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Wang AL, Lahousse L, Dahlin A, Edris A, McGeachie M, Lutz SM, Sordillo JE, Brusselle G, Lasky-Su J, Weiss ST, Iribarren C, Lu MX, Tantisira KG, Wu AC. Novel genetic variants associated with inhaled corticosteroid treatment response in older adults with asthma. Thorax 2023; 78:432-441. [PMID: 35501119 PMCID: PMC9810110 DOI: 10.1136/thoraxjnl-2021-217674] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 04/01/2022] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Older adults have the greatest burden of asthma and poorest outcomes. The pharmacogenetics of inhaled corticosteroid (ICS) treatment response is not well studied in older adults. METHODS A genome-wide association study of ICS response was performed in asthmatics of European ancestry in Genetic Epidemiology Research on Adult Health and Aging (GERA) by fitting Cox proportional hazards regression models, followed by validation in the Mass General Brigham (MGB) Biobank and Rotterdam Study. ICS response was measured using two definitions in asthmatics on ICS treatment: (1) absence of oral corticosteroid (OCS) bursts using prescription records and (2) absence of asthma-related exacerbations using diagnosis codes. A fixed-effect meta-analysis was performed for each outcome. The validated single-nucleotide polymorphisms (SNPs) were functionally annotated to standard databases. RESULTS In 5710 subjects in GERA, 676 subjects in MGB Biobank, and 465 subjects in the Rotterdam Study, four novel SNPs on chromosome six near PTCHD4 validated across all cohorts and met genome-wide significance on meta-analysis for the OCS burst outcome. In 4541 subjects in GERA and 505 subjects in MGB Biobank, 152 SNPs with p<5 × 10-5 were validated across these two cohorts for the asthma-related exacerbation outcome. The validated SNPs included methylation and expression quantitative trait loci for CPED1, CRADD and DST for the OCS burst outcome and GM2A, SNW1, CACNA1C, DPH1, and RPS10 for the asthma-related exacerbation outcome. CONCLUSIONS Multiple novel SNPs associated with ICS response were identified in older adult asthmatics. Several SNPs annotated to genes previously associated with asthma and other airway or allergic diseases, including PTCHD4.
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Affiliation(s)
- Alberta L Wang
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ahmed Edris
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Joanne E Sordillo
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Guy Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Carlos Iribarren
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, California, USA
| | - Meng X Lu
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, California, USA
| | - Kelan G Tantisira
- Division of Pediatric Respiratory Medicine, Rady's Children's Hospital-San Diego, University of California San Diego School of Medicine, San Diego, California, USA
| | - Ann C Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
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2
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Wang J, Tan L, Yu X, Cao X, Jia B, Chen R, Li J. lncRNA ZNRD1-AS1 promotes malignant lung cell proliferation, migration, and angiogenesis via the miR-942/TNS1 axis and is positively regulated by the m 6A reader YTHDC2. Mol Cancer 2022; 21:229. [PMID: 36581942 PMCID: PMC9801573 DOI: 10.1186/s12943-022-01705-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
RATIONALE Lung cancer is the most prevalent form of cancer and has a high mortality rate, making it a global public health concern. The N6-methyladenosine (m6A) modification is a highly dynamic and reversible process that is involved in a variety of essential biological processes. Using in vitro, in vivo, and multi-omics bioinformatics, the present study aims to determine the function and regulatory mechanisms of the long non-coding (lnc)RNA zinc ribbon domain-containing 1-antisense 1 (ZNRD1-AS1). METHODS The RNAs that were bound to the m6A 'reader' were identified using YTH domain-containing 2 (YTHDC2) RNA immunoprecipitation (RIP)-sequencing. Utilizing methylated RIP PCR/quantitative PCR, pull-down, and RNA stability assays, m6A modification and ZNRD1-AS1 regulation were analyzed. Using bioinformatics, the expression levels and clinical significance of ZNRD1-AS1 in lung cancer were evaluated. Using fluorescent in situ hybridization and quantitative PCR assays, the subcellular location of ZNRD1-AS1 was determined. Using cell migration, proliferation, and angiogenesis assays, the biological function of ZNRD1-AS1 in lung cancer was determined. In addition, the tumor suppressor effect of ZNRD1-AS1 in vivo was validated using a xenograft animal model. Through bioinformatics analysis and in vitro assays, the downstream microRNAs (miRs) and competing endogenous RNAs were also predicted and validated. RESULTS This study provided evidence that m6A modification mediates YTHDC2-mediated downregulation of ZNRD1-AS1 in lung cancer and cigarette smoke-exposed cells. Low levels of ZNRD1-AS1 expression were linked to adverse clinicopathological characteristics, immune infiltration, and prognosis. ZNRD1-AS1 overexpression was shown to suppress lung cancer cell proliferation, migration, and angiogenesis in vitro and in vivo, and to reduce tumor growth in nude mice. ZNRD1-AS1 expression was shown to be controlled by treatment of cells with either the methylation inhibitor 3-Deazaadenosine or the demethylation inhibitor Meclofenamic. Furthermore, the miR-942/tensin 1 (TNS1) axis was demonstrated to be the downstream regulatory signaling pathway of ZNRD1-AS1. CONCLUSIONS ZNRD1-AS1 serves an important function and has clinical relevance in lung cancer. In addition, the findings suggested that m6A modification could mediate the regulation of the ZNRD1-AS1/miR-942/TNS1 axis via the m6A reader YTHDC2.
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Affiliation(s)
- Jin Wang
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Lirong Tan
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Xueting Yu
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Xiyuan Cao
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Beibei Jia
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Rui Chen
- grid.452666.50000 0004 1762 8363Department of Respiratory Medicine, The Second Affiliated Hospital of Soochow University, Suzhou Jiangsu, 215004 China
| | - Jianxiang Li
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
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3
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Mierke CT. Viscoelasticity, Like Forces, Plays a Role in Mechanotransduction. Front Cell Dev Biol 2022; 10:789841. [PMID: 35223831 PMCID: PMC8864183 DOI: 10.3389/fcell.2022.789841] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Viscoelasticity and its alteration in time and space has turned out to act as a key element in fundamental biological processes in living systems, such as morphogenesis and motility. Based on experimental and theoretical findings it can be proposed that viscoelasticity of cells, spheroids and tissues seems to be a collective characteristic that demands macromolecular, intracellular component and intercellular interactions. A major challenge is to couple the alterations in the macroscopic structural or material characteristics of cells, spheroids and tissues, such as cell and tissue phase transitions, to the microscopic interferences of their elements. Therefore, the biophysical technologies need to be improved, advanced and connected to classical biological assays. In this review, the viscoelastic nature of cytoskeletal, extracellular and cellular networks is presented and discussed. Viscoelasticity is conceptualized as a major contributor to cell migration and invasion and it is discussed whether it can serve as a biomarker for the cells' migratory capacity in several biological contexts. It can be hypothesized that the statistical mechanics of intra- and extracellular networks may be applied in the future as a powerful tool to explore quantitatively the biomechanical foundation of viscoelasticity over a broad range of time and length scales. Finally, the importance of the cellular viscoelasticity is illustrated in identifying and characterizing multiple disorders, such as cancer, tissue injuries, acute or chronic inflammations or fibrotic diseases.
