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Imamoto T, Kawasaki T, Sato H, Tatsumi K, Ishii D, Yoshioka K, Hasegawa Y, Ohara O, Suzuki T. Different Transcriptome Features of Peripheral Blood Mononuclear Cells in Non-Emphysematous Chronic Obstructive Pulmonary Disease. Int J Mol Sci 2023; 25:66. [PMID: 38203236 PMCID: PMC10779039 DOI: 10.3390/ijms25010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Non-emphysematous chronic obstructive pulmonary disease (COPD), which is defined based on chest computed tomography findings, presented different transcriptome features of peripheral blood mononuclear cells (PBMCs) compared with emphysematous COPD. Enrichment analysis of transcriptomic data in COPD demonstrated that the "Hematopoietic cell lineage" pathway in Kyoto Encyclopedia of Genes and Genomes pathway analysis was highly upregulated, suggesting that cellular dynamic dysregulation in COPD lungs is affected by pathologically modified PBMCs. The differentially expressed genes (DEGs) upregulated in PBMCs reflected the disease state of non-emphysematous COPD. Upregulated DEGs such as XCL1, PRKCZ, TMEM102, CD200R1, and AQP1 activate T lymphocytes and eosinophils. Upregulating keratan sulfate biosynthesis and metabolic processes is associated with protection against the destruction of the distal airways. ITGA3 upregulation augments interactions with extracellular matrix proteins, and COL6A1 augments the profibrotic mast cell phenotype during alveolar collagen VI deposition. Upregulating HSPG2, PDGFRB, and PAK4 contributes to the thickening of the airway wall, and upregulating SERPINF1 expression explains the better-preserved vascular bed. Therefore, gene expression and pathway analysis in PBMCs in patients with non-emphysematous COPD represented type 2 immune responses and airway remodeling features. Therefore, these patients have asthmatic potential despite no clinical signs of asthma, in contrast to those with emphysematous COPD.
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Affiliation(s)
- Takuro Imamoto
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Takeshi Kawasaki
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Hironori Sato
- Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Koichiro Tatsumi
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Daisuke Ishii
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Keiichiro Yoshioka
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Yoshinori Hasegawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Takuji Suzuki
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
- Synergy Institute for Futuristic Mucosal Vaccine Research and Development, Chiba University, Chiba 260-8670, Japan
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2
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Jin Y, Li Y, He S, Ge Y, Zhao Y, Zhu K, He A, Li S, Yan S, Cao C. ATM participates in fine particulate matter-induced airway inflammation through regulating DNA damage and DNA damage response. ENVIRONMENTAL TOXICOLOGY 2023; 38:2668-2678. [PMID: 37483094 DOI: 10.1002/tox.23901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/20/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023]
Abstract
The relationship between fine particulate matter (PM2.5) and chronic airway inflammatory diseases, such as chronic obstructive pulmonary disease and asthma, have garnered public attention, while the detailed mechanisms of PM2.5-induced airway inflammation remain unclear. This study reveals that PM2.5 induces airway inflammation both in vivo and in vitro, and, moreover, identifies DNA damage and DNA damage repair (DDR) as results of this exposure. Ataxia telangiectasia-mutated heterozygous (ATM+/- ) and wild-type C57BL/6 (WT) mice were exposed to PM2.5. The results show that, following exposure to PM2.5, the number of neutrophils in broncho alveolar lavage fluid and the mRNA expression of CXCL-1 in lung tissues of the ATM+/- mice were lower than those of the WT mice. The mRNA expression of FANCD2 and FANCI were also down-regulated. Human bronchial epithelial (HBE) cells were transfected with ATM-siRNA to induce down-regulation of ATM gene expression and were subsequently stimulated with PM2.5. The results show that the mRNA expression of TNF-α decreased in the ATM-siRNA-transfected cells. The mRNA expression of CXCL-1 and CXCL-2 in peritoneal macrophages, derived from ATM-null mice in which experiments showed that the protein expression of FANCD2 and FANCI decreased, were also decreased after PM2.5 exposure in ATM-siRNA-transfected HBE cells. In conclusion, PM2.5-induced airway inflammation is alleviated in ATM+/- mice compared with WT mice. ATM promotes PM2.5-induced airway inflammation, which may be attributed to the regulation of DNA damage and DDR.
