1
|
Shu HM, Lin CQ, He B, Wang W, Wang L, Wu T, He HJ, Wang HJ, Zhou HP, Ding GZ. Pyroptosis-Related Genes as Diagnostic Markers in Chronic Obstructive Pulmonary Disease and Its Correlation with Immune Infiltration. Int J Chron Obstruct Pulmon Dis 2024; 19:1491-1513. [PMID: 38957709 PMCID: PMC11217143 DOI: 10.2147/copd.s438686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) stands as a predominant cause of global morbidity and mortality. This study aims to elucidate the relationship between pyroptosis-related genes (PRGs) and COPD diagnosis in the context of immune infiltration, ultimately proposing a PRG-based diagnostic model for predicting COPD outcomes. Methods Clinical data and PRGs of COPD patients were sourced from the GEO database. The "ConsensusClusterPlus" package was employed to generate molecular subtypes derived from PRGs that were identified through differential expression analysis and LASSO Cox analysis. A diagnostic signature including eight genes (CASP4, CASP5, ELANE, GPX4, NLRP1, GSDME, NOD1and IL18) was also constructed. Immune cell infiltration calculated by the ESTIMATE score, Stroma scores and Immune scores were also compared on the basis of pyroptosis-related molecular subtypes and the risk signature. We finally used qRT - PCR to detect the expression levels of eight genes in COPD patient and normal. Results The diagnostic model, anchored on eight PRGs, underwent validation with an independent experimental cohort. The area under the receiver operating characteristic (ROC) curves (AUC) for the diagnostic model showcased values of 0.809, 0.765, and 0.956 for the GSE76925, GSE8545, and GSE5058 datasets, respectively. Distinct expression patterns and clinical attributes of PRGs were observed between the comparative groups, with functional analysis underscoring a disparity in immune-related functions between them. Conclusion In this study, we developed a potential as diagnostic biomarkers for COPD and have a significant role in modulating the immune response. Such insights pave the way for novel diagnostic and therapeutic strategies for COPD.
Collapse
Affiliation(s)
- Hong-Mei Shu
- Department of Pulmonary and Critical Care Medicine, Anqing Municipal Hospital, Anhui, People’s Republic of China
| | - Chang-Qing Lin
- Department of Pulmonary and Critical Care Medicine, Anqing Municipal Hospital, Anhui, People’s Republic of China
| | - Bei He
- Department of Pulmonary and Critical Care Medicine, Anqing Municipal Hospital, Anhui, People’s Republic of China
| | - Wang Wang
- Department of Pulmonary and Critical Care Medicine, Anqing Municipal Hospital, Anhui, People’s Republic of China
| | - Ling Wang
- Department of Pulmonary and Critical Care Medicine, Anqing Municipal Hospital, Anhui, People’s Republic of China
| | - Ting Wu
- Department of Pulmonary and Critical Care Medicine, Anqing Municipal Hospital, Anhui, People’s Republic of China
| | - Hai-Juan He
- Department of Pulmonary and Critical Care Medicine, Anqing Municipal Hospital, Anhui, People’s Republic of China
| | - Hui-Juan Wang
- Department of Pulmonary and Critical Care Medicine, Anqing Municipal Hospital, Anhui, People’s Republic of China
| | - He-Ping Zhou
- Neurosurgery Department, Anqing Municipal Hospital, Anhui, People’s Republic of China
| | - Guo-Zheng Ding
- Department of Pulmonary and Critical Care Medicine, Anqing Municipal Hospital, Anhui, People’s Republic of China
| |
Collapse
|
2
|
Zhang Z, Yu H, Wang Q, Ding Y, Wang Z, Zhao S, Bian T. A Macrophage-Related Gene Signature for Identifying COPD Based on Bioinformatics and ex vivo Experiments. J Inflamm Res 2023; 16:5647-5665. [PMID: 38050560 PMCID: PMC10693783 DOI: 10.2147/jir.s438308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023] Open
Abstract
Background This study aims to investigate the association between immune cells and the development of COPD, while providing a new method for the diagnosis of COPD according to the changes in immune microenvironment. Methods In this study, the "CIBERSORT" algorithm was used to estimate the tissue infiltration of 22 types of immune cells in GSE20257 and GSE10006. The "limma" package was used for differentially expressed analysis. The key modules associated with vital immune cells were identified using WGCNA. GO and KEGG enrichment analysis revealed the biological functions of the candidate genes. Ultimately, a novel diagnostic prediction model was constructed via machine learning methods and multivariate logistic regression analysis based on GSE20257. Furthermore, we examined the stability of the model on one internal test set (GSE10006), three external test sets (GSE8545, GSE57148 and GSE76925), one single-cell transcriptome dataset (GSE167295), macrophages (THP-M cells) and lung tissue from COPD patients. Results M0 macrophages (AUC > 0.7 in GSE20257 and GSE10006) were considered as the most important immune cells through exploring the immune microenvironment landscapes in COPD patients and healthy controls. The differentially expressed genes from GSE20257 and GSE10006 were divided into six and five modules via WGCNA, respectively. The green module in GSE20257 (cor = 0.41, P < 0.001) and the brown module in GSE10006 (cor = 0.67, P < 0.001) were highly correlated with M0 macrophages and were selected as key modules. Forty-one intersected genes obtained from two modules were primarily involved in regulation of cytokine production, regulation of innate immune response, specific granule, phagosome, lysosome, ferroptosis, and other biological processes. On the basis of the candidate genetic markers further characterized via the "Boruta" and "LASSO" algorithm for COPD, a diagnostic model comprising CLEC5A, FTL and SLC2A3 was constructed, which could accurately distinguish COPD patients from healthy controls in multiple datasets. GSE20257 as the training set has an AUC of 0.916. The AUCs of the internal test set and three external test sets were 0.873, 0.932, 0.675 and 0.688, respectively. Single-cell sequencing analysis suggested that CLEC5A, FTL and SLC2A3 were expressed in macrophages from COPD patients. The expressions of CLEC5A, FTL and SLC2A3 were up-regulated in THP-M cells and lung tissue from COPD patients. Conclusion According to the variations of immune microenvironment in COPD patients, we constructed and validated a novel macrophage M0-associated diagnostic model with satisfactory predictive value. CLEC5A, FTL and SLC2A3 are expected to be promising targets of immunotherapy in COPD.
Collapse
Affiliation(s)
- Zheming Zhang
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
- Department of Respiratory Medicine, Wuxi People’s Hospital, Nanjing Medical University, Wuxi, People’s Republic of China
| | - Haoda Yu
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
- Department of Respiratory Medicine, Wuxi People’s Hospital, Nanjing Medical University, Wuxi, People’s Republic of China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, People’s Republic of China
| | - Yu Ding
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
- Department of Respiratory Medicine, Wuxi People’s Hospital, Nanjing Medical University, Wuxi, People’s Republic of China
| | - Ziteng Wang
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
- Department of Respiratory Medicine, Wuxi People’s Hospital, Nanjing Medical University, Wuxi, People’s Republic of China
| | - Songyun Zhao
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
| | - Tao Bian
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
- Department of Respiratory Medicine, Wuxi People’s Hospital, Nanjing Medical University, Wuxi, People’s Republic of China
| |
Collapse
|
3
|
Faiz A, Mahbub RM, Boedijono FS, Tomassen MI, Kooistra W, Timens W, Nawijn M, Hansbro PM, Johansen MD, Pouwels SD, Heijink IH, Massip F, de Biase MS, Schwarz RF, Adcock IM, Chung KF, van der Does A, Hiemstra PS, Goulaouic H, Xing H, Abdulai R, de Rinaldis E, Cunoosamy D, Harel S, Lederer D, Nivens MC, Wark PA, Kerstjens HAM, Hylkema MN, Brandsma CA, van den Berge M. IL-33 Expression Is Lower in Current Smokers at both Transcriptomic and Protein Levels. Am J Respir Crit Care Med 2023; 208:1075-1087. [PMID: 37708400 PMCID: PMC10867944 DOI: 10.1164/rccm.202210-1881oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 09/14/2023] [Indexed: 09/16/2023] Open
Abstract
Rationale: IL-33 is a proinflammatory cytokine thought to play a role in the pathogenesis of asthma and chronic obstructive pulmonary disease (COPD). A recent clinical trial using an anti-IL-33 antibody showed a reduction in exacerbation and improved lung function in ex-smokers but not current smokers with COPD. Objectives: This study aimed to understand the effects of smoking status on IL-33. Methods: We investigated the association of smoking status with the level of gene expression of IL-33 in the airways in eight independent transcriptomic studies of lung airways. Additionally, we performed Western blot analysis and immunohistochemistry for IL-33 in lung tissue to assess protein levels. Measurements and Main Results: Across the bulk RNA-sequencing datasets, IL-33 gene expression and its signaling pathway were significantly lower in current versus former or never-smokers and increased upon smoking cessation (P < 0.05). Single-cell sequencing showed that IL-33 is predominantly expressed in resting basal epithelial cells and decreases during the differentiation process triggered by smoke exposure. We also found a higher transitioning of this cellular subpopulation into a more differentiated cell type during chronic smoking, potentially driving the reduction of IL-33. Protein analysis demonstrated lower IL-33 levels in lung tissue from current versus former smokers with COPD and a lower proportion of IL-33-positive basal cells in current versus ex-smoking controls. Conclusions: We provide strong evidence that cigarette smoke leads to an overall reduction in IL-33 expression in transcriptomic and protein level, and this may be due to the decrease in resting basal cells. Together, these findings may explain the clinical observation that a recent antibody-based anti-IL-33 treatment is more effective in former than current smokers with COPD.