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Affiliation(s)
- Claudia Tanja Mierke
- Faculty of Physics and Earth Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, University of Leipzig, Leipzig, Germany
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4
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Xie B, Laxman B, Hashemifar S, Stern R, Gilliam TC, Maltsev N, White SR. Chemokine expression in the early response to injury in human airway epithelial cells. PLoS One 2018; 13:e0193334. [PMID: 29534074 PMCID: PMC5849294 DOI: 10.1371/journal.pone.0193334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/08/2018] [Indexed: 12/22/2022] Open
Abstract
Basal airway epithelial cells (AEC) constitute stem/progenitor cells within the central airways and respond to mucosal injury in an ordered sequence of spreading, migration, proliferation, and differentiation to needed cell types. However, dynamic gene transcription in the early events after mucosal injury has not been studied in AEC. We examined gene expression using microarrays following mechanical injury (MI) in primary human AEC grown in submersion culture to generate basal cells and in the air-liquid interface to generate differentiated AEC (dAEC) that include goblet and ciliated cells. A select group of ~150 genes was in differential expression (DE) within 2-24 hr after MI, and enrichment analysis of these genes showed over-representation of functional categories related to inflammatory cytokines and chemokines. Network-based gene prioritization and network reconstruction using the PINTA heat kernel diffusion algorithm demonstrated highly connected networks that were richer in differentiated AEC compared to basal cells. Similar experiments done in basal AEC collected from asthmatic donor lungs demonstrated substantial changes in DE genes and functional categories related to inflammation compared to basal AEC from normal donors. In dAEC, similar but more modest differences were observed. We demonstrate that the AEC transcription signature after MI identifies genes and pathways that are important to the initiation and perpetuation of airway mucosal inflammation. Gene expression occurs quickly after injury and is more profound in differentiated AEC, and is altered in AEC from asthmatic airways. Our data suggest that the early response to injury is substantially different in asthmatic airways, particularly in basal airway epithelial cells.
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Affiliation(s)
- Bingqing Xie
- Department of Human Genetics, University of Chicago, Chicago, IL, United States of America
- Illinois Institute of Technology, Chicago, IL, United States of America
| | - Bharathi Laxman
- Department of Medicine, University of Chicago, Chicago, IL, United States of America
| | - Somaye Hashemifar
- Department of Human Genetics, University of Chicago, Chicago, IL, United States of America
- Toyota Technological Institute at Chicago, Chicago, IL, United States of America
| | - Randi Stern
- Department of Medicine, University of Chicago, Chicago, IL, United States of America
| | - T. Conrad Gilliam
- Department of Human Genetics, University of Chicago, Chicago, IL, United States of America
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, Chicago, IL, United States of America
| | - Steven R. White
- Department of Medicine, University of Chicago, Chicago, IL, United States of America
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5
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Zhang H, Yang J, Walters MS, Staudt MR, Strulovici-Barel Y, Salit J, Mezey JG, Leopold PL, Crystal RG. Mandatory role of HMGA1 in human airway epithelial normal differentiation and post-injury regeneration. Oncotarget 2018; 9:14324-14337. [PMID: 29581847 PMCID: PMC5865673 DOI: 10.18632/oncotarget.24511] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/20/2018] [Indexed: 12/11/2022] Open
Abstract
Due to high levels of expression in aggressive tumors, high mobility group AT-hook 1 (HMGA1) has recently attracted attention as a potential anti-tumor target. However, HMGA1 is also expressed in normal somatic progenitor cells, raising the question: how might systemic anti-HMGA1 therapies affect the structure and function of normal tissue differentiation? In the present study, RNA sequencing data demonstrated HMGA1 is highly expressed in human airway basal stem/progenitor cells (BC), but decreases with BC differentiation in air-liquid interface cultures (ALI). BC collected from nonsmokers, healthy smokers, and smokers with chronic obstructive pulmonary disease (COPD) displayed a range of HMGA1 expression levels. Low initial expression levels of HMGA1 in BC were associated with decreased ability to maintain a differentiated ALI epithelium. HMGA1 down-regulation in BC diminished BC proliferation, suppressed gene expression related to normal proliferation and differentiation, decreased airway epithelial resistance, suppressed junctional and cell polarity gene expression, and delayed wound closure of airway epithelium following injury. Furthermore, silencing of HMGA1 in airway BC in ALI increased the expression of genes associated with airway remodeling in COPD including squamous, epithelial-mesenchymal transition (EMT), and inflammatory genes. Together, the data suggests HMGA1 plays a central role in normal airway differentiation, and thus caution should be used to monitor airway epithelial structure and function in the context of systemic HMGA1-targeted therapies.
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Affiliation(s)
- Haijun Zhang
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jing Yang
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Matthew S Walters
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Michelle R Staudt
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Philip L Leopold
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
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6
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Narożna B, Langwinski W, Jackson C, Lackie P, Holloway JW, Szczepankiewicz A. MicroRNA-328 is involved in wound repair process in human bronchial epithelial cells. Respir Physiol Neurobiol 2017; 242:59-65. [PMID: 28347890 DOI: 10.1016/j.resp.2017.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 03/06/2017] [Accepted: 03/24/2017] [Indexed: 12/26/2022]
Abstract
Our aim was to investigate the role of microRNA on epithelial wound repair by global microRNA silencing. We have also analysed the influence of five miRNAs (miR-328, miR-342, miR-411, miR-609, miR-888, previously identified) on wound repair in 16HBE14o-bronchial epithelial cell line. Cells were transfected with siRNAs against human DROSHA and DICER1 or miRNA mimics or inhibitors. Wounding assays were performed and the cells were observed using time-lapse microscopy. The area of damage was calculated at chosen time points, followed by data analysis. Cells with silenced global miRNA expression showed a significantly slower repair rate compared to the control cells (p=0.001). For miR-328, we observed significantly delayed repair in cells transfected with the inhibitor compared to control (p=0.02). Global microRNA silencing significantly decreased the repair rate of airway epithelial cells in vitro, indicating an important role of miRNA in the regulation of wound repair and that miR-328, possibly involved in actin pathway, may be a potent modifier of this process.
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Affiliation(s)
- Beata Narożna
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 27/33 Szpitalna St., 60-572 Poznan, Poland
| | - Wojciech Langwinski
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 27/33 Szpitalna St., 60-572 Poznan, Poland
| | - Claire Jackson
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Peter Lackie
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Aleksandra Szczepankiewicz
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 27/33 Szpitalna St., 60-572 Poznan, Poland.
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Zhang H, Fu W, Xu Z. Re-epithelialization: a key element in tracheal tissue engineering. Regen Med 2015; 10:1005-23. [PMID: 26388452 DOI: 10.2217/rme.15.68] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Trachea-tissue engineering is a thriving new field in regenerative medicine that is reaching maturity and yielding numerous promising results. In view of the crucial role that the epithelium plays in the trachea, re-epithelialization of tracheal substitutes has gradually emerged as the focus of studies in tissue-engineered trachea. Recent progress in our understanding of stem cell biology, growth factor interactions and transplantation immunobiology offer the prospect of optimization of a tissue-engineered tracheal epithelium. In addition, advances in cell culture technology and successful applications of clinical transplantation are opening up new avenues for the construction of a tissue-engineered tracheal epithelium. Therefore, this review summarizes current advances, unresolved obstacles and future directions in the reconstruction of a tissue-engineered tracheal epithelium.