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Affiliation(s)
- Yan Jin
- Department of Respiratory and Critical Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Municipal Hospital Affiliated to Taizhou University, Taizhou, China
| | - Yiting Li
- Department of Respiratory and Critical Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Shiyi He
- Department of Respiratory and Critical Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yijun Ge
- Department of Respiratory and Critical Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yun Zhao
- Department of Respiratory and Critical Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Ke Zhu
- Department of Respiratory and Critical Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Andong He
- Department of Respiratory and Critical Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Siyu Li
- Department of Respiratory and Critical Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Siyu Yan
- Department of Respiratory and Critical Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Chao Cao
- Department of Respiratory and Critical Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
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3
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Bateman G, Guo-Parke H, Rodgers AM, Linden D, Bailey M, Weldon S, Kidney JC, Taggart CC. Airway Epithelium Senescence as a Driving Mechanism in COPD Pathogenesis. Biomedicines 2023; 11:2072. [PMID: 37509711 PMCID: PMC10377597 DOI: 10.3390/biomedicines11072072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Cellular senescence is a state of permanent cell cycle arrest triggered by various intrinsic and extrinsic stressors. Cellular senescence results in impaired tissue repair and remodeling, loss of physiological integrity, organ dysfunction, and changes in the secretome. The systemic accumulation of senescence cells has been observed in many age-related diseases. Likewise, cellular senescence has been implicated as a risk factor and driving mechanism in chronic obstructive pulmonary disease (COPD) pathogenesis. Airway epithelium exhibits hallmark features of senescence in COPD including activation of the p53/p21WAF1/CIP1 and p16INK4A/RB pathways, leading to cell cycle arrest. Airway epithelial senescent cells secrete an array of inflammatory mediators, the so-called senescence-associated secretory phenotype (SASP), leading to a persistent low-grade chronic inflammation in COPD. SASP further promotes senescence in an autocrine and paracrine manner, potentially contributing to the onset and progression of COPD. In addition, cellular senescence in COPD airway epithelium is associated with telomere dysfunction, DNA damage, and oxidative stress. This review discusses the potential mechanisms of airway epithelial cell senescence in COPD, the impact of cellular senescence on the development and severity of the disease, and highlights potential targets for modulating cellular senescence in airway epithelium as a potential therapeutic approach in COPD.
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Affiliation(s)
- Georgia Bateman
- Airway Innate Immunity Research Group, Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, Belfast BT9 7AE, UK
| | - Hong Guo-Parke
- Airway Innate Immunity Research Group, Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, Belfast BT9 7AE, UK
| | - Aoife M Rodgers
- Airway Innate Immunity Research Group, Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, Belfast BT9 7AE, UK
| | - Dermot Linden
- Airway Innate Immunity Research Group, Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, Belfast BT9 7AE, UK
| | - Melanie Bailey
- Department of Respiratory Medicine, Mater Hospital Belfast, Belfast BT14 6AB, UK
| | - Sinéad Weldon
- Airway Innate Immunity Research Group, Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, Belfast BT9 7AE, UK
| | - Joseph C Kidney
- Department of Respiratory Medicine, Mater Hospital Belfast, Belfast BT14 6AB, UK
| | - Clifford C Taggart
- Airway Innate Immunity Research Group, Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, Belfast BT9 7AE, UK
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4
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Mumby S, Adcock IM. Recent evidence from omic analysis for redox signalling and mitochondrial oxidative stress in COPD. J Inflamm (Lond) 2022; 19:10. [PMID: 35820851 PMCID: PMC9277949 DOI: 10.1186/s12950-022-00308-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022] Open
Abstract
COPD is driven by exogenous and endogenous oxidative stress derived from inhaled cigarette smoke, air pollution and reactive oxygen species from dysregulated mitochondria in activated inflammatory cells within the airway and lung. This is compounded by the loss in antioxidant defences including FOXO and NRF2 and other antioxidant transcription factors together with various key enzymes that attenuate oxidant effects. Oxidative stress enhances inflammation; airway remodelling including fibrosis and emphysema; post-translational protein modifications leading to autoantibody generation; DNA damage and cellular senescence. Recent studies using various omics technologies in the airways, lungs and blood of COPD patients has emphasised the importance of oxidative stress, particularly that derived from dysfunctional mitochondria in COPD and its role in immunity, inflammation, mucosal barrier function and infection. Therapeutic interventions targeting oxidative stress should overcome the deleterious pathologic effects of COPD if targeted to the lung. We require novel, more efficacious antioxidant COPD treatments among which mitochondria-targeted antioxidants and Nrf2 activators are promising.