Collapse
Affiliation(s)
- Alen Faiz
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Rashad M. Mahbub
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Fia Sabrina Boedijono
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
| | - Milan I. Tomassen
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Wierd Kooistra
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn Nawijn
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Philip M. Hansbro
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
| | - Simon D. Pouwels
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Irene H. Heijink
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Florian Massip
- Centre for Computational Biology, Mines ParisTech, Paris Sciences et Lettres Research University, Paris, France
- Cancer and Genome: Bioinformatics, Biostatistics and Epidemiology of Complex Systems Institut Curie, Paris, France
- Institut Nationale de la Santé et de la Recherche Médicale U900, Paris, France
| | - Maria Stella de Biase
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Computational Cancer Biology, Center for Integrated Oncology, Cancer Research Center Cologne Essen, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Ian M. Adcock
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Kian F. Chung
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Anne van der Does
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Pieter S. Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | | | | | - Sivan Harel
- Regeneron Pharmaceuticals, Tarrytown, New York
| | | | | | - Peter A. Wark
- Centre for Asthma & Respiratory Disease, The University of Newcastle, Newcastle, New South Wales, Australia; and
- Hunter Medical Research Institute, Vaccines, Infection, Viruses & Asthma Newcastle, New South Wales, Australia
| | - Huib A. M. Kerstjens
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Machteld N. Hylkema
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - the Cambridge Lung Cancer Early Detection Programme
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
- Centre for Computational Biology, Mines ParisTech, Paris Sciences et Lettres Research University, Paris, France
- Cancer and Genome: Bioinformatics, Biostatistics and Epidemiology of Complex Systems Institut Curie, Paris, France
- Institut Nationale de la Santé et de la Recherche Médicale U900, Paris, France
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Computational Cancer Biology, Center for Integrated Oncology, Cancer Research Center Cologne Essen, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
- Sanofi, Chilly-Mazarin, France
- Sanofi, Cambridge, Massachusetts
- Regeneron Pharmaceuticals, Tarrytown, New York
- Centre for Asthma & Respiratory Disease, The University of Newcastle, Newcastle, New South Wales, Australia; and
- Hunter Medical Research Institute, Vaccines, Infection, Viruses & Asthma Newcastle, New South Wales, Australia
| |
Collapse
|
4
|
Zhang Y, Wang L, Liu Y, Yan F. Mettl3-mediated transcriptome-wide m6A methylation induced by cigarette smoking in human bronchial epithelial cells. Toxicol In Vitro 2023; 89:105584. [PMID: 36924977 DOI: 10.1016/j.tiv.2023.105584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/17/2023] [Accepted: 03/13/2023] [Indexed: 03/16/2023]
Abstract
Cigarette smoke exposure is a well-recognized causative factor for Chronic obstructive pulmonary disease (COPD), but the molecular mechanisms responsible for this effect need to be further investigated. An expanding number of studies suggest that m6A modification is involved in the progression of various diseases. Nevertheless, evidence on the regulatory function of m6A modification in human bronchial epithelial cells exposed to cigarette smoke is scarce. In this study, we investigated for the first time the effect of cigarette smoke exposure on contributing to high Mettl3 expression in HBE cells in vitro, an essential m6A writer. To investigate the pattern of m6A modification in HBE cells following cigarette smoke exposure, Mettl3 was down-regulated in HBE cells and a MeRIP-seq analysis revealed differences in m6A methylation between wild-type (WT) and Mettl3 knockdown HBE cells exposed to CSE. There were 1584 significantly hypomethylated genes engaged in multicellular organismal developments. We identified 200 differentially expressed genes with hypomethylated m6A peaks in conjunction with Mettl3 knockdown, among four candidate genes (NR1H4, TSPEAR, ACSBG1, and SLC5A5) that could be further explored in COPD. According to the research, cigarette smoke may control the behavior of human bronchial epithelial cells through m6A modification in COPD, providing a unique molecular mechanism.
Collapse
Affiliation(s)
- Yaping Zhang
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, China.
| | - Lixing Wang
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, China
| | - Yifei Liu
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, China
| | - Furong Yan
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, China
| |
Collapse
|
5
|
Gene Expression Trajectories from Normal Nonsmokers to COPD Smokers and Disease Progression Discriminant Modeling in Response to Cigarette Smoking. DISEASE MARKERS 2022; 2022:9354286. [PMID: 36157207 PMCID: PMC9493146 DOI: 10.1155/2022/9354286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
Background Cigarette smoking (CS) is considered to the predominant risk factor contributing to the etiopathogenesis of chronic obstructive pulmonary disease (COPD); meanwhile, genetic predisposition likely plays a role in determining disease susceptibility. Objectives We aimed to investigate gene expression trajectories from normal nonsmokers to COPD smokers and disease progression discriminant modeling in response to cigarette smoking. Methods Small airway epithelial samples of human with different smoking status using fiberoptic bronchoscopy and corresponding rat lung tissues following 0, 3, and 6 months of CS exposure were obtained. The expression of the significant overlapping genes between human and rats was confirmed in 16HBE cells, rat lung tissues, and human peripheral PBMC using qRT-PCR. Binary logistic regression analysis was carried out to establish discrimination models. Results The integrated bioinformatic analysis of 8 human GEO datasets (293 individuals) and 9 rat transcriptome databases revealed 13 overlapping genes between humans and rats in response to smoking exposure during COPD progression. Of these, 5 genes (AKR1C3/Akr1c3, ERP27/Erp27, AHRR/Ahrr, KCNMB2/Kcnmb2, and MRC1/Mrc1) were consistently identified in both the human and rat and validated by qRT-PCR. Among them, ERP27/Erp27, KCNMB2/Kcnmb2, and MRC1/Mrc1 were newly identified. On the basis of the overlapping gene panel, discriminant models were established with the receiver operating characteristic curve (AUC) of 0.98 (AKR1C3/Akr1c3 + ERP27/Erp27) and 0.99 (AHRR/Ahrr + KCNMB2/Kcnmb2) in differentiating progressive COPD from normal nonsmokers. In addition, we also found that DEG obtained from each expression profile dataset was better than combined analysis as more genes could be identified. Conclusion This study identified 5 DEG candidates of COPD progression in response to smoking and developed effective and convenient discriminant models that can accurately predict the disease progression.
Collapse
|
6
|
Fantauzzi MF, Aguiar JA, Tremblay BJM, Mansfield MJ, Yanagihara T, Chandiramohan A, Revill S, Ryu MH, Carlsten C, Ask K, Stämpfli M, Doxey AC, Hirota JA. Expression of endocannabinoid system components in human airway epithelial cells: impact of sex and chronic respiratory disease status. ERJ Open Res 2020; 6:00128-2020. [PMID: 33344628 PMCID: PMC7737429 DOI: 10.1183/23120541.00128-2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Cannabis smoking is the dominant route of delivery, with the airway epithelium functioning as the site of first contact. The endocannabinoid system is responsible for mediating the physiological effects of inhaled phytocannabinoids. The expression of the endocannabinoid system in the airway epithelium and contribution to normal physiological responses remains to be defined. To begin to address this knowledge gap, a curated dataset of 1090 unique human bronchial brushing gene expression profiles was created. The dataset included 616 healthy subjects, 136 subjects with asthma, and 338 subjects with COPD. A 32-gene endocannabinoid signature was analysed across all samples with sex and disease-specific analyses performed. Immunohistochemistry and immunoblots were performed to probe in situ and in vitro protein expression. CB1, CB2, and TRPV1 protein signal is detectable in human airway epithelial cells in situ and in vitro, justifying examining the downstream endocannabinoid pathway. Sex status was associated with differential expression of 7 of 32 genes. In contrast, disease status was associated with differential expression of 21 of 32 genes in people with asthma and 26 of 32 genes in people with COPD. We confirm at the protein level that TRPV1, the most differentially expressed candidate in our analyses, was upregulated in airway epithelial cells from people with asthma relative to healthy subjects. Our data demonstrate that the endocannabinoid system is expressed in human airway epithelial cells with expression impacted by disease status and minimally by sex. The data suggest that cannabis consumers may have differential physiological responses in the respiratory mucosa.