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Affiliation(s)
- Hengyi Zhang
- Department of Pediatric Cardiothoracic Surgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
| | - Wei Fu
- Department of Pediatric Cardiothoracic Surgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China.,Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
| | - Zhiwei Xu
- Department of Pediatric Cardiothoracic Surgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
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8
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Muhammad SA, Fatima N, Syed NIH, Wu X, Yang XF, Chen JY. MicroRNA Expression Profiling of Human Respiratory Epithelium Affected by Invasive Candida Infection. PLoS One 2015; 10:e0136454. [PMID: 26313489 PMCID: PMC4551683 DOI: 10.1371/journal.pone.0136454] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/03/2015] [Indexed: 11/18/2022] Open
Abstract
Invasive candidiasis is potentially life-threatening systemic fungal infection caused by Candida albicans (C. albicans). Candida enters the blood stream and disseminate throughout the body and it is often observed in hospitalized patients, immunocompromised individuals or those with chronic diseases. This infection is opportunistic and risk starts with the colonization of C. albicans on mucocutaneous surfaces and respiratory epithelium. MicroRNAs (miRNAs) are small non-coding RNAs which are involved in the regulation of virtually every cellular process. They regulate and control the levels of mRNA stability and post-transcriptional gene expression. Aberrant expression of miRNAs has been associated in many disease states, and miRNA-based therapies are in progress. In this study, we investigated possible variations of miRNA expression profiles of respiratory epithelial cells infected by invasive Candida species. For this purpose, respiratory epithelial tissues of infected individuals from hospital laboratory were accessed before their treatment. Invasive Candida infection was confirmed by isolation of Candia albicans from the blood cultures of the same infected individuals. The purity of epithelial tissues was assessed by flow cytometry (FACSCalibur cytometer; BD Biosciences, Heidelberg, Germany) using statin antibody (S-44). TaqMan quantitative real-time PCR (in a TaqMan Low Density Array format) was used for miRNA expression profiling. MiRNAs investigated, the levels of expression of 55 miRNA were significantly altered in infected tissues. Some miRNAs showed dramatic increase (miR-16-1) or decrease of expression (miR-17-3p) as compared to control. Gene ontology enrichment analysis of these miRNA-targeted genes suggests that Candidal infection affect many important biological pathways. In summary, disturbance in miRNA expression levels indicated the change in cascade of pathological processes and the regulation of respiratory epithelial functions following invasive Candidal infection. These findings contribute to our understanding of host cell response to Candidal systemic infections.
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Affiliation(s)
- Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University (BZU), Multan, Pakistan
| | - Nighat Fatima
- Department of Pharmacy, COMSATS Institute of Information Technology, Abbottabad, 22060, Pakistan
| | | | - Xiaogang Wu
- Institute for Systems Biology (ISB), Seattle, WA, United States of America
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Jake Y Chen
- Indiana Center for Systems Biology and Personalized Medicine, Indiana University-Purdue University, Indianapolis, IN, United States of America; School of Informatics and Computing, Indiana University, Indianapolis, IN, United States of America; Department of Computer and Information Science, School of Science Purdue University, Indianapolis, IN, United States of America; Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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9
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Clarke LA, Botelho HM, Sousa L, Falcao AO, Amaral MD. Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators. Genomics 2015. [PMID: 26225835 DOI: 10.1016/j.ygeno.2015.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A meta-analysis of 13 independent microarray data sets was performed and gene expression profiles from cystic fibrosis (CF), similar disorders (COPD: chronic obstructive pulmonary disease, IPF: idiopathic pulmonary fibrosis, asthma), environmental conditions (smoking, epithelial injury), related cellular processes (epithelial differentiation/regeneration), and non-respiratory "control" conditions (schizophrenia, dieting), were compared. Similarity among differentially expressed (DE) gene lists was assessed using a permutation test, and a clustergram was constructed, identifying common gene markers. Global gene expression values were standardized using a novel approach, revealing that similarities between independent data sets run deeper than shared DE genes. Correlation of gene expression values identified putative gene regulators of the CF transmembrane conductance regulator (CFTR) gene, of potential therapeutic significance. Our study provides a novel perspective on CF epithelial gene expression in the context of other lung disorders and conditions, and highlights the contribution of differentiation/EMT and injury to gene signatures of respiratory disease.
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Affiliation(s)
- Luka A Clarke
- University of Lisboa, Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Hugo M Botelho
- University of Lisboa, Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Lisete Sousa
- University of Lisboa, Faculty of Sciences, DEIO and CEAUL, Portugal
| | - Andre O Falcao
- University of Lisboa, Faculty of Sciences, Department of Informatics, Portugal
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
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Abstract
A characteristic feature of the human airway epithelium is the presence of ciliated cells bearing motile cilia, specialized cell surface projections containing axonemes composed of microtubules and dynein arms, which provide ATP-driven motility. In the airways, cilia function in concert with airway mucus to mediate the critical function of mucociliary clearance, cleansing the airways of inhaled particles and pathogens. The prototypical disorder of respiratory cilia is primary ciliary dyskinesia, an inherited disorder that leads to impaired mucociliary clearance, to repeated chest infections, and to the progressive destruction of lung architecture. Numerous acquired lung diseases are also marked by abnormalities in both cilia structure and function. In this review we summarize current knowledge regarding airway ciliated cells and cilia, how they function to maintain a healthy epithelium, and how disorders of cilia structure and function contribute to inherited and acquired lung disease.
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11
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McErlean P, Berdnikovs S, Favoreto S, Shen J, Biyasheva A, Barbeau R, Eisley C, Barczak A, Ward T, Schleimer RP, Erle DJ, Boushey HA, Avila PC. Asthmatics with exacerbation during acute respiratory illness exhibit unique transcriptional signatures within the nasal mucosa. Genome Med 2014; 6:1. [PMID: 24433494 PMCID: PMC3971347 DOI: 10.1186/gm520] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/08/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Acute respiratory illness is the leading cause of asthma exacerbations yet the mechanisms underlying this association remain unclear. To address the deficiencies in our understanding of the molecular events characterizing acute respiratory illness-induced asthma exacerbations, we undertook a transcriptional profiling study of the nasal mucosa over the course of acute respiratory illness amongst individuals with a history of asthma, allergic rhinitis and no underlying respiratory disease. METHODS Transcriptional profiling experiments were performed using the Agilent Whole Human Genome 4X44K array platform. Time point-based microarray and principal component analyses were conducted to identify and distinguish acute respiratory illness-associated transcriptional profiles over the course of our study. Gene enrichment analysis was conducted to identify biological processes over-represented within each acute respiratory illness-associated profile, and gene expression was subsequently confirmed by quantitative polymerase chain reaction. RESULTS We found that acute respiratory illness is characterized by dynamic, time-specific transcriptional profiles whose magnitudes of expression are influenced by underlying respiratory disease and the mucosal repair signature evoked during acute respiratory illness. Most strikingly, we report that people with asthma who experience acute respiratory illness-induced exacerbations are characterized by a reduced but prolonged inflammatory immune response, inadequate activation of mucosal repair, and the expression of a newly described exacerbation-specific transcriptional signature. CONCLUSION Findings from our study represent a significant contribution towards clarifying the complex molecular interactions that typify acute respiratory illness-induced asthma exacerbations.