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5
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Nucera F, Mumby S, Paudel KR, Dharwal V, DI Stefano A, Casolaro V, Hansbro PM, Adcock IM, Caramori G. Role of oxidative stress in the pathogenesis of COPD. Minerva Med 2022; 113:370-404. [PMID: 35142479 DOI: 10.23736/s0026-4806.22.07972-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chronic inhalation of cigarette smoke is a prominent cause of chronic obstructive pulmonary disease (COPD) and provides an important source of exogenous oxidants. In addition, several inflammatory and structural cells are a source of endogenous oxidants in the lower airways of COPD patients, even in former smokers. This suggests that oxidants play a key role in the pathogenesis of COPD. This oxidative stress is counterbalanced by the protective effects of the various endogenous antioxidant defenses of the lower airways. A large amount of data from animal models and patients with COPD have shown that both the stable phase of the disease, and during exacerbations, have increased oxidative stress in the lower airways compared with age-matched smokers with normal lung function. Thus, counteracting the increased oxidative stress may produce clinical benefits in COPD patients. Smoking cessation is currently the most effective treatment of COPD patients and reduces oxidative stress in the lower airways. In addition, many drugs used to treat COPD have some antioxidant effects, however, it is still unclear if their clinical efficacy is related to pharmacological modulation of the oxidant/antioxidant balance. Several new antioxidant compounds are in development for the treatment of COPD.
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Affiliation(s)
- Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Messina, Italy -
| | - Sharon Mumby
- Airways Diseases Section, Faculty of Medicine, Imperial College London, National Heart and Lung Institute, London, UK
| | - Keshav R Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, Australia
| | - Vivek Dharwal
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, Australia
| | - Antonino DI Stefano
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell'Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, IRCCS, Veruno, Novara, Italy
| | - Vincenzo Casolaro
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, Australia
| | - Ian M Adcock
- Airways Diseases Section, Faculty of Medicine, Imperial College London, National Heart and Lung Institute, London, UK
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Messina, Italy
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6
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Xu J, Li L, Ren J, Zhong X, Xie C, Zheng A, Abudukadier A, Tuerxun M, Zhang S, Tang L, Hairoula D, Zou X. Whole-Exome Sequencing Implicates the USP34 rs777591A > G Intron Variant in Chronic Obstructive Pulmonary Disease in a Kashi Cohort. Front Cell Dev Biol 2022; 9:792027. [PMID: 35198563 PMCID: PMC8859106 DOI: 10.3389/fcell.2021.792027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022] Open
Abstract
Genetic factors are important factors in chronic obstructive pulmonary disease (COPD) onset. Plenty of risk and new causative genes for COPD have been identified in patients of the Chinese Han population. In contrast, we know considerably little concerning the genetics in the Kashi COPD population (Uyghur). This study aims at clarifying the genetic maps regarding COPD susceptibility in Kashi (China). Whole-exome sequencing (WES) was used to analyze three Uyghur families with COPD in Kashi (eight patients and one healthy control). Sanger sequencing was also used to verify the WES results in 541 unrelated Uyghur COPD patients and 534 Uyghur healthy controls. WES showed 72 single nucleotide variants (SNVs), two deletions, and small insertions (InDels), 26 copy number variants (CNVs), and 34 structural variants (SVs), including g.71230620T > A (rs12449210T > A, NC_000,016.10) in the HYDIN axonemal central pair apparatus protein (HYDIN) gene and g.61190482A > G (rs777591A > G, NC_000002.12) in the ubiquitin-specific protease 34 (USP34) gene. After Sanger sequencing, we found that rs777591“AA” under different genetic models except for the dominant model (adjusted OR = 0.8559, 95%CI 0.6568–1.115, p > .05), could significantly reduce COPD risk, but rs12449210T > A was not related to COPD. In stratified analysis of smoking status, rs777591“AA” reduced COPD risk significantly among the nonsmoker group. Protein and mRNA expression of USP34 in cigarette smoke extract-treated BEAS-2b cells increased significantly compared with those in the control group. Our findings associate the USP34 rs777591“AA” genotype as a protector factor in COPD.