Collapse
Affiliation(s)
- Matthew F Fantauzzi
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | | | | | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Toyoshi Yanagihara
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada
| | - Abiram Chandiramohan
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada
| | - Spencer Revill
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada
| | - Min Hyung Ryu
- Division of Respiratory Medicine, Dept of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chris Carlsten
- Division of Respiratory Medicine, Dept of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kjetil Ask
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Martin Stämpfli
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Andrew C Doxey
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada.,Dept of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jeremy A Hirota
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.,Dept of Biology, University of Waterloo, Waterloo, ON, Canada.,Division of Respiratory Medicine, Dept of Medicine, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
7
|
Immunomodulatory Effects of Hydrolyzed Seawater Pearl Tablet (HSPT) on Th1/Th2 Functionality in a Mice Model of Chronic Obstructive Pulmonary Disease (COPD) Induced by Cigarette Smoke. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:5931652. [PMID: 33281913 PMCID: PMC7688355 DOI: 10.1155/2020/5931652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/09/2020] [Accepted: 10/30/2020] [Indexed: 11/17/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is predicted to become the third leading cause of death around the world. The present study is designed to investigate whether hydrolyzed seawater pearl tablet (HSPT) has immunoregulatory effects on the Th1/Th2 functionality in cigarette smoke-induced COPD model mice. The determination of the amino acid composition of HSPT was carried out by high-performance liquid chromatography (HPLC) with precolumn phenylisothiocyanate (PITC) derivatization. COPD model mice were constructed by cigarette smoking (CS) treatment and HSPT was administered. HSPT inhibited the infiltration of inflammation in the airway of the lung, reduced influx of eosinophils (EOSs), lymphocytes (LYMs), neutrophils (NEUs), and macrophages (MACs) in the bronchoalveolar lavage fluid (BALF), decreased the levels of IFN-γ, IL-2, IL-4, and IL-10 in the serum and lung, and decreased the expression of aforementioned cytokines in the spleen and lung in CS-treated mice. Besides, HSPT also had the ability to reduce the amount of CD3+CD4+ T cells and modulate the Th1/Th2 balance. Taken together, this study supports the consensus that CS is a critical factor to induce and aggravate COPD. HSPT could regulate the balance of Th1/Th2 in CS-induced COPD model mice, indicating its effects on inhibiting the development of COPD.
Collapse
|
8
|
Yin J, Kasper B, Petersen F, Yu X. Association of Cigarette Smoking, COPD, and Lung Cancer With Expression of SARS-CoV-2 Entry Genes in Human Airway Epithelial Cells. Front Med (Lausanne) 2020; 7:619453. [PMID: 33425965 PMCID: PMC7793919 DOI: 10.3389/fmed.2020.619453] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 enters into human airway epithelial cells via membrane fusion or endocytosis, and this process is dependent on ACE2, TMPRSS2, and cathepsin L. In this study, we examined the expression profiles of the three SARS-CoV-2 entry genes in primary human airway epithelial cells isolated from smokers, non-smokers, patients with chronic obstructive pulmonary disease or lung cancer. An exhaustive search of the GEO database was performed to identify eligible data on 1st June 2020. In total, 46 GEO datasets comprising transcriptomic data of 3,053 samples were identified as eligible data for further analysis. All meta-analysis were performed using RStudio. Standardized mean difference was utilized to assess the effect size of a factor on the expression of targeted genes and 95% confidence intervals (CIs) were calculated. This study revealed that (i) cigarette smoking is associated with an increased expression of ACE2 and TMPRSS2 and a decreased expression of cathepsin L; (ii) significant alternations in expression of ACE2, TMPRSS2, and cathepsin L were observed between current smokers and former smokers, but not between former smokers and never smokers; (iii) when compared with healthy controls with identical smoking status, patients with COPD or lung cancer showed negligible changes in expression of ACE2, TMPRSS2, and cathepsin L. Therefore, this study implicates cigarette smoking might contribute to the development of COVID-19 by affecting the expression of SARS-CoV-2 entry genes, while smoking cessation could be effective to reduce the potential risk.
Collapse
Affiliation(s)
- Junping Yin
- Division of Pulmonary Immune Diseases, Department of Asthma and Allergy, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Brigitte Kasper
- Division of Pulmonary Immune Diseases, Department of Asthma and Allergy, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Frank Petersen
- Division of Pulmonary Immune Diseases, Department of Asthma and Allergy, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Xinhua Yu
- Division of Pulmonary Immune Diseases, Department of Asthma and Allergy, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| |
Collapse
|
9
|
Ricciardi L, Giurato G, Memoli D, Pietrafesa M, Dal Col J, Salvato I, Nigro A, Vatrella A, Caramori G, Casolaro V, Stellato C. Posttranscriptional Gene Regulatory Networks in Chronic Airway Inflammatory Diseases: In silico Mapping of RNA-Binding Protein Expression in Airway Epithelium. Front Immunol 2020; 11:579889. [PMID: 33178205 PMCID: PMC7596416 DOI: 10.3389/fimmu.2020.579889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Posttranscriptional gene regulation (PTGR) contributes to inflammation through alterations in messenger RNA (mRNA) turnover and translation rates. RNA-binding proteins (RBPs) coordinate these processes but their role in lung inflammatory diseases is ill-defined. We evaluated the expression of a curated list of mRNA-binding RBPs (mRBPs) in selected Gene Expression Omnibus (GEO) transcriptomic databases of airway epithelium isolated from chronic obstructive pulmonary disease (COPD), severe asthma (SA) and matched control subjects, hypothesizing that global changes in mRBPs expression could be used to infer their pathogenetic roles and identify novel disease-related regulatory networks. Methods: A published list of 692 mRBPs [Nat Rev Genet 2014] was searched in GEO datasets originated from bronchial brushings of stable COPD patients (C), smokers (S), non-smokers (NS) controls with normal lung function (n = 6/12/12) (GEO ID: GSE5058) and of (SA) and healthy control (HC) (n = 6/12) (GSE63142). Fluorescence intensity data were extracted and normalized on the medians for fold change (FC) comparisons. FCs were set at ≥ |1.5| with a false discovery rate (FDR) of ≤ 0.05. Pearson correlation maps and heatmaps were generated using tMEV tools v4_9_0.45. DNA sequence motifs were searched using PScan-ChIP. Gene Ontology (GO) was performed with Ingenuity Pathway Analysis (IPA) tool. Results: Significant mRBP expression changes were detected for S/NS, COPD/NS and COPD/S (n = 41, 391, 382, respectively). Of those, 32% of genes changed by FC ≥ |1.5| in S/NS but more than 60% in COPD/NS and COPD/S (n = 13, 267, 257, respectively). Genes were predominantly downregulated in COPD/NS (n = 194, 73%) and COPD/S (n = 202, 79%), less so in S/NS (n = 4, 31%). Unsupervised cluster analysis identified in 4 out of 12 S the same mRBP pattern seen in C, postulating subclinical COPD. Significant DNA motifs enrichment for transcriptional regulation was found for downregulated RBPs. Correlation analysis identified five clusters of co-expressed mRBPs. GO analysis revealed significant enrichments in canonical pathways both specific and shared among comparisons. Unexpectedly, no significant mRBPs modulation was found in SA compared to controls. Conclusions: Airway epithelial mRBPs profiling reveals a COPD-specific global downregulation of RBPs shared by a subset of control smokers, the potential of functional cooperation by coexpressed RBPs and significant impact on relevant pathogenetic pathways in COPD. Elucidation of PTGR in COPD could identify disease biomarkers or pathways for therapeutic targeting.
Collapse
Affiliation(s)
- Luca Ricciardi
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Mariagrazia Pietrafesa
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Ilaria Salvato
- Pulmonology, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Alessandro Vatrella
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Gaetano Caramori
- Pulmonology, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Vincenzo Casolaro
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| |
Collapse
|
10
|
Huang X, Lv D, Yang X, Li M, Zhang H. m6A RNA methylation regulators could contribute to the occurrence of chronic obstructive pulmonary disease. J Cell Mol Med 2020; 24:12706-12715. [PMID: 32961012 PMCID: PMC7686997 DOI: 10.1111/jcmm.15848] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/04/2020] [Accepted: 08/19/2020] [Indexed: 12/21/2022] Open
Abstract
N6‐methyladenosine (m6A) RNA methylation, the most prevalent internal chemical modification of mRNA, has been reported to participate in the progression of various tumours via the dynamic regulation of m6A RNA methylation regulators. However, the role of m6A RNA methylation regulators in chronic obstructive pulmonary disease (COPD) has never been reported. This study aimed to determine the expression and potential functions of m6A RNA methylation regulators in COPD. Four gene expression data sets were acquired from Gene Expression Omnibus. Gene ontology function, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses, weighted correlation network analysis and protein‐protein interaction network analysis were performed. The correlation analyses of m6A RNA methylation regulators and key COPD genes were also performed. We found that the mRNA expressions of IGF2BP3, FTO, METTL3 and YTHDC2, which have the significant associations with some key genes enriched in the signalling pathway and biological processes that promote the development progression of COPD, are highly correlated with the occurrence of COPD. In conclusion, six central m6A RNA methylation regulators could contribute to the occurrence of COPD. This study provides important evidence for further examination of the role of m6A RNA methylation in COPD.