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Affiliation(s)
- Peter McErlean
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sergejs Berdnikovs
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Silvio Favoreto
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Junqing Shen
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Assel Biyasheva
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rebecca Barbeau
- Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility, University of California San Francisco, San Francisco, CA, USA
| | - Chris Eisley
- Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Barczak
- Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility, University of California San Francisco, San Francisco, CA, USA
| | - Theresa Ward
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Robert P Schleimer
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - David J Erle
- Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Homer A Boushey
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Pedro C Avila
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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12
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Walters MS, Gomi K, Ashbridge B, Moore MAS, Arbelaez V, Heldrich J, Ding BS, Rafii S, Staudt MR, Crystal RG. Generation of a human airway epithelium derived basal cell line with multipotent differentiation capacity. Respir Res 2013; 14:135. [PMID: 24298994 PMCID: PMC3907041 DOI: 10.1186/1465-9921-14-135] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 10/22/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND As the multipotent progenitor population of the airway epithelium, human airway basal cells (BC) replenish the specialized differentiated cell populations of the mucociliated airway epithelium during physiological turnover and repair. Cultured primary BC divide a limited number of times before entering a state of replicative senescence, preventing the establishment of long-term replicating cultures of airway BC that maintain their original phenotype. METHODS To generate an immortalized human airway BC cell line, primary human airway BC obtained by brushing the airway epithelium of healthy nonsmokers were infected with a retrovirus expressing human telomerase (hTERT). The resulting immortalized cell line was then characterized under non-differentiating and differentiating air-liquid interface (ALI) culture conditions using ELISA, TaqMan quantitative PCR, Western analysis, and immunofluorescent and immunohistochemical staining analysis for cell type specific markers. In addition, the ability of the cell line to respond to environmental stimuli under differentiating ALI culture was assessed. RESULTS We successfully generated an immortalized human airway BC cell line termed BCi-NS1 via expression of hTERT. A single cell derived clone from the parental BCi-NS1 cells, BCi-NS1.1, retains characteristics of the original primary cells for over 40 passages and demonstrates a multipotent differentiation capacity into secretory (MUC5AC, MUC5B), goblet (TFF3), Clara (CC10) and ciliated (DNAI1, FOXJ1) cells on ALI culture. The cells can respond to external stimuli such as IL-13, resulting in alteration of the normal differentiation process. CONCLUSION Development of immortalized human airway BC that retain multipotent differentiation capacity over long-term culture should be useful in understanding the biology of BC, the response of BC to environmental stress, and as a target for assessment of pharmacologic agents.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York NY, USA.
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13
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Szczepankiewicz A, Lackie PM, Holloway JW. Altered microRNA expression profile during epithelial wound repair in bronchial epithelial cells. BMC Pulm Med 2013; 13:63. [PMID: 24188858 PMCID: PMC4229315 DOI: 10.1186/1471-2466-13-63] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 10/31/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Airway epithelial cells provide a protective barrier against environmental particles including potential pathogens. Epithelial repair in response to tissue damage is abnormal in asthmatic airway epithelium in comparison to the repair of normal epithelium after damage. The complex mechanisms coordinating the regulation of the processes involved in wound repair requires the phased expression of networks of genes. Small non-coding RNA molecules termed microRNAs (miRNAs) play a critical role in such coordinated regulation of gene expression. We aimed to establish if the phased expression of specific miRNAs is correlated with the repair of mechanically induced damage to the epithelium. METHODS To investigate the possible involvement of miRNA in epithelial repair, we analyzed miRNA expression profiles during epithelial repair in a cell culture model using TaqMan-based quantitative real-time PCR in a TaqMan Low Density Array format. The expression of 754 miRNA genes at seven time points in a 48-hour period during the wound repair process was profiled using the bronchial epithelial cell line 16HBE14o- growing in monolayer. RESULTS The expression levels of numerous miRNAs were found to be altered during the wound repair process. These miRNA genes were clustered into 3 different patterns of expression that correlate with the further regulation of several biological pathways involved in wound repair. Moreover, it was observed that expression of some miRNA genes were significantly altered only at one time point, indicating their involvement in a specific stage of the epithelial wound repair. CONCLUSIONS In summary, miRNA expression is modulated during the normal repair processes in airway epithelium in vitro suggesting a potential role in regulation of wound repair.
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Affiliation(s)
- Aleksandra Szczepankiewicz
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 27/33 Szpitalna St,, 60-572 Poznan, Poland.
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14
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Roth HM, Wadsworth SJ, Kahn M, Knight DA. The airway epithelium in asthma: developmental issues that scar the airways for life? Pulm Pharmacol Ther 2012; 25:420-6. [PMID: 23022283 DOI: 10.1016/j.pupt.2012.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 08/19/2012] [Accepted: 09/11/2012] [Indexed: 11/30/2022]
Abstract
While allergies are very common, affecting ∼40% of the population in most Western countries, only a proportion of allergic people develop asthma. This highlights the importance of tissue and cell specific mechanisms that contribute to the disease. As the interface between the inhaled environment and the internal environment of the lung, the epithelium normally possesses numerous mechanisms to maintain an effective protective barrier. However, the inability of the airway epithelium of asthmatics to effectively defend the lung against normally innocuous inhaled agents strongly suggests that asthma must involve defects in the epithelial barrier rather than being primarily an allergic disease. Evidence is accumulating that in asthma, the epithelium does not go through normal stages of development and differentiation and as a consequence, remain somewhat "immature". This in turn leads to a chronic cycle of dysregulated damage and repair which ultimately impacts on the airways function by increasing inflammation, but also by initiating processes that ultimately lead to changes to the structure and function of the airway.
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Affiliation(s)
- Hollis M Roth
- UBC James Hogg Research Centre, Institute for Heart + Lung Health, Canada
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15
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Yahaya B. Understanding cellular mechanisms underlying airway epithelial repair: selecting the most appropriate animal models. ScientificWorldJournal 2012; 2012:961684. [PMID: 23049478 PMCID: PMC3461624 DOI: 10.1100/2012/961684] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 08/07/2012] [Indexed: 12/18/2022] Open
Abstract
Understanding the mechanisms underlying the process of regeneration and repair of airway epithelial structures demands close characterization of the associated cellular and molecular events. The choice of an animal model system to study these processes and the role of lung stem cells is debatable since ideally the chosen animal model should offer a valid comparison with the human lung. Species differences may include the complex three-dimensional lung structures, cellular composition of the lung airway as well as transcriptional control of the molecular events in response to airway epithelium regeneration, and repair following injury. In this paper, we discuss issues related to the study of the lung repair and regeneration including the role of putative stem cells in small- and large-animal models. At the end of this paper, the author discuss the potential for using sheep as a model which can help bridge the gap between small-animal model systems and humans.
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Affiliation(s)
- B Yahaya
- Cluster for Regenerative Medicine, Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bandar Putra Bertam, Penang, Kepala Batas, Malaysia.
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16
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Curradi G, Walters MS, Ding BS, Rafii S, Hackett NR, Crystal RG. Airway basal cell vascular endothelial growth factor-mediated cross-talk regulates endothelial cell-dependent growth support of human airway basal cells. Cell Mol Life Sci 2012; 69:2217-31. [PMID: 22382924 DOI: 10.1007/s00018-012-0922-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Revised: 12/19/2011] [Accepted: 01/10/2012] [Indexed: 12/16/2022]
Abstract
The human airway epithelium is a pseudostratified heterogenous layer comprised of ciliated, secretory, intermediate, and basal cells. As the stem/progenitor population of the airway epithelium, airway basal cells differentiate into ciliated and secretory cells to replenish the airway epithelium during physiological turnover and repair. Transcriptome analysis of airway basal cells revealed high expression of vascular endothelial growth factor A (VEGFA), a gene not typically associated with the function of this cell type. Using cultures of primary human airway basal cells, we demonstrate that basal cells express all of the three major isoforms of VEGFA (121, 165 and 189) but lack functional expression of the classical VEGFA receptors VEGFR1 and VEGFR2. The VEGFA is actively secreted by basal cells and while it appears to have no direct autocrine function on basal cell growth and proliferation, it functions in a paracrine manner to activate MAPK signaling cascades in endothelium via VEGFR2-dependent signaling pathways. Using a cytokine- and serum-free co-culture system of primary human airway basal cells and human endothelial cells revealed that basal cell-secreted VEGFA activated endothelium to express mediators that, in turn, stimulate and support basal cell proliferation and growth. These data demonstrate novel VEGFA-mediated cross-talk between airway basal cells and endothelium, the purpose of which is to modulate endothelial activation and in turn stimulate and sustain basal cell growth.