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Affiliation(s)
- Jingran Xu
- Department of Medical College, Shihezi University, Shihezi, China
| | - Li Li
- Department of Respiratory and Critical Care Medicine, First People’s Hospital of Kashi, Kashi, China
| | - Jie Ren
- Department of Respiratory and Critical Care Medicine, First People’s Hospital of Kashi, Kashi, China
| | - Xuemei Zhong
- Department of Respiratory and Critical Care Medicine, First People’s Hospital of Kashi, Kashi, China
| | - Chengxin Xie
- Department of Respiratory and Critical Care Medicine, First People’s Hospital of Kashi, Kashi, China
| | - Aifang Zheng
- Department of Respiratory and Critical Care Medicine, First People’s Hospital of Kashi, Kashi, China
| | - Ayiguzali Abudukadier
- Department of Respiratory and Critical Care Medicine, First People’s Hospital of Kashi, Kashi, China
| | - Maimaitiaili Tuerxun
- Department of Respiratory and Critical Care Medicine, First People’s Hospital of Kashi, Kashi, China
| | - Sujie Zhang
- Department of Medical College, Shihezi University, Shihezi, China
| | - Lifeng Tang
- Department of Medical College, Shihezi University, Shihezi, China
- Department of Respiratory and Critical Care Medicine, First People’s Hospital of Kashi, Kashi, China
| | - Dilare Hairoula
- Department of Medical College, Shihezi University, Shihezi, China
- Department of Respiratory and Critical Care Medicine, First People’s Hospital of Kashi, Kashi, China
| | - Xiaoguang Zou
- Department of Medical College, Shihezi University, Shihezi, China
- Department of Respiratory and Critical Care Medicine, First People’s Hospital of Kashi, Kashi, China
- *Correspondence: Xiaoguang Zou,
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7
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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: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [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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8
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Zhuang Y, Hobbs BD, Hersh CP, Kechris K. Identifying miRNA-mRNA Networks Associated With COPD Phenotypes. Front Genet 2021; 12:748356. [PMID: 34777474 PMCID: PMC8581181 DOI: 10.3389/fgene.2021.748356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/27/2021] [Indexed: 11/21/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by expiratory airflow limitation and symptoms such as shortness of breath. Although many studies have demonstrated dysregulated microRNA (miRNA) and gene (mRNA) expression in the pathogenesis of COPD, how miRNAs and mRNAs systematically interact and contribute to COPD development is still not clear. To gain a deeper understanding of the gene regulatory network underlying COPD pathogenesis, we used Sparse Multiple Canonical Correlation Network (SmCCNet) to integrate whole blood miRNA and RNA-sequencing data from 404 participants in the COPDGene study to identify novel miRNA-mRNA networks associated with COPD-related phenotypes including lung function and emphysema. We hypothesized that phenotype-directed interpretable miRNA-mRNA networks from SmCCNet would assist in the discovery of novel biomarkers that traditional single biomarker discovery methods (such as differential expression) might fail to discover. Additionally, we investigated whether adjusting -omics and clinical phenotypes data for covariates prior to integration would increase the statistical power for network identification. Our study demonstrated that partial covariate adjustment for age, sex, race, and CT scanner model (in the quantitative emphysema networks) improved network identification when compared with no covariate adjustment. However, further adjustment for current smoking status and relative white blood cell (WBC) proportions sometimes weakened the power for identifying lung function and emphysema networks, a phenomenon which may be due to the correlation of smoking status and WBC counts with the COPD-related phenotypes. With partial covariate adjustment, we found six miRNA-mRNA networks associated with COPD-related phenotypes. One network consists of 2 miRNAs and 28 mRNAs which had a 0.33 correlation (p = 5.40E-12) to forced expiratory volume in 1 s (FEV1) percent predicted. We also found a network of 5 miRNAs and 81 mRNAs that had a 0.45 correlation (p = 8.80E-22) to percent emphysema. The miRNA-mRNA networks associated with COPD traits provide a systems view of COPD pathogenesis and complements biomarker identification with individual miRNA or mRNA expression data.
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Affiliation(s)
- Yonghua Zhuang
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Katerina Kechris
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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9
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Tang Y, Chen Z, Fang Z, Zhao J, Zhou Y, Tang C. Multi-Omics study on biomarker and pathway discovery of chronic obstructive pulmonary disease. J Breath Res 2021; 15. [PMID: 34280912 DOI: 10.1088/1752-7163/ac15ea] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a common heterogeneous respiratory disease characterized by persistent and incompletely reversible airflow limitation. Due to the heterogeneity and phenotypes complexity of COPD, traditionally diagnostic methods can only give limited information on predicted results and treatment, which are not sufficient for accurate diagnosis and evaluation. With the development of omics technologies in recent years, genomics, proteomics, and metabolomics are widely used in the study of COPD, providing good tools for discovering biomarkers to diagnose and elucidate the complex mechanism of COPD. In this review, we summarized the biomarkers of COPD based on metabolomic, proteomic and transcriptomic studies that have been reported in recent years. Furthermore, protein-protein interactions and multi-omics integrated analysis were carried out to explore the important metabolites and proteins that involved in significant pathways in the progression of COPD for explanation the pathogenesis of COPD. Finally, the prospective and challenges in the study of COPD were proposed. It is expected that this review will provide some references for the development of diagnostic methods and elucidation of the pathogenesis of COPD.