Collapse
Affiliation(s)
- Xinwei Huang
- Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China.,Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Dongjin Lv
- Department of Medical Oncology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, China
| | - Xiao Yang
- Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Min Li
- Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Hong Zhang
- Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China.,Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
11
|
Bailey KL, Smith H, Mathai SK, Huber J, Yacoub M, Yang IV, Wyatt TA, Kechris K, Burnham EL. Alcohol Use Disorders Are Associated With a Unique Impact on Airway Epithelial Cell Gene Expression. Alcohol Clin Exp Res 2020; 44:1571-1584. [PMID: 32524622 PMCID: PMC7484391 DOI: 10.1111/acer.14395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/28/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Alcohol use disorders (AUDs) and cigarette smoking both increase risk for the development of community-acquired pneumonia (CAP), likely through adverse effects on proximal airway mucociliary clearance and pathogen recognition. Smoking-related alterations on airway gene expression are well described, but little is known about the impact of AUDs. We measured gene expression in human airway epithelial cells (AECs), hypothesizing that AUDs would be associated with novel differences in gene expression that could alter risk for CAP. METHODS Bronchoscopy with airway brushings was performed in participants with AUDs and controls to obtain AECs. An AUD Identification Test was used to define AUD. RNA was extracted from AECs, and mRNA expression data were collected on an Agilent micro-array. Differential expression analyses were performed on the filtered and normalized data with correction for multiple testing. Enrichment analyses were performed using clusterProfiler. RESULTS Expression data from 19 control and 18 AUD participants were evaluated. After adjustment for smoking, AUDs were associated with significant differential expression of 520 AEC genes, including genes for ribosomal proteins and genes involved in protein folding. Enrichment analyses indicated significant differential expression of 24 pathways in AUDs, including those implicated in protein targeting to membrane and viral gene expression. Smoking-associated AEC gene expression differences mirrored previous reports, but differed from those associated with AUDs. CONCLUSIONS AUDs have a distinct impact on AEC gene expression that may influence proximal airway function independent of smoking. Alcohol-associated alterations may influence risk for CAP through modifying key mechanisms important in protecting proximal airway integrity.
Collapse
Affiliation(s)
- Kristina L. Bailey
- University of Nebraska Medical Center, Department of Internal Medicine. Division of Pulmonary, Critical Care, Sleep and Allergy
- VA Nebraska-Western Iowa Health Care System
| | - Harry Smith
- University of Colorado Anschutz Medical Campus, Department of Biostatistics and Informatics, Colorado School of Public Health
| | - Susan K. Mathai
- Baylor University Medical Center, Center for Advanced Heart & Lung Disease
| | - Jonathan Huber
- University of Colorado Anschutz Medical Campus, Department of Medicine, Division of Allergy & Clinical Immunology
| | - Mark Yacoub
- University of Colorado Anschutz Medical Campus, Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine
| | - Ivana V. Yang
- University of Colorado Anschutz Medical Campus, Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine
- University of Colorado Anschutz Medical Campus, Department of Medicine, Division of Biomedical Informatics and Personalized Medicine
| | - Todd A. Wyatt
- VA Nebraska-Western Iowa Health Care System
- University of Nebraska Medical Center, Department of Environmental, Agricultural, & Occupational Health
| | - Katerina Kechris
- University of Colorado Anschutz Medical Campus, Department of Biostatistics and Informatics, Colorado School of Public Health
- University of Colorado Anschutz Medical Campus, Department of Medicine, Division of Biomedical Informatics and Personalized Medicine
| | - Ellen L. Burnham
- University of Colorado Anschutz Medical Campus, Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine
| |
Collapse
|
12
|
Matsumura K, Ito S. Novel biomarker genes which distinguish between smokers and chronic obstructive pulmonary disease patients with machine learning approach. BMC Pulm Med 2020; 20:29. [PMID: 32013930 PMCID: PMC6998147 DOI: 10.1186/s12890-020-1062-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is combination of progressive lung diseases. The diagnosis of COPD is generally based on the pulmonary function testing, however, difficulties underlie in prognosis of smokers or early stage of COPD patients due to the complexity and heterogeneity of the pathogenesis. Computational analyses of omics technologies are expected as one of the solutions to resolve such complexities. Methods We obtained transcriptomic data by in vitro testing with exposures of human bronchial epithelial cells to the inducers for early events of COPD to identify the potential descriptive marker genes. With the identified genes, the machine learning technique was employed with the publicly available transcriptome data obtained from the lung specimens of COPD and non-COPD patients to develop the model that can reflect the risk continuum across smoking and COPD. Results The expression levels of 15 genes were commonly altered among in vitro tissues exposed to known inducible factors for earlier events of COPD (exposure to cigarette smoke, DNA damage, oxidative stress, and inflammation), and 10 of these genes and their corresponding proteins have not previously reported as COPD biomarkers. Although these genes were able to predict each group with 65% accuracy, the accuracy with which they were able to discriminate COPD subjects from smokers was only 29%. Furthermore, logistic regression enabled the conversion of gene expression levels to a numerical index, which we named the “potential risk factor (PRF)” index. The highest significant index value was recorded in COPD subjects (0.56 at the median), followed by smokers (0.30) and non-smokers (0.02). In vitro tissues exposed to cigarette smoke displayed dose-dependent increases of PRF, suggesting its utility for prospective risk estimation of tobacco products. Conclusions Our experimental-based transcriptomic analysis identified novel genes associated with COPD, and the 15 genes could distinguish smokers and COPD subjects from non-smokers via machine-learning classification with remarkable accuracy. We also suggested a PRF index that can quantitatively reflect the risk continuum across smoking and COPD pathogenesis, and we believe it will provide an improved understanding of smoking effects and new insights into COPD.
Collapse
Affiliation(s)
- Kazushi Matsumura
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc., 6-2 Umegaoka, Aoba-ku, Yokohama, Kanagawa, 227-8512, Japan.
| | - Shigeaki Ito
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc., 6-2 Umegaoka, Aoba-ku, Yokohama, Kanagawa, 227-8512, Japan
| |
Collapse
|
13
|
Kopa PN, Pawliczak R. Effect of smoking on gene expression profile – overall mechanism, impact on respiratory system function, and reference to electronic cigarettes. Toxicol Mech Methods 2018; 28:397-409. [DOI: 10.1080/15376516.2018.1461289] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Paulina Natalia Kopa
- Department of Immunopathology, Division of Allergology, Immunology and Dermatology, Faculty of Biomedical Sciences and Postgraduate Training, Medical University of Lodz, Lodz, Poland
| | - Rafał Pawliczak
- Department of Immunopathology, Division of Allergology, Immunology and Dermatology, Faculty of Biomedical Sciences and Postgraduate Training, Medical University of Lodz, Lodz, Poland
| |
Collapse
|
14
|
A large lung gene expression study identifying IL1B as a novel player in airway inflammation in COPD airway epithelial cells. Inflamm Res 2018; 67:539-551. [DOI: 10.1007/s00011-018-1145-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/22/2018] [Accepted: 03/24/2018] [Indexed: 01/21/2023] Open
|
15
|
Aghapour M, Raee P, Moghaddam SJ, Hiemstra PS, Heijink IH. Airway Epithelial Barrier Dysfunction in Chronic Obstructive Pulmonary Disease: Role of Cigarette Smoke Exposure. Am J Respir Cell Mol Biol 2018; 58:157-169. [DOI: 10.1165/rcmb.2017-0200tr] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Pourya Raee
- Department of Basic Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Seyed Javad Moghaddam
- Department of Pulmonary Medicine, Division of Internal Medicine, the University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Pieter S. Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands; and
| | - Irene H. Heijink
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| |
Collapse
|
16
|
Talikka M, Martin F, Sewer A, Vuillaume G, Leroy P, Luettich K, Chaudhary N, Peck MJ, Peitsch MC, Hoeng J. Mechanistic Evaluation of the Impact of Smoking and Chronic Obstructive Pulmonary Disease on the Nasal Epithelium. CLINICAL MEDICINE INSIGHTS-CIRCULATORY RESPIRATORY AND PULMONARY MEDICINE 2017; 11:1179548417710928. [PMID: 28620266 PMCID: PMC5466113 DOI: 10.1177/1179548417710928] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/04/2017] [Indexed: 12/27/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the major causes of chronic morbidity and mortality worldwide. The development of markers of COPD onset is hampered by the lack of accessibility to the primary target tissue, and there is a need to consider other sample sources as surrogates for biomarker research. Airborne toxicants pass through the nasal epithelium before reaching the lower airways, and the similarity with bronchial histology makes it an attractive surrogate for lower airways. In this work, we describe the transcriptomics findings from the nasal epithelia of subjects enrolled in a clinical study focusing on the identification of COPD biomarkers. Transcriptomic data were analyzed using the biological network approach that enabled us to pinpoint the biological processes affected in the upper respiratory tract in response to smoking and mild-to-moderate COPD. Our results indicated that nasal and lower airway immune responses were considerably different in COPD subjects and caution should be exercised when using upper airway samples as a surrogate for the lower airway. Nevertheless, the network approach described here could present a sensitive means of identifying smokers at risk of developing COPD.