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Affiliation(s)
- Giacomo Curradi
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10065, USA
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17
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Engineering airway epithelium. J Biomed Biotechnol 2012; 2012:982971. [PMID: 22523471 PMCID: PMC3304574 DOI: 10.1155/2012/982971] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/28/2011] [Accepted: 10/30/2011] [Indexed: 12/11/2022] Open
Abstract
Airway epithelium is constantly presented with injurious signals, yet under healthy circumstances, the epithelium maintains its innate immune barrier and mucociliary elevator function. This suggests that airway epithelium has regenerative potential (I. R. Telford and C. F. Bridgman, 1990). In practice, however, airway regeneration is problematic because of slow turnover and dedifferentiation of epithelium thereby hindering regeneration and increasing time necessary for full maturation and function. Based on the anatomy and biology of the airway epithelium, a variety of tissue engineering tools available could be utilized to overcome the barriers currently seen in airway epithelial generation. This paper describes the structure, function, and repair mechanisms in native epithelium and highlights specific and manipulatable tissue engineering signals that could be of great use in the creation of artificial airway epithelium.
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18
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Stewart CE, Nijmeh HS, Brightling CE, Sayers I. uPAR regulates bronchial epithelial repair in vitro and is elevated in asthmatic epithelium. Thorax 2011; 67:477-87. [PMID: 22139533 PMCID: PMC3358731 DOI: 10.1136/thoraxjnl-2011-200508] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background The asthma-associated gene urokinase plasminogen activator receptor (uPAR) may be involved in epithelial repair and airway remodelling. These processes are not adequately targeted by existing asthma therapies. A fuller understanding of the pathways involved in remodelling may lead to development of new therapeutic opportunities. uPAR expression in the lung epithelium of normal subjects and patients with asthma was investigated and the contribution of uPAR to epithelial wound repair in vitro was studied using primary bronchial epithelial cells (NHBECs). Methods Bronchial biopsy sections from normal subjects and patients with asthma were immunostained for uPAR. NHBECs were used in a scratch wound model to investigate the contribution of the plasminogen pathway to repair. The pathway was targeted via blocking of the interaction between urokinase plasminogen activator (uPA) and uPAR and overexpression of uPAR. The rate of wound closure and activation of intracellular signalling pathways and matrix metalloproteinases (MMPs) were measured. Results uPAR expression was significantly increased in the bronchial epithelium of patients with asthma compared with controls. uPAR expression was increased during wound repair in monolayer and air-liquid interface-differentiated NHBEC models. Blocking the uPA–uPAR interaction led to attenuated wound repair via changes in Erk1/2, Akt and p38MAPK signalling. Cells engineered to have raised levels of uPAR showed attenuated repair via sequestration of uPA by soluble uPAR. Conclusions The uPAR pathway is required for efficient epithelial wound repair. Increased uPAR expression, as seen in the bronchial epithelium of patients with asthma, leads to attenuated wound repair which may contribute to the development and progression of airway remodelling in asthma. This pathway may therefore represent a potential novel therapeutic target for the treatment of asthma.
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Affiliation(s)
- Ceri E Stewart
- Division of Therapeutics and Molecular Medicine, Nottingham Respiratory Biomedical Research Unit, University Hospital of Nottingham, Nottingham NG7 2UH, UK
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19
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Santa Maria PL, Redmond SL, McInnes RL, Atlas MD, Ghassemifar R. Tympanic membrane wound healing in rats assessed by transcriptome profiling. Laryngoscope 2011; 121:2199-213. [PMID: 21919009 DOI: 10.1002/lary.22150] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 06/14/2011] [Indexed: 11/06/2022]
Abstract
OBJECTIVES/HYPOTHESIS The aim of this study is to elucidate transcriptional changes that occur in response to tympanic membrane (TM) perforation in rats and to infer key genes and molecular events in the healing process. STUDY DESIGN A prospective cohort study of 393 male Sprague-Dawley (Rattus norvegicus) rats. METHODS Sprague-Dawley rats were randomly allocated into either control or perforation groups spanning a 7-day time period. Perforation groups consisted of 12-hour, 24-hour, 36-hour, 2-day, 3-day, 4-day, 5-day, six-day, and 7-day time points. The left TMs of all perforation groups were perforated and the RNA extracted at the specified time point postperforation. Subsequent analysis was performed using Agilent's 4 × 44 k whole rat genome arrays (40 in total) to assess wound-healing gene expression over a 7-day time period. RESULTS Over a 7-day time course and at nine time points that encompassed the wounding and progression of healing, a total of 3,262 genes were differentially expressed. In this study the transcripts most upregulated occurred at 12 hours. These were Stefin A2 (344-fold), Stefin 2 (143-fold), and Natriuretic peptide precursor type B (222-fold). Those most downregulated also occurred at 12 hours. These were alcohol dehydrogenase 7 (13.1-fold) and gamma-butyrobetaine hydroxylase (10.4-fold). Results were validated by quantitative real-time polymerase chain reaction. CONCLUSIONS The findings of this study provide a baseline against which to identify disease-related molecular signatures, biomarkers, and to develop new treatments for TM conditions based on molecular evidence.
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Affiliation(s)
- Peter L Santa Maria
- Ear Sciences Centre, School of Surgery, The University of Western Australia, Perth, Australia.
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20
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Yahaya B, Baker A, Tennant P, Smith SH, Shaw DJ, McLachlan G, Collie DDS. Analysis of airway epithelial regeneration and repair following endobronchial brush biopsy in sheep. Exp Lung Res 2011; 37:519-35. [PMID: 21895444 DOI: 10.3109/01902148.2011.605513] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Understanding the fundamental processes involved in repairing the airway wall following injury is fundamental to understanding the way in which these processes are perturbed during disease pathology. Indeed complex diseases such as asthma and chronic obstructive pulmonary disease (COPD) have at their core evidence of airway wall remodeling processes that play a crucial functional role in these diseases. The authors sought to understand the dynamic cellular events that occur during bronchial airway epithelial repair in sheep. The injury was induced by endobronchial brush biopsy (BBr), a process that causes epithelial débridement and induces a consequential repair process. In addition, the current experimental protocol allowed for the time-dependent changes in airway wall morphology to be studied both within and between animals. The initial débridement was followed by evidence of dedifferentiation in the intact epithelium at the wound margins, followed by proliferation of cells both within the epithelium and in the deeper wall structures, notably in association with the submucosal glands and smooth muscle bundles. Seven days after injury, although the airway wall was thickened at the site of damage, the epithelial layer was intact, with evidence of redifferentiation. These studies, in demonstrating broad agreement with previous studies in small animals, indicate the wider relevance of this system as a comparative model and should provide a solid basis upon which to further characterize the critical cellular and molecular interactions that underlie both effective restitution and pathological repair.
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Affiliation(s)
- B Yahaya
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian Kelantan, Malaysia.