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Affiliation(s)
- Yuqing Tang
- Ningbo University Medical School, The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China, Ningbo, Zhejiang, 315020, CHINA
| | - Zhengjun Chen
- Ningbo University Medical School, The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China, Ningbo, Zhejiang, 315020, CHINA
| | - Zhiling Fang
- Ningbo University Medical School, Ningbo University School of Medicine, Ningbo 315211, China, Ningbo, Zhejiang, 315211, CHINA
| | - Jinshun Zhao
- Ningbo University Medical School, Ningbo University School of Medicine, Ningbo 315211, China, Ningbo, Zhejiang, 315211, CHINA
| | - Yuping Zhou
- Ningbo University Medical School, The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China, Ningbo, Zhejiang, 315020, CHINA
| | - Chunlan Tang
- Ningbo University Medical School, The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China, Ningbo, Zhejiang, 315020, CHINA
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10
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Skerrett-Byrne DA, Bromfield EG, Murray HC, Jamaluddin MFB, Jarnicki AG, Fricker M, Essilfie AT, Jones B, Haw TJ, Hampsey D, Anderson AL, Nixon B, Scott RJ, Wark PAB, Dun MD, Hansbro PM. Time-resolved proteomic profiling of cigarette smoke-induced experimental chronic obstructive pulmonary disease. Respirology 2021; 26:960-973. [PMID: 34224176 DOI: 10.1111/resp.14111] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/01/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND OBJECTIVE Chronic obstructive pulmonary disease (COPD) is the third leading cause of illness and death worldwide. Current treatments aim to control symptoms with none able to reverse disease or stop its progression. We explored the major molecular changes in COPD pathogenesis. METHODS We employed quantitative label-based proteomics to map the changes in the lung tissue proteome of cigarette smoke-induced experimental COPD that is induced over 8 weeks and progresses over 12 weeks. RESULTS Quantification of 7324 proteins enabled the tracking of changes to the proteome. Alterations in protein expression profiles occurred in the induction phase, with 18 and 16 protein changes at 4- and 6-week time points, compared to age-matched controls, respectively. Strikingly, 269 proteins had altered expression after 8 weeks when the hallmark pathological features of human COPD emerge, but this dropped to 27 changes at 12 weeks with disease progression. Differentially expressed proteins were validated using other mouse and human COPD bronchial biopsy samples. Major changes in RNA biosynthesis (heterogeneous nuclear ribonucleoproteins C1/C2 [HNRNPC] and RNA-binding protein Musashi homologue 2 [MSI2]) and modulators of inflammatory responses (S100A1) were notable. Mitochondrial dysfunction and changes in oxidative stress proteins also occurred. CONCLUSION We provide a detailed proteomic profile, identifying proteins associated with the pathogenesis and disease progression of COPD establishing a platform to develop effective new treatment strategies.
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Affiliation(s)
- David A Skerrett-Byrne
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,Pregnancy and Reproduction Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Elizabeth G Bromfield
- Pregnancy and Reproduction Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia.,Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Heather C Murray
- University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - M Fairuz B Jamaluddin
- University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Andrew G Jarnicki
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria, Australia
| | - Michael Fricker
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Ama T Essilfie
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,Queensland Institute of Medical Research, Herston, Queensland, Australia
| | - Bernadette Jones
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Tatt J Haw
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Daniel Hampsey
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Amanda L Anderson
- Pregnancy and Reproduction Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Brett Nixon
- Pregnancy and Reproduction Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Rodney J Scott
- University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Peter A B Wark
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Matthew D Dun
- University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia.,Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
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11
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Nouws J, Wan F, Finnemore E, Roque W, Kim SJ, Bazan I, Li CX, Skold CM, Dai Q, Yan X, Chioccioli M, Neumeister V, Britto CJ, Sweasy J, Bindra R, Wheelock ÅM, Gomez JL, Kaminski N, Lee PJ, Sauler M. MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary disease. JCI Insight 2021; 6:134218. [PMID: 33290275 PMCID: PMC7934877 DOI: 10.1172/jci.insight.134218] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/02/2020] [Indexed: 12/27/2022] Open
Abstract
The pathogenesis of chronic obstructive pulmonary disease (COPD) involves aberrant responses to cellular stress caused by chronic cigarette smoke (CS) exposure. However, not all smokers develop COPD and the critical mechanisms that regulate cellular stress responses to increase COPD susceptibility are not understood. Because microRNAs are well-known regulators of cellular stress responses, we evaluated microRNA expression arrays performed on distal parenchymal lung tissue samples from 172 subjects with and without COPD. We identified miR-24-3p as the microRNA that best correlated with radiographic emphysema and validated this finding in multiple cohorts. In a CS exposure mouse model, inhibition of miR-24-3p increased susceptibility to apoptosis, including alveolar type II epithelial cell apoptosis, and emphysema severity. In lung epithelial cells, miR-24-3p suppressed apoptosis through the BH3-only protein BIM and suppressed homology-directed DNA repair and the DNA repair protein BRCA1. Finally, we found BIM and BRCA1 were increased in COPD lung tissue, and BIM and BRCA1 expression inversely correlated with miR-24-3p. We concluded that miR-24-3p, a regulator of the cellular response to DNA damage, is decreased in COPD, and decreased miR-24-3p increases susceptibility to emphysema through increased BIM and apoptosis.