Collapse
Affiliation(s)
- Marja Talikka
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Florian Martin
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Alain Sewer
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Grégory Vuillaume
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Patrice Leroy
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Karsta Luettich
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Nveed Chaudhary
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Michael J Peck
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Manuel C Peitsch
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Julia Hoeng
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| |
Collapse
|
17
|
Moses E, Wang T, Corbett S, Jackson GR, Drizik E, Perdomo C, Perdomo C, Kleerup E, Brooks D, O'Connor G, Dubinett S, Hayden P, Lenburg ME, Spira A. Molecular Impact of Electronic Cigarette Aerosol Exposure in Human Bronchial Epithelium. Toxicol Sci 2016; 155:248-257. [PMID: 27701119 DOI: 10.1093/toxsci/kfw198] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Little evidence is available regarding the physiological effects of exposure to electronic cigarette (ECIG) aerosol. We sought to determine the molecular impact of ECIG aerosol exposure in human bronchial epithelial cells (HBECs). Gene-expression profiling was conducted in primary grown at air liquid interface and exposed to 1 of 4 different ECIG aerosols, traditional tobacco cigarette (TCIG) smoke, or clean air. Findings were validated experimentally with quantitative polymerase chain reaction and a reactive oxygen species immunoassay. Using gene set enrichment analysis, signatures of in vitro ECIG exposure were compared with those generated from bronchial epithelial brushings of current TCIG smokers and former TCIG smokers currently using ECIGs. We found 546 genes differentially expressed across the ECIG, TCIG, and air-exposed groups of HBECs (ANOVA; FDR q < .05; fold change > 1.5). A subset of these changes were shared between TCIG- and ECIG-exposed HBECs. ECIG exposure induced genes involved in oxidative and xenobiotic stress pathways and increased a marker of reactive oxygen species production in a dose-dependent manner. ECIG exposure decreased expression of genes involved in cilia assembly and movement. Furthermore, gene-expression differences observed in vitro were concordant with differences observed in airway epithelium collected from ECIG users (q < .01). In summary, our data suggest that ECIG aerosol can induce gene-expression changes in bronchial airway epithelium in vitro, some of which are shared with TCIG smoke. These changes were generally less pronounced than the effects of TCIG exposure and were more pronounced in ECIG products containing nicotine than those without nicotine. Our data further suggest that the gene-expression alterations seen with the in vitro exposure system reflects the physiological effects experienced in vivo by ECIG users.
Collapse
Affiliation(s)
- Elizabeth Moses
- Section of Computational Biomedicine, Department of Medicine Boston University School of Medicine, Boston, Massachusetts 02118
| | - Teresa Wang
- Section of Computational Biomedicine, Department of Medicine Boston University School of Medicine, Boston, Massachusetts 02118
| | - Sean Corbett
- Section of Computational Biomedicine, Department of Medicine Boston University School of Medicine, Boston, Massachusetts 02118
| | | | - Eduard Drizik
- Section of Computational Biomedicine, Department of Medicine Boston University School of Medicine, Boston, Massachusetts 02118
| | - Catalina Perdomo
- Section of Computational Biomedicine, Department of Medicine Boston University School of Medicine, Boston, Massachusetts 02118
| | - Claudia Perdomo
- University of California Los Angeles, Los Angeles, California 90095
| | - Eric Kleerup
- University of California Los Angeles, Los Angeles, California 90095
| | - Daniel Brooks
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts 02118
| | - George O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Steven Dubinett
- University of California Los Angeles, Los Angeles, California 90095
| | | | - Marc E Lenburg
- Section of Computational Biomedicine, Department of Medicine Boston University School of Medicine, Boston, Massachusetts 02118;
| | - Avrum Spira
- Section of Computational Biomedicine, Department of Medicine Boston University School of Medicine, Boston, Massachusetts 02118.,Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts 02118
| |
Collapse
|
18
|
Shen Y, Wolkowicz MJ, Kotova T, Fan L, Timko MP. Transcriptome sequencing reveals e-cigarette vapor and mainstream-smoke from tobacco cigarettes activate different gene expression profiles in human bronchial epithelial cells. Sci Rep 2016; 6:23984. [PMID: 27041137 PMCID: PMC4819171 DOI: 10.1038/srep23984] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/17/2016] [Indexed: 12/04/2022] Open
Abstract
Electronic cigarettes (e-cigarettes) generate an aerosol vapor (e-vapor) thought to represent a less risky alternative to main stream smoke (MSS) of conventional tobacco cigarettes. RNA-seq analysis was used to examine the transcriptomes of differentiated human bronchial epithelial (HBE) cells exposed to air, MSS from 1R5F tobacco reference cigarettes, and e-vapor with and without added nicotine in an in vitro air-liquid interface model for cellular exposure. Our results indicate that while e-vapor does not elicit many of the cell toxicity responses observed in MSS-exposed HBE cells, e-vapor exposure is not benign, but elicits discrete transcriptomic signatures with and without added nicotine. Among the cellular pathways with the most significantly enriched gene expression following e-vapor exposure are the phospholipid and fatty acid triacylglycerol metabolism pathways. Our data suggest that alterations in cellular glycerophopholipid biosynthesis are an important consequences of e-vapor exposure. Moreover, the presence of nicotine in e-vapor elicits a cellular response distinct from e-vapor alone including alterations of cytochrome P450 function, retinoid metabolism, and nicotine catabolism. These studies establish a baseline for future analysis of e-vapor and e-vapor additives that will better inform the FDA and other governmental bodies in discussions of the risks and future regulation of these products.
Collapse
Affiliation(s)
- Yifei Shen
- Research Center for Air Pollution and Health and Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | | | - Tatyana Kotova
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Lonjiang Fan
- Research Center for Air Pollution and Health and Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Michael P. Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22903, USA
| |
Collapse
|
19
|
Liu Z, Li W, Lv J, Xie R, Huang H, Li Y, He Y, Jiang J, Chen B, Guo S, Chen L. Identification of potential COPD genes based on multi-omics data at the functional level. MOLECULAR BIOSYSTEMS 2016; 12:191-204. [DOI: 10.1039/c5mb00577a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A novel systematic approach MMMG (Methylation–MicroRNA–MRNA–GO) to identify potential COPD genes and their classifying performance evaluation.
Collapse
Affiliation(s)
- Zhe Liu
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| | - Wan Li
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| | - Junjie Lv
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| | - Ruiqiang Xie
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| | - Hao Huang
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| | - Yiran Li
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| | - Yuehan He
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| | - Jing Jiang
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| | - Binbin Chen
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| | - Shanshan Guo
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| | - Lina Chen
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin
- China
| |
Collapse
|
20
|
Boue S, Fields B, Hoeng J, Park J, Peitsch MC, Schlage WK, Talikka M, Binenbaum I, Bondarenko V, Bulgakov OV, Cherkasova V, Diaz-Diaz N, Fedorova L, Guryanova S, Guzova J, Igorevna Koroleva G, Kozhemyakina E, Kumar R, Lavid N, Lu Q, Menon S, Ouliel Y, Peterson SC, Prokhorov A, Sanders E, Schrier S, Schwaitzer Neta G, Shvydchenko I, Tallam A, Villa-Fombuena G, Wu J, Yudkevich I, Zelikman M. Enhancement of COPD biological networks using a web-based collaboration interface. F1000Res 2015; 4:32. [PMID: 25767696 PMCID: PMC4350443 DOI: 10.12688/f1000research.5984.2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/14/2015] [Indexed: 01/06/2023] Open
Abstract
The construction and application of biological network models is an approach that offers a holistic way to understand biological processes involved in disease. Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease of the airways for which therapeutic options currently are limited after diagnosis, even in its earliest stage. COPD network models are important tools to better understand the biological components and processes underlying initial disease development. With the increasing amounts of literature that are now available, crowdsourcing approaches offer new forms of collaboration for researchers to review biological findings, which can be applied to the construction and verification of complex biological networks. We report the construction of 50 biological network models relevant to lung biology and early COPD using an integrative systems biology and collaborative crowd-verification approach. By combining traditional literature curation with a data-driven approach that predicts molecular activities from transcriptomics data, we constructed an initial COPD network model set based on a previously published non-diseased lung-relevant model set. The crowd was given the opportunity to enhance and refine the networks on a website ( https://bionet.sbvimprover.com/) and to add mechanistic detail, as well as critically review existing evidence and evidence added by other users, so as to enhance the accuracy of the biological representation of the processes captured in the networks. Finally, scientists and experts in the field discussed and refined the networks during an in-person jamboree meeting. Here, we describe examples of the changes made to three of these networks: Neutrophil Signaling, Macrophage Signaling, and Th1-Th2 Signaling. We describe an innovative approach to biological network construction that combines literature and data mining and a crowdsourcing approach to generate a comprehensive set of COPD-relevant models that can be used to help understand the mechanisms related to lung pathobiology. Registered users of the website can freely browse and download the networks.