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21
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Hackett NR, Shaykhiev R, Walters MS, Wang R, Zwick RK, Ferris B, Witover B, Salit J, Crystal RG. The human airway epithelial basal cell transcriptome. PLoS One 2011; 6:e18378. [PMID: 21572528 PMCID: PMC3087716 DOI: 10.1371/journal.pone.0018378] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 03/05/2011] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The human airway epithelium consists of 4 major cell types: ciliated, secretory, columnar and basal cells. During natural turnover and in response to injury, the airway basal cells function as stem/progenitor cells for the other airway cell types. The objective of this study is to better understand human airway epithelial basal cell biology by defining the gene expression signature of this cell population. METHODOLOGY/PRINCIPAL FINDINGS Bronchial brushing was used to obtain airway epithelium from healthy nonsmokers. Microarrays were used to assess the transcriptome of basal cells purified from the airway epithelium in comparison to the transcriptome of the differentiated airway epithelium. This analysis identified the "human airway basal cell signature" as 1,161 unique genes with >5-fold higher expression level in basal cells compared to differentiated epithelium. The basal cell signature was suppressed when the basal cells differentiated into a ciliated airway epithelium in vitro. The basal cell signature displayed overlap with genes expressed in basal-like cells from other human tissues and with that of murine airway basal cells. Consistent with self-modulation as well as signaling to other airway cell types, the human airway basal cell signature was characterized by genes encoding extracellular matrix components, growth factors and growth factor receptors, including genes related to the EGF and VEGF pathways. Interestingly, while the basal cell signature overlaps that of basal-like cells of other organs, the human airway basal cell signature has features not previously associated with this cell type, including a unique pattern of genes encoding extracellular matrix components, G protein-coupled receptors, neuroactive ligands and receptors, and ion channels. CONCLUSION/SIGNIFICANCE The human airway epithelial basal cell signature identified in the present study provides novel insights into the molecular phenotype and biology of the stem/progenitor cells of the human airway epithelium.
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Affiliation(s)
- Neil R. Hackett
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Renat Shaykhiev
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Matthew S. Walters
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Rui Wang
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Rachel K. Zwick
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Barbara Ferris
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Bradley Witover
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
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Wang R, Ahmed J, Wang G, Hassan I, Strulovici-Barel Y, Hackett NR, Crystal RG. Down-regulation of the canonical Wnt β-catenin pathway in the airway epithelium of healthy smokers and smokers with COPD. PLoS One 2011; 6:e14793. [PMID: 21490961 PMCID: PMC3072378 DOI: 10.1371/journal.pone.0014793] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Accepted: 02/14/2011] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The Wnt pathway mediates differentiation of epithelial tissues; depending on the tissue types, Wnt can either drive or inhibit the differentiation process. We hypothesized that key genes in the Wnt pathway are suppressed in the human airway epithelium under the stress of cigarette smoking, a stress associated with dysregulation of the epithelial differentiated state. METHODOLOGY/PRINCIPAL FINDINGS Microarrays were used to assess the expression of Wnt-related genes in the small airway epithelium (SAE) obtained via bronchoscopy and brushing of healthy nonsmokers, healthy smokers, and smokers with COPD. Thirty-three of 56 known Wnt-related genes were expressed in the SAE. Wnt pathway downstream mediators β-catenin and the transcription factor 7-like 1 were down-regulated in healthy smokers and smokers with COPD, as were many Wnt target genes. Among the extracellular regulators that suppress the Wnt pathway, secreted frizzled-related protein 2 (SFRP2), was up-regulated 4.3-fold in healthy smokers and 4.9-fold in COPD smokers, an observation confirmed by TaqMan Real-time PCR, Western analysis and immunohistochemistry. Finally, cigarette smoke extract mediated up-regulation of SFRP2 and down-regulation of Wnt target genes in airway epithelial cells in vitro. CONCLUSIONS/SIGNIFICANCE Smoking down-regulates the Wnt pathway in the human airway epithelium. In the context that Wnt pathway plays an important role in differentiation of epithelial tissues, the down-regulation of Wnt pathway may contribute to the dysregulation of airway epithelium differentiation observed in smoking-related airway disorders.
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Affiliation(s)
- Rui Wang
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Joumana Ahmed
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Guoqing Wang
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Ibrahim Hassan
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Yael Strulovici-Barel
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Neil R. Hackett
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
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Herranz C, Melero JA, Martínez I. Reduced innate immune response, apoptosis, and virus release in cells cured of respiratory syncytial virus persistent infection. Virology 2011; 410:56-63. [DOI: 10.1016/j.virol.2010.10.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 08/25/2010] [Accepted: 10/24/2010] [Indexed: 12/24/2022]
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Abstract
Airway epithelia are continuously damaged by airborne pollutants, pathogens and allergens, and they rely on intrinsic mechanisms to restore barrier integrity. Epithelial repair is a multi-step process including cell migration into the wounded area, proliferation, differentiation and matrix deposition. Each step requires the secretion of various molecules, including growth factors, integrins and matrix metalloproteinases. Evidence is emerging that purinergic signaling promotes repair in human airway epithelia. An injury induces ATP release, which binds P2Y(2) receptors (P2Y(2)Rs) to initiate protein kinase C (PKC)-dependent oxidative activation of TNFα-converting enzyme (TACE), which then releases the membrane-bound ligands of the epidermal growth factor receptor (EGFR). The P2Y(2)R- and EGFR-dependent signaling cascades converge to induce mediator release, whereas the latter also induces cytoskeletal rearrangement for cell migration and proliferation. Similar roles for purinergic signaling are reported in pulmonary endothelial cells, smooth muscle cells and fibroblasts. In chronic airway diseases, the aberrant regulation of extracellular purines is implicated in the development of airway remodeling by mucus cell metaplasia and hypersecretion, excess collagen deposition, fibrosis and neovascularization. This chapter describes the crosstalk between these signaling cascades and discusses the impact of deregulated purinergic signaling in chronic lung diseases.
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Lee JS, Kim JH, Bae JS, Kim JY, Park TJ, Pasaje CF, Park BL, Cheong HS, Uh ST, Park JS, Jang AS, Kim MK, Choi IS, Park CS, Shin HD. Association of CACNG6 polymorphisms with aspirin-intolerance asthmatics in a Korean population. BMC MEDICAL GENETICS 2010; 11:138. [PMID: 20860846 PMCID: PMC2954844 DOI: 10.1186/1471-2350-11-138] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/23/2010] [Indexed: 12/13/2022]
Abstract
BACKGROUND Aspirin-intolerant asthma (AIA) occurs in the lower and upper airways through excessive production of leukotrienes upon administration of non-steroidal anti-inflammatory drugs (NSAIDs). One of the three symptoms of AIA is nasal polyposis, a chronic inflammatory disease that is related to the function of calcium ion in recruitment of immune cells during airway inflammation. It has been implicated that bronchodilation in the airway is related to Ca(2+) regulation. The calcium channel, voltage-dependent, gamma subunit 6 (CACNG6) gene encodes a protein that stabilizes the calcium channel. METHODS To study the associations between AIA and polymorphisms in CACNG6 gene, eight variants were genotyped in 102 AIA cases and 429 aspirin-tolerant asthma (ATA) controls. Logistic analyses were used to evaluate the associations of CACNG6 polymorphisms with AIA. RESULTS Statistical analyses revealed that a single nucleotide polymorphism (SNP; rs192808C > T; P = 0.0004, Pcorr = 0.0029, OR = 2.88 in co-dominant model; P = 0.0005, Pcorr = 0.0036, OR = 2.99 in dominant model) in intron and a haplotype unique to this variant (CACNG6_BL1_ht6; P = 0.003, Pcorr = 0.02, OR = 2.57 in co-dominant model, P = 0.001, Pcorr = 0.0087, OR = 2.81 in dominant model) were significantly associated with the risk of AIA. CONCLUSIONS Our results suggest that the CACNG6 variants might be associated with the risk of AIA in a Korean population.