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Affiliation(s)
- Jessica Nouws
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Feng Wan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Anatomy, Beijing University of Chinese Medicine, Beijing, China
| | - Eric Finnemore
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Willy Roque
- Department of Internal Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - So-Jin Kim
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Isabel Bazan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Chuan-Xing Li
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - C Magnus Skold
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Qile Dai
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Maurizio Chioccioli
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Veronique Neumeister
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Clemente J Britto
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joann Sweasy
- Department of Radiation Oncology, University of Arizona College of Medicine, Tucson, Arizona, USA.,Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ranjit Bindra
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Åsa M Wheelock
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jose L Gomez
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Patty J Lee
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Section of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Maor Sauler
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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12
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Omote N, Sauler M. Non-coding RNAs as Regulators of Cellular Senescence in Idiopathic Pulmonary Fibrosis and Chronic Obstructive Pulmonary Disease. Front Med (Lausanne) 2020; 7:603047. [PMID: 33425948 PMCID: PMC7785852 DOI: 10.3389/fmed.2020.603047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
Cellular senescence is a cell fate implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD). Cellular senescence occurs in response to cellular stressors such as oxidative stress, DNA damage, telomere shortening, and mitochondrial dysfunction. Whether these stresses induce cellular senescence or an alternative cell fate depends on the type and magnitude of cellular stress, but also on intrinsic factors regulating the cellular stress response. Non-coding RNAs, including both microRNAs and long non-coding RNAs, are key regulators of cellular stress responses and susceptibility to cellular senescence. In this review, we will discuss cellular mechanisms that contribute to senescence in IPF and COPD and highlight recent advances in our understanding of how these processes are influenced by non-coding RNAs. We will also discuss the potential therapeutic role for targeting non-coding RNAs to treat these chronic lung diseases.
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Affiliation(s)
- Norihito Omote
- Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
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13
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Kobayashi Y, Tata A, Konkimalla A, Katsura H, Lee RF, Ou J, Banovich NE, Kropski JA, Tata PR. Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis. Nat Cell Biol 2020; 22:934-946. [PMID: 32661339 PMCID: PMC7461628 DOI: 10.1038/s41556-020-0542-8] [Citation(s) in RCA: 274] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Abstract
Stem cells undergo dynamic changes in response to injury to regenerate lost cells. However, the identity of transitional states and the mechanisms that drive their trajectories remain understudied. Using lung organoids, multiple in vivo repair models, single-cell transcriptomics and lineage tracing, we find that alveolar type-2 epithelial cells undergoing differentiation into type-1 cells acquire pre-alveolar type-1 transitional cell state (PATS) en route to terminal maturation. Transitional cells undergo extensive stretching during differentiation, making them vulnerable to DNA damage. Cells in the PATS show an enrichment of TP53, TGFβ, DNA-damage-response signalling and cellular senescence. Gain and loss of function as well as genomic binding assays revealed a direct transcriptional control of PATS by TP53 signalling. Notably, accumulation of PATS-like cells in human fibrotic lungs was observed, suggesting persistence of the transitional state in fibrosis. Our study thus implicates a transient state associated with senescence in normal epithelial tissue repair and its abnormal persistence in disease conditions.
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Affiliation(s)
- Yoshihiko Kobayashi
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Arvind Konkimalla
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC, USA
| | - Hiroaki Katsura
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Rebecca F Lee
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Jianhong Ou
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Regeneration Next, Duke University, Durham, NC, USA
| | | | - Jonathan A Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
- Regeneration Next, Duke University, Durham, NC, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.