Collapse
Affiliation(s)
- The sbv IMPROVER project team (in alphabetical order)
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
- Private, Washington DC, USA
- USAMRIID, Attn: MCMR-UIZ-R, 1425 Porter Street, Frederick, MD, 21702-5011, USA
- Private, Boston, MA, USA
- Institute of Microbial Technology, Chandigarh, 160036, India
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
- AnalyzeDat Consulting Services, Ernakulam, India
- Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
- Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
| | - Stephanie Boue
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Brett Fields
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Jennifer Park
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
| | - Manuel C. Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Walter K. Schlage
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - The Challenge Best Performers (in alphabetical order)
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
- Private, Washington DC, USA
- USAMRIID, Attn: MCMR-UIZ-R, 1425 Porter Street, Frederick, MD, 21702-5011, USA
- Private, Boston, MA, USA
- Institute of Microbial Technology, Chandigarh, 160036, India
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
- AnalyzeDat Consulting Services, Ernakulam, India
- Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
- Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
| | - Ilona Binenbaum
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
| | - Vladimir Bondarenko
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
| | - Oleg V. Bulgakov
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
| | | | - Norberto Diaz-Diaz
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
| | - Larisa Fedorova
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
| | - Svetlana Guryanova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
| | | | | | | | - Rahul Kumar
- Institute of Microbial Technology, Chandigarh, 160036, India
| | - Noa Lavid
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
| | - Qingxian Lu
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
| | - Swapna Menon
- AnalyzeDat Consulting Services, Ernakulam, India
| | - Yael Ouliel
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
| | | | - Alexander Prokhorov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
| | - Edward Sanders
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
| | - Sarah Schrier
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | | | - Irina Shvydchenko
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
| | - Aravind Tallam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
| | | | - John Wu
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
| | - Ilya Yudkevich
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
| | - Mariya Zelikman
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
| |
Collapse
|
21
|
Boue S, Fields B, Hoeng J, Park J, Peitsch MC, Schlage WK, Talikka M, Binenbaum I, Bondarenko V, Bulgakov OV, Cherkasova V, Diaz-Diaz N, Fedorova L, Guryanova S, Guzova J, Igorevna Koroleva G, Kozhemyakina E, Kumar R, Lavid N, Lu Q, Menon S, Ouliel Y, Peterson SC, Prokhorov A, Sanders E, Schrier S, Schwaitzer Neta G, Shvydchenko I, Tallam A, Villa-Fombuena G, Wu J, Yudkevich I, Zelikman M. Enhancement of COPD biological networks using a web-based collaboration interface. F1000Res 2015; 4:32. [PMID: 25767696 PMCID: PMC4350443 DOI: 10.12688/f1000research.5984.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2015] [Indexed: 11/20/2022] Open
Abstract
The construction and application of biological network models is an approach that offers a holistic way to understand biological processes involved in disease. Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease of the airways for which therapeutic options currently are limited after diagnosis, even in its earliest stage. COPD network models are important tools to better understand the biological components and processes underlying initial disease development. With the increasing amounts of literature that are now available, crowdsourcing approaches offer new forms of collaboration for researchers to review biological findings, which can be applied to the construction and verification of complex biological networks. We report the construction of 50 biological network models relevant to lung biology and early COPD using an integrative systems biology and collaborative crowd-verification approach. By combining traditional literature curation with a data-driven approach that predicts molecular activities from transcriptomics data, we constructed an initial COPD network model set based on a previously published non-diseased lung-relevant model set. The crowd was given the opportunity to enhance and refine the networks on a website ( https://bionet.sbvimprover.com/) and to add mechanistic detail, as well as critically review existing evidence and evidence added by other users, so as to enhance the accuracy of the biological representation of the processes captured in the networks. Finally, scientists and experts in the field discussed and refined the networks during an in-person jamboree meeting. Here, we describe examples of the changes made to three of these networks: Neutrophil Signaling, Macrophage Signaling, and Th1-Th2 Signaling. We describe an innovative approach to biological network construction that combines literature and data mining and a crowdsourcing approach to generate a comprehensive set of COPD-relevant models that can be used to help understand the mechanisms related to lung pathobiology. Registered users of the website can freely browse and download the networks.
Collapse
Affiliation(s)
- The sbv IMPROVER project team (in alphabetical order)
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
- Private, Washington DC, USA
- USAMRIID, Attn: MCMR-UIZ-R, 1425 Porter Street, Frederick, MD, 21702-5011, USA
- Private, Boston, MA, USA
- Institute of Microbial Technology, Chandigarh, 160036, India
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
- AnalyzeDat Consulting Services, Ernakulam, India
- Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
- Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
| | - Stephanie Boue
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Brett Fields
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Jennifer Park
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
| | - Manuel C. Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Walter K. Schlage
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - The Challenge Best Performers (in alphabetical order)
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
- Private, Washington DC, USA
- USAMRIID, Attn: MCMR-UIZ-R, 1425 Porter Street, Frederick, MD, 21702-5011, USA
- Private, Boston, MA, USA
- Institute of Microbial Technology, Chandigarh, 160036, India
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
- AnalyzeDat Consulting Services, Ernakulam, India
- Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
- Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
| | - Ilona Binenbaum
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
| | - Vladimir Bondarenko
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
| | - Oleg V. Bulgakov
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
| | | | - Norberto Diaz-Diaz
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
| | - Larisa Fedorova
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
| | - Svetlana Guryanova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
| | | | | | | | - Rahul Kumar
- Institute of Microbial Technology, Chandigarh, 160036, India
| | - Noa Lavid
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
| | - Qingxian Lu
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
| | - Swapna Menon
- AnalyzeDat Consulting Services, Ernakulam, India
| | - Yael Ouliel
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
| | | | - Alexander Prokhorov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
| | - Edward Sanders
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
| | - Sarah Schrier
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | | | - Irina Shvydchenko
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
| | - Aravind Tallam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
| | | | - John Wu
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
| | - Ilya Yudkevich
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
| | - Mariya Zelikman
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
| |
Collapse
|
22
|
Hobbs BD, Hersh CP. Integrative genomics of chronic obstructive pulmonary disease. Biochem Biophys Res Commun 2014; 452:276-86. [PMID: 25078622 PMCID: PMC4172635 DOI: 10.1016/j.bbrc.2014.07.086] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/18/2014] [Indexed: 01/21/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex disease with both environmental and genetic determinants, the most important of which is cigarette smoking. There is marked heterogeneity in the development of COPD among persons with similar cigarette smoking histories, which is likely partially explained by genetic variation. Genomic approaches such as genomewide association studies and gene expression studies have been used to discover genes and molecular pathways involved in COPD pathogenesis; however, these "first generation" omics studies have limitations. Integrative genomic studies are emerging which can combine genomic datasets to further examine the molecular underpinnings of COPD. Future research in COPD genetics will likely use network-based approaches to integrate multiple genomic data types in order to model the complex molecular interactions involved in COPD pathogenesis. This article reviews the genomic research to date and offers a vision for the future of integrative genomic research in COPD.
Collapse
Affiliation(s)
- Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States.
| |
Collapse
|
23
|
Vucic EA, Chari R, Thu KL, Wilson IM, Cotton AM, Kennett JY, Zhang M, Lonergan KM, Steiling K, Brown CJ, McWilliams A, Ohtani K, Lenburg ME, Sin DD, Spira A, MacAulay CE, Lam S, Lam WL. DNA methylation is globally disrupted and associated with expression changes in chronic obstructive pulmonary disease small airways. Am J Respir Cell Mol Biol 2014; 50:912-22. [PMID: 24298892 PMCID: PMC4068945 DOI: 10.1165/rcmb.2013-0304oc] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 12/03/2013] [Indexed: 01/06/2023] Open
Abstract
DNA methylation is an epigenetic modification that is highly disrupted in response to cigarette smoke and involved in a wide spectrum of malignant and nonmalignant diseases, but surprisingly not previously assessed in small airways of patients with chronic obstructive pulmonary disease (COPD). Small airways are the primary sites of airflow obstruction in COPD. We sought to determine whether DNA methylation patterns are disrupted in small airway epithelia of patients with COPD, and evaluate whether changes in gene expression are associated with these disruptions. Genome-wide methylation and gene expression analysis were performed on small airway epithelial DNA and RNA obtained from the same patient during bronchoscopy, using Illumina's Infinium HM27 and Affymetrix's Genechip Human Gene 1.0 ST arrays. To control for known effects of cigarette smoking on DNA methylation, methylation and gene expression profiles were compared between former smokers with and without COPD matched for age, pack-years, and years of smoking cessation. Our results indicate that aberrant DNA methylation is (1) a genome-wide phenomenon in small airways of patients with COPD, and (2) associated with altered expression of genes and pathways important to COPD, such as the NF-E2-related factor 2 oxidative response pathway. DNA methylation is likely an important mechanism contributing to modulation of genes important to COPD pathology. Because these methylation events may underlie disease-specific gene expression changes, their characterization is a critical first step toward the development of epigenetic markers and an opportunity for developing novel epigenetic therapeutic interventions for COPD.