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Affiliation(s)
- Jin Sol Lee
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
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Schiller KR, Maniak PJ, O'Grady SM. Cystic fibrosis transmembrane conductance regulator is involved in airway epithelial wound repair. Am J Physiol Cell Physiol 2010; 299:C912-21. [PMID: 20686068 DOI: 10.1152/ajpcell.00215.2010] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The role of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) in airway epithelial wound repair was investigated using normal human bronchial epithelial (NHBE) cells and a human airway epithelial cell line (Calu-3) of serous gland origin. Measurements of wound repair were performed using continuous impedance sensing to determine the time course for wound closure. Control experiments showed that the increase in impedance corresponding to cell migration into the wound was blocked by treatment with the actin polymerization inhibitor, cytochalasin D. Time lapse imaging revealed that NHBE and Calu-3 cell wound closure was dependent on cell migration, and that movement occurred as a collective sheet of cells. Selective inhibition of CFTR activity with CFTR(inh)-172 or short hairpin RNA silencing of CFTR expression produced a significant delay in wound repair. The CF cell line UNCCF1T also exhibited significantly slower migration than comparable normal airway epithelial cells. Inhibition of CFTR-dependent anion transport by treatment with CFTR(inh)-172 slowed wound closure to the same extent as silencing CFTR protein expression, indicating that ion transport by CFTR plays a critical role in migration. Moreover, morphologic analysis of migrating cells revealed that CFTR inhibition or silencing significantly reduced lamellipodia protrusion. These findings support the conclusion that CFTR participates in airway epithelial wound repair by a mechanism involving anion transport that is coupled to the regulation of lamellipodia protrusion at the leading edge of the cell.
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Affiliation(s)
- Katherine R Schiller
- Graduate Program in Comparative Molecular Biosciences, University of Minnesota, St. Paul, Minnesota 55108, USA
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Mehrani H, Ghanei M, Aslani J, Golmanesh L. Bronchoalveolar lavage fluid proteomic patterns of sulfur mustard-exposed patients. Proteomics Clin Appl 2009; 3:1191-200. [PMID: 21136943 DOI: 10.1002/prca.200900001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2009] [Revised: 03/16/2009] [Accepted: 06/25/2009] [Indexed: 11/11/2022]
Abstract
Sulfur mustard is an alkylating agent that reacts with ocular, respiratory, cutaneous, and bone marrow tissues. Main late respiratory complications are chronic obstructive pulmonary disease, bronchiectasis, asthma, and bronchiolitis obliterans. The aim of the present study was to identify differentially expressed proteins in bronchoalveolar lavage (BAL) fluid of control healthy and sulfur mustard-exposed lung disease patients. The BAL protein profile of ten healthy and 30 exposed patients with mild, moderate, and severe conditions (ten males in each group) were separated with 2-D SDS-PAGE and differentially expressed protein spots were successfully identified with MALDI TOF TOF MS. Among the differentially expressed proteins we observed a significant increase in vitamin D binding protein isoforms, haptoglobin isoforms, and fibrinogen especially in exposed moderate and severe lung diseases patients (p<0.01). Moreover, compared with healthy controls, significant decreases was noted in calcyphosine, surfactant protein A, and transthyretin in these patients (p<0.01). Apolipoprotein A1 was detected in all patients' BAL fluid but none of the healthy controls. Furthermore, S100 calcium-binding protein A8 was only detected in BAL fluid of moderate and severe groups. These findings will be useful to improve current methods of monitoring and helps to identify new therapeutic targets for treatment of this complicated illness.
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Affiliation(s)
- Hossein Mehrani
- Laboratory of Proteomics, Faculty of Medicine and Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran. ,
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Turetz ML, O'Connor TP, Tilley AE, Strulovici-Barel Y, Salit J, Dang D, Teater M, Mezey J, Clark AG, Crystal RG. Trachea epithelium as a "canary" for cigarette smoking-induced biologic phenotype of the small airway epithelium. Clin Transl Sci 2009; 2:260-72. [PMID: 20443905 PMCID: PMC3875387 DOI: 10.1111/j.1752-8062.2009.00129.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The initial site of smoking-induced lung disease is the small airway epithelium, which is difficult and time consuming to sample by fiberoptic bronchoscopy. We developed a rapid, office-based procedure to obtain trachea epithelium without conscious sedation from healthy nonsmokers (n= 26) and healthy smokers (n= 19, 27 +/- 15 pack-year). Gene expression differences (fold change >1.5, p < 0.01, Benjamini-Hochberg correction) were assessed with Affymetrix microarrays. A total of 1,057 probe sets were differentially expressed in healthy smokers versus nonsmokers, representing >500 genes. Trachea gene expression was compared to an independent group of small airway epithelial samples (n= 23 healthy nonsmokers, n= 19 healthy smokers, 25 +/- 12 pack-year). The trachea epithelium is more sensitive to smoking, responding with threefold more differentially expressed genes than small airway epithelium. The trachea transcriptome paralleled the small airway epithelium, with 156 of 167 (93%) genes that are significantly up- and downregulated by smoking in the small airway epithelium showing similar direction and magnitude of response to smoking in the trachea. Trachea epithelium can be obtained without conscious sedation, representing a less invasive surrogate "canary" for smoking-induced changes in the small airway epithelium. This should prove useful in epidemiologic studies correlating gene expression with clinical outcome in assessing smoking-induced lung disease.
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Affiliation(s)
- Meredith L Turetz
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College New York, New York, USA
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29
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Abstract
The adult human bronchial tree is covered with a continuous layer of epithelial cells that play a critical role in maintaining the conduit for air, and which are central to the defenses of the lung against inhaled environmental concomitants. The epithelial sheet functions as an interdependent unit with the other lung components. Importantly, the structure and/or function of airway epithelium is deranged in major lung disorders, including chronic obstructive pulmonary disease, asthma, and bronchogenic carcinoma. Investigations regarding the airway epithelium have led to many advances over the past few decades, but new developments in genetics and stem cell/progenitor cell biology have opened the door to understanding how the airway epithelium is developed and maintained, and how it responds to environmental stress. This article provides an overview of the current state of knowledge regarding airway epithelial stem/progenitor cells, gene expression, cell-cell interactions, and less frequent cell types, and discusses the challenges for future areas of investigation regarding the airway epithelium in health and disease.
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30
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Kazeros A, Harvey BG, Carolan BJ, Vanni H, Krause A, Crystal RG. Overexpression of apoptotic cell removal receptor MERTK in alveolar macrophages of cigarette smokers. Am J Respir Cell Mol Biol 2008; 39:747-57. [PMID: 18587056 DOI: 10.1165/rcmb.2007-0306oc] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Mononuclear phagocytes play an important role in the removal of apoptotic cells by expressing cell surface receptors that recognize and remove apoptotic cells. Based on the knowledge that cigarette smoking is associated with increased lung cell turnover, we hypothesized that alveolar macrophages (AMs) of normal cigarette smokers may exhibit enhanced expression of apoptotic cell removal receptor genes. AMs obtained by bronchoalveolar lavage of normal nonsmokers (n = 11) and phenotypic normal smokers (n = 13; 36 +/- 6 pack-years) were screened for mRNA expression of all known apoptotic cell removal receptors using Affymetrix HG-U133 Plus 2.0 microarray chips with TaqMan RT-PCR confirmation. Of the 14 known apoptotic receptors expressed, only MER tyrosine kinase (MERTK), a transmembrane tyrosine kinase receptor, was significantly up-regulated in smokers. MERTK expression was then assessed in AMs of smokers versus nonsmokers by TaqMan RT-PCR, immunocytochemistry, Western analysis, and flow analysis. Smoker AMs had up-regulation of MERTK mRNA levels (smoker vs. nonsmoker: 3.6-fold by microarray, P < 0.003; 9.5-fold by TaqMan RT-PCR, P < 0.02). Immunocytochemistry demonstrated a qualitative increase in MERTK protein expression on AMs of smokers. Increased protein expression of MERTK on AMs of smokers was confirmed by Western and flow analyses (P < 0.007 and P < 0.0002, respectively). MERTK, a cell surface receptor that recognizes apoptotic cells, is expressed on human AMs, and its expression is up-regulated in AMs of cigarette smokers. This up-regulation of MERTK may reflect an increased demand for removal of apoptotic cells in smokers, an observation with implications for the development of chronic obstructive pulmonary disease, a disorder associated with dysregulated apoptosis of lung parenchymal cells.