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14
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Tejwani V, Yun X, Sikka G, Shimoda L, Suresh K. Airway Epithelial Genomic Signatures in Steroid-Resistant COPD; Role for SMAD3 in Vascular Remodeling in Pulmonary Hypertension; Regulation of Lung Endothelial Cell Function by VEGFR3. Am J Respir Cell Mol Biol 2020; 61:392-394. [PMID: 31038982 DOI: 10.1165/rcmb.2019-0075ro] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Vickram Tejwani
- Division of Pulmonary/Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Xin Yun
- Division of Pulmonary/Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Gautam Sikka
- Division of Pulmonary/Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Larissa Shimoda
- Division of Pulmonary/Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Karthik Suresh
- Division of Pulmonary/Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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15
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Thun GA, Derdak S, Castro-Giner F, Apunte-Ramos K, Águeda L, Wjst M, Boland A, Deleuze JF, Kolsum U, Heiss-Neumann MS, Nowinski A, Gorecka D, Hohlfeld JM, Welte T, Brightling CE, Parr DG, Prasse A, Müller-Quernheim J, Greulich T, Stendardo M, Boschetto P, Barta I, Döme B, Gut M, Singh D, Ziegler-Heitbrock L, Gut IG. High degree of polyclonality hinders somatic mutation calling in lung brush samples of COPD cases and controls. Sci Rep 2019; 9:20158. [PMID: 31882973 PMCID: PMC6934450 DOI: 10.1038/s41598-019-56618-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 12/04/2019] [Indexed: 11/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is induced by cigarette smoking and characterized by inflammation of airway tissue. Since smokers with COPD have a higher risk of developing lung cancer than those without, we hypothesized that they carry more mutations in affected tissue. We called somatic mutations in airway brush samples from medium-coverage whole genome sequencing data from healthy never and ex-smokers (n = 8), as well as from ex-smokers with variable degrees of COPD (n = 4). Owing to the limited concordance of resulting calls between the applied tools we built a consensus, a strategy that was validated with high accuracy for cancer data. However, consensus calls showed little promise of representing true positives due to low mappability of corresponding sequence reads and high overlap with positions harbouring known genetic polymorphisms. A targeted re-sequencing approach suggested that only few mutations would survive stringent verification testing and that our data did not allow the inference of any difference in the mutational load of bronchial brush samples between former smoking COPD cases and controls. High polyclonality in airway brush samples renders medium-depth sequencing insufficient to provide the resolution to detect somatic mutations. Deep sequencing data of airway biopsies are needed to tackle the question.
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Affiliation(s)
- Gian-Andri Thun
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sophia Derdak
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Francesc Castro-Giner
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Katherine Apunte-Ramos
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Lidia Águeda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Matthias Wjst
- Helmholtz-Zentrum München, National Research Centre for Environmental Health, Institute of Lung Biology and Disease, Neuherberg, Germany
- Institute of Medical Statistics, Epidemiology and Medical Informatics, Technical University Munich, Munich, Germany
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Umme Kolsum
- University of Manchester, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Adam Nowinski
- 2nd Department of Respiratory Medicine, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Dorota Gorecka
- 2nd Department of Respiratory Medicine, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Jens M Hohlfeld
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of the German Center of Lung Research, Hannover, Germany
- Department of Respiratory Medicine, Hannover Medical School, Member of the German Center of Lung Research, Hannover, Germany
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, Member of the German Center of Lung Research, Hannover, Germany
| | - Christopher E Brightling
- Department of Infection, Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, UK
| | - David G Parr
- Department of Respiratory Medicine, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
| | - Antje Prasse
- Department of Respiratory Medicine, Hannover Medical School, Member of the German Center of Lung Research, Hannover, Germany
- Department of Pneumology, University Medical Center, Freiburg, Germany
| | | | - Timm Greulich
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, Philipps-University, Marburg, Germany
| | - Mariarita Stendardo
- Department of Medical Sciences, University of Ferrara and University-Hospital of Ferrara, Ferrara, Italy
| | - Piera Boschetto
- Department of Medical Sciences, University of Ferrara and University-Hospital of Ferrara, Ferrara, Italy
| | - Imre Barta
- Department of Pathophysiology, National Koranyi Institute for Pulmonology, Budapest, Hungary
| | - Balázs Döme
- Department of Tumorbiology, National Koranyi Institute for Pulmonology, Budapest, Hungary
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Dave Singh
- University of Manchester, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Ivo G Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
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16
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Otálora-Otálora BA, Florez M, López-Kleine L, Canas Arboleda A, Grajales Urrego DM, Rojas A. Joint Transcriptomic Analysis of Lung Cancer and Other Lung Diseases. Front Genet 2019; 10:1260. [PMID: 31867044 PMCID: PMC6908522 DOI: 10.3389/fgene.2019.01260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/14/2019] [Indexed: 12/09/2022] Open
Abstract