Collapse
Affiliation(s)
- Emily A. Vucic
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Raj Chari
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Kelsie L. Thu
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Ian M. Wilson
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Allison M. Cotton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Y. Kennett
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - May Zhang
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Kim M. Lonergan
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Katrina Steiling
- Division of Computational Biomedicine, Department of Medicine, Boston University Medical Center, Boston, Massachusetts; and
| | - Carolyn J. Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Annette McWilliams
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Keishi Ohtani
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Marc E. Lenburg
- Division of Computational Biomedicine, Department of Medicine, Boston University Medical Center, Boston, Massachusetts; and
| | - Don D. Sin
- University of British Columbia James Hogg Research Centre and the Institute of Heart and Lung Health, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Avrum Spira
- Division of Computational Biomedicine, Department of Medicine, Boston University Medical Center, Boston, Massachusetts; and
| | - Calum E. MacAulay
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Wan L. Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| |
Collapse
|
24
|
Van Dyck E, Nazarov PV, Muller A, Nicot N, Bosseler M, Pierson S, Van Moer K, Palissot V, Mascaux C, Knolle U, Ninane V, Nati R, Bremnes RM, Vallar L, Berchem G, Schlesser M. Bronchial airway gene expression in smokers with lung or head and neck cancer. Cancer Med 2014; 3:322-36. [PMID: 24497500 PMCID: PMC3987082 DOI: 10.1002/cam4.190] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/30/2013] [Accepted: 11/01/2013] [Indexed: 01/10/2023] Open
Abstract
Cigarette smoking is the major cause of cancers of the respiratory tract, including non-small cell lung cancer (NSCLC) and head and neck cancer (HNC). In order to better understand carcinogenesis of the lung and upper airways, we have compared the gene expression profiles of tumor-distant, histologically normal bronchial biopsy specimens obtained from current smokers with NSCLC or HNC (SC, considered as a single group), as well as nonsmokers (NS) and smokers without cancer (SNC). RNA from a total of 97 biopsies was used for gene expression profiling (Affymetrix HG-U133 Plus 2.0 array). Differentially expressed genes were used to compare NS, SNC, and SC, and functional analysis was carried out using Ingenuity Pathway Analysis (IPA). Smoking-related cancer of the respiratory tract was found to affect the expression of genes encoding xenobiotic biotransformation proteins, as well as proteins associated with crucial inflammation/immunity pathways and other processes that protect the airway from the chemicals in cigarette smoke or contribute to carcinogenesis. Finally, we used the prediction analysis for microarray (PAM) method to identify gene signatures of cigarette smoking and cancer, and uncovered a 15-gene signature that distinguished between SNC and SC with an accuracy of 83%. Thus, gene profiling of histologically normal bronchial biopsy specimens provided insight into cigarette-induced carcinogenesis of the respiratory tract and gene signatures of cancer in smokers.
Collapse
Affiliation(s)
- Eric Van Dyck
- Département d'Oncologie, CRP-Santé du Luxembourg, Luxembourg
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Didon L, Zwick RK, Chao IW, Walters MS, Wang R, Hackett NR, Crystal RG. RFX3 modulation of FOXJ1 regulation of cilia genes in the human airway epithelium. Respir Res 2013; 14:70. [PMID: 23822649 PMCID: PMC3710277 DOI: 10.1186/1465-9921-14-70] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 06/10/2013] [Indexed: 11/30/2022] Open
Abstract
Background Ciliated cells play a central role in cleansing the airways of inhaled contaminants. They are derived from basal cells that include the airway stem/progenitor cells. In animal models, the transcription factor FOXJ1 has been shown to induce differentiation to the ciliated cell lineage, and the RFX transcription factor-family has been shown to be necessary for, but not sufficient to induce, correct cilia development. Methods To test the hypothesis that FOXJ1 and RFX3 cooperatively induce expression of ciliated genes in the differentiation process of basal progenitor cells toward a ciliated cell linage in the human airway epithelium, primary human airway basal cells were assessed under conditions of in vitro differentiation induced by plasmid-mediated gene transfer of FOXJ1 and/or RFX3. TaqMan PCR was used to quantify mRNA levels of basal, secretory, and cilia-associated genes. Results Basal cells, when cultured in air-liquid interface, differentiated into a ciliated epithelium, expressing FOXJ1 and RFX3. Transfection of FOXJ1 into resting basal cells activated promoters and induced expression of ciliated cell genes as well as both FOXJ1 and RFX3, but not basal cell genes. Transfection of RFX3 induced expression of RFX3 but not FOXJ1, nor the expression of cilia-related genes. The combination of FOXJ1 + RFX3 enhanced ciliated gene promoter activity and mRNA expression beyond that due to FOXJ1 alone. Corroborating immunoprecipitation studies demonstrated an interaction between FOXJ1 and RFX3. Conclusion FOXJ1 is an important regulator of cilia gene expression during ciliated cell differentiation, with RFX3 as a transcriptional co-activator to FOXJ1, helping to induce the expression of cilia genes in the process of ciliated cell differentiation of basal/progenitor cells.
Collapse
Affiliation(s)
- Lukas Didon
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | | | | | | |
Collapse
|
26
|
Mariani TJ, Martinez F. Chronic obstructive pulmonary disease genomics: yesterday, discovering population biomarkers; tomorrow, defining disease clusters. Am J Respir Crit Care Med 2013; 187:900-2. [PMID: 23634854 DOI: 10.1164/rccm.201302-0340ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
|
27
|
Brody JS. Transcriptome alterations induced by cigarette smoke. Int J Cancer 2012; 131:2754-62. [PMID: 22961494 DOI: 10.1002/ijc.27829] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 08/16/2012] [Indexed: 12/24/2022]
Abstract
Cigarette smoke alters the transcriptome of multiple tissues; those directly exposed to toxic products and those exposed to circulating components and metabolic products of tobacco smoke. In most tissues and organs that have been studied, the smoking transcriptome is characterized by increased expression of antioxidant and xenobiotic genes as well as a wide spectrum of inflammation-related genes, and potential oncogenic genes. Smoking is associated with an increased incidence of cancer in a number of organs both those directly exposed (lungs and airways) and those indirectly exposed (bladder, liver, pancreas). Individual transcriptomic responses vary, based to some degree on as yet to be clarified genetic factors, and likely how and what the individual has smoked. The complexity of individual responses to tobacco exposure and of smoking-related cancers in various organs is beginning to be revealed in transcriptomic and whole genome sequencing studies, of both tumors and cytologically normal appearing cells that have been exposed to cigarette smoke or its products creating a genomic "field of injury." The recent application of next generation sequencing to defining the transcriptome alterations induced by cigarette smoke holds the promise of discovering new approaches to personalized prevention and treatment of smoking-related lung diseases in the future.
Collapse
Affiliation(s)
- Jerome S Brody
- Boston University School of Medicine, Pulmonary Center (R-3), Boston, MA 02118, USA.
| |
Collapse
|
28
|
Fourtounis J, Wang IM, Mathieu MC, Claveau D, Loo T, Jackson AL, Peters MA, Therien AG, Boie Y, Crackower MA. Gene expression profiling following NRF2 and KEAP1 siRNA knockdown in human lung fibroblasts identifies CCL11/Eotaxin-1 as a novel NRF2 regulated gene. Respir Res 2012; 13:92. [PMID: 23061798 PMCID: PMC3546844 DOI: 10.1186/1465-9921-13-92] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 10/10/2012] [Indexed: 01/21/2023] Open
Abstract
Background Oxidative Stress contributes to the pathogenesis of many diseases. The NRF2/KEAP1 axis is a key transcriptional regulator of the anti-oxidant response in cells. Nrf2 knockout mice have implicated this pathway in regulating inflammatory airway diseases such as asthma and COPD. To better understand the role the NRF2 pathway has on respiratory disease we have taken a novel approach to define NRF2 dependent gene expression in a relevant lung system. Methods Normal human lung fibroblasts were transfected with siRNA specific for NRF2 or KEAP1. Gene expression changes were measured at 30 and 48 hours using a custom Affymetrix Gene array. Changes in Eotaxin-1 gene expression and protein secretion were further measured under various inflammatory conditions with siRNAs and pharmacological tools. Results An anti-correlated gene set (inversely regulated by NRF2 and KEAP1 RNAi) that reflects specific NRF2 regulated genes was identified. Gene annotations show that NRF2-mediated oxidative stress response is the most significantly regulated pathway, followed by heme metabolism, metabolism of xenobiotics by Cytochrome P450 and O-glycan biosynthesis. Unexpectedly the key eosinophil chemokine Eotaxin-1/CCL11 was found to be up-regulated when NRF2 was inhibited and down-regulated when KEAP1 was inhibited. This transcriptional regulation leads to modulation of Eotaxin-1 secretion from human lung fibroblasts under basal and inflammatory conditions, and is specific to Eotaxin-1 as NRF2 or KEAP1 knockdown had no effect on the secretion of a set of other chemokines and cytokines. Furthermore, the known NRF2 small molecule activators CDDO and Sulphoraphane can also dose dependently inhibit Eotaxin-1 release from human lung fibroblasts. Conclusions These data uncover a previously unknown role for NRF2 in regulating Eotaxin-1 expression and further the mechanistic understanding of this pathway in modulating inflammatory lung disease.