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Affiliation(s)
- Angeliki Kazeros
- Division of Pulmonary and Critical Care, Weill Medical College of Cornell University, New York, New York 10065, USA
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31
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Wagh AA, Roan E, Chapman KE, Desai LP, Rendon DA, Eckstein EC, Waters CM. Localized elasticity measured in epithelial cells migrating at a wound edge using atomic force microscopy. Am J Physiol Lung Cell Mol Physiol 2008; 295:L54-60. [PMID: 18487359 DOI: 10.1152/ajplung.00475.2007] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Restoration of lung homeostasis following injury requires efficient wound healing by the epithelium. The mechanisms of lung epithelial wound healing include cell spreading and migration into the wounded area and later cell proliferation. We hypothesized that mechanical properties of cells vary near the wound edge, and this may provide cues to direct cell migration. To investigate this hypothesis, we measured variations in the stiffness of migrating human bronchial epithelial cells (16HBE cells) approximately 2 h after applying a scratch wound. We used atomic force microscopy (AFM) in contact mode to measure the cell stiffness in 1.5-microm square regions at different locations relative to the wound edge. In regions far from the wound edge (>2.75 mm), there was substantial variation in the elastic modulus in specific cellular regions, but the median values measured from multiple fields were consistently lower than 5 kPa. At the wound edge, cell stiffness was significantly lower within the first 5 microm but increased significantly between 10 and 15 microm before decreasing again below the median values away from the wound edge. When cells were infected with an adenovirus expressing a dominant negative form of RhoA, cell stiffness was significantly decreased compared with cells infected with a control adenovirus. In addition, expression of dominant negative RhoA abrogated the peak increase in stiffness near the wound edge. These results suggest that cells near the wound edge undergo localized changes in cellular stiffness that may provide signals for cell spreading and migration.
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Affiliation(s)
- Ajay A Wagh
- Department of Physiology, The University of Tennessee Health Science Center, Memphis, Tennessee 38163-0001, USA
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32
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Ammous Z, Hackett NR, Butler MW, Raman T, Dolgalev I, O'Connor TP, Harvey BG, Crystal RG. Variability in small airway epithelial gene expression among normal smokers. Chest 2008; 133:1344-1353. [PMID: 18339782 DOI: 10.1378/chest.07-2245] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Despite overwhelming data that cigarette smoking causes COPD, only a minority of long-term smokers are affected, strongly suggesting that genetic factors modify susceptibility to this disease. We hypothesized that individual variations exist in the response to cigarette smoking, with variability among smokers in expression levels of protective/susceptibility genes. METHODS Affymetrix arrays and quantitative polymerase chain reaction were used to assess the variability of gene expression in the small airway epithelium obtained by fiberoptic bronchoscopy of 18 normal nonsmokers, 18 normal smokers, and 18 smokers with COPD. RESULTS We identified 201 probe sets representing 152 smoking-responsive genes that were significantly up-regulated or down-regulated, and assessed the coefficient of variation in expression levels among the study population. Variation was a reproducible property of each gene as assessed by different microarray probe sets and real-time polymerase chain reaction, and was observed in both normal smokers and smokers with COPD. Greater individual variability was found in smokers with COPD than in normal smokers. The majority of these highly variable smoking-responsive genes were in the functional categories of signal transduction, xenobiotic degradation, metabolism, transport, oxidant related, and transcription. A similar pattern of the same highly variable genes was observed in an independent data set. CONCLUSIONS We propose that genetic diversity is likely within this subset of genes, with highly variable individual-to-individual responses of the small airway epithelium to smoking, and that this subset of genes represents putative candidates for assessment of susceptibility/protection from disease in future gene-based epidemiologic studies of smokers' risk for COPD.
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Affiliation(s)
- Zeinab Ammous
- Weill Cornell Medical College in Qatar, Education City, Doha, Qatar
| | - Neil R Hackett
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY
| | - Marcus W Butler
- Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, New York, NY
| | - Tina Raman
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY
| | - Igor Dolgalev
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY
| | - Timothy P O'Connor
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY
| | - Ben-Gary Harvey
- Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, New York, NY
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY.
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Beane J, Sebastiani P, Liu G, Brody JS, Lenburg ME, Spira A. Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. Genome Biol 2007; 8:R201. [PMID: 17894889 PMCID: PMC2375039 DOI: 10.1186/gb-2007-8-9-r201] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 09/17/2007] [Accepted: 09/25/2007] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Tobacco use remains the leading preventable cause of death in the US. The risk of dying from smoking-related diseases remains elevated for former smokers years after quitting. The identification of irreversible effects of tobacco smoke on airway gene expression may provide insights into the causes of this elevated risk. RESULTS Using oligonucleotide microarrays, we measured gene expression in large airway epithelial cells obtained via bronchoscopy from never, current, and former smokers (n = 104). Linear models identified 175 genes differentially expressed between current and never smokers, and classified these as irreversible (n = 28), slowly reversible (n = 6), or rapidly reversible (n = 139) based on their expression in former smokers. A greater percentage of irreversible and slowly reversible genes were down-regulated by smoking, suggesting possible mechanisms for persistent changes, such as allelic loss at 16q13. Similarities with airway epithelium gene expression changes caused by other environmental exposures suggest that common mechanisms are involved in the response to tobacco smoke. Finally, using irreversible genes, we built a biomarker of ever exposure to tobacco smoke capable of classifying an independent set of former and current smokers with 81% and 100% accuracy, respectively. CONCLUSION We have categorized smoking-related changes in airway gene expression by their degree of reversibility upon smoking cessation. Our findings provide insights into the mechanisms leading to reversible and persistent effects of tobacco smoke that may explain former smokers increased risk for developing tobacco-induced lung disease and provide novel targets for chemoprophylaxis. Airway gene expression may also serve as a sensitive biomarker to identify individuals with past exposure to tobacco smoke.
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Affiliation(s)
- Jennifer Beane
- Bioinformatics Program, Boston University, Cummington Street, Boston, MA 02215, USA
- The Pulmonary Center, Boston University Medical Center, Albany Street, Boston, MA 02118, USA
| | - Paola Sebastiani
- School of Public Health, Boston University, Albany Street, Boston, MA 02118, USA
| | - Gang Liu
- The Pulmonary Center, Boston University Medical Center, Albany Street, Boston, MA 02118, USA
| | - Jerome S Brody
- The Pulmonary Center, Boston University Medical Center, Albany Street, Boston, MA 02118, USA
| | - Marc E Lenburg
- The Pulmonary Center, Boston University Medical Center, Albany Street, Boston, MA 02118, USA
- Department of Genetics and Genomics, Boston University, Albany Street, Boston, MA 02118, USA
| | - Avrum Spira
- Bioinformatics Program, Boston University, Cummington Street, Boston, MA 02215, USA
- The Pulmonary Center, Boston University Medical Center, Albany Street, Boston, MA 02118, USA
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