Background: Epidemiological and clinical evidence points cancer comorbidity with pulmonary chronic disease. The acquisition of some hallmarks of cancer by cells affected with lung pathologies as a cell adaptive mechanism to a shear stress, suggests that could be associated with the establishment of tumoral processes. Objective: To propose a bioinformatic pipeline for the identification of all deregulated genes and the transcriptional regulators (TFs) that are coexpressed during lung cancer establishment, and therefore could be important for the acquisition of the hallmarks of cancer. Methods: Ten microarray datasets (six of lung cancer, four of lung diseases) comparing normal and diseases-related lung tissue were selected to identify hub differentiated expressed genes (DEGs) in common between lung pathologies and lung cancer, along with transcriptional regulators through the utilization of specialized libraries from R language. DAVID bioinformatics tool for gene enrichment analyses was used to identify genes with experimental evidence associated to tumoral processes and signaling pathways. Coexpression networks of DEGs and TFs in lung cancer establishment were created with Coexnet library, and a survival analysis of the main hub genes was made. Results: Two hundred ten DEGs were identified in common between lung cancer and other lung diseases related to the acquisition of tumoral characteristics, which are coexpressed in a lung cancer network with TFs, suggesting that could be related to the establishment of the tumoral pathology in lung. The comparison of the coexpression networks of lung cancer and other lung diseases allowed the identification of common connectivity patterns (CCPs) with DEGs and TFs correlated to important tumoral processes and signaling pathways, that haven´t been studied to experimentally validate their role in the early stages of lung cancer. Some of the TFs identified showed a correlation between its expression levels and the survival of lung cancer patients. Conclusion: Our findings indicate that lung diseases share genes with lung cancer which are coexpressed in lung cancer, and might be able to explain the epidemiological observations that point to direct and inverse comorbid associations between some chronic lung diseases and lung cancer and represent a complex transcriptomic scenario.
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Affiliation(s)
| | - Mauro Florez
- Departamento de Estadística, Grupo de Investigación en Bioinformática y Biología de sistemas – GiBBS, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Liliana López-Kleine
- Departamento de Estadística, Grupo de Investigación en Bioinformática y Biología de sistemas – GiBBS, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Adriana Rojas
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
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17
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Devadoss D, Long C, Langley RJ, Manevski M, Nair M, Campos MA, Borchert G, Rahman I, Chand HS. Long Noncoding Transcriptome in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2019; 61:678-688. [PMID: 31486667 PMCID: PMC6890411 DOI: 10.1165/rcmb.2019-0184tr] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022] Open
Abstract
Chronic airway inflammation from recurring exposures to noxious environmental stimuli results in a progressive and irreversible airflow limitation and the lung parenchymal damage that characterizes chronic obstructive pulmonary disease (COPD). The large variability observed in the onset and progression of COPD is primarily driven by complex gene-environment interactions. The transcriptomic and epigenetic memory potential of lung epithelial and innate immune cells drive responses, such as mucus hyperreactivity and airway remodeling, that are tightly regulated by various molecular mechanisms, for which several candidate susceptibility genes have been described. However, the recently described noncoding RNA species, in particular the long noncoding RNAs, may also have an important role in modulating pulmonary responses to chronic inhalation of toxic substances and the development of COPD. This review outlines the features of long noncoding RNAs that have been implicated in regulating the airway inflammatory responses to cigarette smoke exposure and their possible association with COPD pathogenesis. As COPD continues to debilitate the increasingly aging population and contribute to higher morbidity and mortality rates worldwide, the search for better biomarkers and alternative therapeutic options is pivotal.
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Affiliation(s)
- Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Christopher Long
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Raymond J. Langley
- Department of Pharmacology, University of South Alabama, Mobile, Alabama
| | - Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Madhavan Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Michael A. Campos
- Pulmonary Section, Miami Veterans Administration Medical Center, Miami, Florida
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Miller School of Medicine, University of Miami, Coral Gables, Florida; and
| | - Glen Borchert
- Department of Pharmacology, University of South Alabama, Mobile, Alabama
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
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18
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Adcock IM, Mumby S, Caramori G. Breaking news: DNA damage and repair pathways in COPD and implications for pathogenesis and treatment. Eur Respir J 2018; 52:52/4/1801718. [PMID: 30287495 DOI: 10.1183/13993003.01718-2018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Ian M Adcock
- Airways Disease Section, National Heart & Lung Institute, Imperial College, London, UK
| | - Sharon Mumby
- Airways Disease Section, National Heart & Lung Institute, Imperial College, London, UK
| | - Gaetano Caramori
- Unità Operativa Complessa di Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF) Università degli Studi di Messina, Messina, Italy
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