Collapse
Affiliation(s)
- Jimmy Fourtounis
- Department of Respiratory and Immunology, Merck Research Laboratories, Boston, Massachusetts 02115, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Hackett NR, Butler MW, Shaykhiev R, Salit J, Omberg L, Rodriguez-Flores JL, Mezey JG, Strulovici-Barel Y, Wang G, Didon L, Crystal RG. RNA-Seq quantification of the human small airway epithelium transcriptome. BMC Genomics 2012; 13:82. [PMID: 22375630 PMCID: PMC3337229 DOI: 10.1186/1471-2164-13-82] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 02/29/2012] [Indexed: 01/04/2023] Open
Abstract
Background The small airway epithelium (SAE), the cell population that covers the human airway surface from the 6th generation of airway branching to the alveoli, is the major site of lung disease caused by smoking. The focus of this study is to provide quantitative assessment of the SAE transcriptome in the resting state and in response to chronic cigarette smoking using massive parallel mRNA sequencing (RNA-Seq). Results The data demonstrate that 48% of SAE expressed genes are ubiquitous, shared with many tissues, with 52% enriched in this cell population. The most highly expressed gene, SCGB1A1, is characteristic of Clara cells, the cell type unique to the human SAE. Among other genes expressed by the SAE are those related to Clara cell differentiation, secretory mucosal defense, and mucociliary differentiation. The high sensitivity of RNA-Seq permitted quantification of gene expression related to infrequent cell populations such as neuroendocrine cells and epithelial stem/progenitor cells. Quantification of the absolute smoking-induced changes in SAE gene expression revealed that, compared to ubiquitous genes, more SAE-enriched genes responded to smoking with up-regulation, and those with the highest basal expression levels showed most dramatic changes. Smoking had no effect on SAE gene splicing, but was associated with a shift in molecular pattern from Clara cell-associated towards the mucus-secreting cell differentiation pathway with multiple features of cancer-associated molecular phenotype. Conclusions These observations provide insights into the unique biology of human SAE by providing quantit-ative assessment of the global transcriptome under physiological conditions and in response to the stress of chronic cigarette smoking.
Collapse
Affiliation(s)
- Neil R Hackett
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Biologic phenotyping of the human small airway epithelial response to cigarette smoking. PLoS One 2011; 6:e22798. [PMID: 21829517 PMCID: PMC3145669 DOI: 10.1371/journal.pone.0022798] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 07/07/2011] [Indexed: 01/23/2023] Open
Abstract
Background The first changes associated with smoking are in the small airway epithelium (SAE). Given that smoking alters SAE gene expression, but only a fraction of smokers develop chronic obstructive pulmonary disease (COPD), we hypothesized that assessment of SAE genome-wide gene expression would permit biologic phenotyping of the smoking response, and that a subset of healthy smokers would have a “COPD-like” SAE transcriptome. Methodology/Principal Findings SAE (10th–12th generation) was obtained via bronchoscopy of healthy nonsmokers, healthy smokers and COPD smokers and microarray analysis was used to identify differentially expressed genes. Individual responsiveness to smoking was quantified with an index representing the % of smoking-responsive genes abnormally expressed (ISAE), with healthy smokers grouped into “high” and “low” responders based on the proportion of smoking-responsive genes up- or down-regulated in each smoker. Smokers demonstrated significant variability in SAE transcriptome with ISAE ranging from 2.9 to 51.5%. While the SAE transcriptome of “low” responder healthy smokers differed from both “high” responders and smokers with COPD, the transcriptome of the “high” responder healthy smokers was indistinguishable from COPD smokers. Conclusion/Significance The SAE transcriptome can be used to classify clinically healthy smokers into subgroups with lesser and greater responses to cigarette smoking, even though these subgroups are indistinguishable by clinical criteria. This identifies a group of smokers with a “COPD-like” SAE transcriptome.
Collapse
|
31
|
Brody JS, Steiling K. Interaction of cigarette exposure and airway epithelial cell gene expression. Annu Rev Physiol 2011; 73:437-56. [PMID: 21090967 DOI: 10.1146/annurev-physiol-012110-142219] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cigarette smoking is responsible for lung cancer and chronic obstructive pulmonary disease (COPD), the leading cause of death from cancer and the second-leading cause of death in the United States. In the United States, 46 million people smoke, with an equal number of former smokers. Moreover, 20-25% of current or former smokers will develop either disease, and smokers with one disease are at increased risk for developing the other. There are no tools for predicting risk of developing either disease; no accepted tools for early diagnosis of potentially curable lung cancer; and no tools for defining molecular pathways or molecular subtypes of these diseases, for predicting rate of progression, or for assessing response to therapy at a biochemical or molecular level. This review discusses current studies and the future potential of measuring global gene expression in epithelial cells that are in the airway field of injury and of using the genomic information derived to begin to answer some of the above questions.
Collapse
Affiliation(s)
- Jerome S Brody
- Pulmonary Center, Boston University School of Medicine, Massachusetts 02218, USA.
| | | |
Collapse
|
32
|
Gál K, Cseh A, Szalay B, Rusai K, Vannay A, Lukácsovits J, Heemann U, Szabó AJ, Losonczy G, Tamási L, Müller V. Effect of cigarette smoke and dexamethasone on Hsp72 system of alveolar epithelial cells. Cell Stress Chaperones 2011; 16:369-78. [PMID: 21188663 PMCID: PMC3118827 DOI: 10.1007/s12192-010-0249-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Revised: 11/08/2010] [Accepted: 12/06/2010] [Indexed: 01/21/2023] Open
Abstract
Smoking is the leading risk factor of chronic obstructive pulmonary disease (COPD) and lung cancer. Corticosteroids are abundantly used in these patients; however, the interaction of smoking and steroid treatment is not fully understood. Heat shock proteins (Hsps) play a central role in the maintenance of cell integrity, apoptosis and cellular steroid action. To better understand cigarette smoke-steroid interaction, we examined the effect of cigarette smoke extract (CSE) and/or dexamethasone (DEX) on changes of intracellular heat shock protein-72 (Hsp72) in lung cells. Alveolar epithelial cells (A549) were exposed to increasing doses (0; 0.1; 1; and 10 μM/μl) of DEX in the medium in the absence(C) and presence of CSE. Apoptosis, necrosis, Hsp72 messenger-ribonucleic acid (mRNA) and protein expression of cells were measured, and the role of Hsp72 on steroid effect examined. CSE reduced the number of viable cells by significantly increasing the number of apoptotic and necrotic cells. DEX dose-dependently decreased the ratio of apoptosis when CSE was administered, without change in necrosis. CSE - DEX co-treatment dose-dependently increased Hsp72 mRNA and protein expression, with the highest level measured in CSE + DEX (10) cells, while significantly lower levels were noted in all respective C groups. Pretreatment with Hsp72 silencing RNA confirmed that increased survival observed following DEX administration in CSE-treated cells was mainly mediated via the Hsp72 system. CSE significantly decreases cell survival by inducing apoptosis and necrosis. DEX significantly increases Hsp72 mRNA and protein expression only in the presence of CSE resulting in increased cellular protection and survival. DEX exerts its cell protective effects by decreasing apoptotic cell death via the Hsp72 system in CSE-treated alveolar epithelial cells.
Collapse
Affiliation(s)
- Krisztina Gál
- Department of Pulmonology, Semmelweis University Budapest, Hungary.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Gower AC, Steiling K, Brothers JF, Lenburg ME, Spira A. Transcriptomic studies of the airway field of injury associated with smoking-related lung disease. PROCEEDINGS OF THE AMERICAN THORACIC SOCIETY 2011; 8:173-9. [PMID: 21543797 PMCID: PMC3159071 DOI: 10.1513/pats.201011-066ms] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 12/30/2010] [Indexed: 12/12/2022]
Abstract
The "field of injury" hypothesis proposes that exposure to an inhaled insult such as cigarette smoke elicits a common molecular response throughout the respiratory tract. This response can therefore be quantified in any airway tissue, including readily accessible epithelial cells in the bronchus, nose, and mouth. High-throughput technologies, such as whole-genome gene expression microarrays, can be employed to catalog the physiological consequences of such exposures in the airway epithelium. Pulmonary diseases such as chronic obstructive pulmonary disease, lung cancer, and asthma are also thought to be associated with a field of injury, and in patients with these diseases, airway epithelial cells can be a useful surrogate for diseased tissue that is often difficult to obtain. Global measurement of mRNA and microRNA expression in these cells can provide useful information about the molecular pathogenesis of such diseases and may be useful for diagnosis and for predicting prognosis and response to therapy. In this review, our aim is to summarize the history and state of the art of such "transcriptomic" studies in the human airway epithelium, especially in smoking and smoking-related lung diseases, and to highlight future directions for this field.
Collapse
Affiliation(s)
- Adam C. Gower
- Bioinformatics Program, Boston University, Section of Computational Biomedicine, Department of Medicine, and Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Katrina Steiling
- Bioinformatics Program, Boston University, Section of Computational Biomedicine, Department of Medicine, and Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - John F. Brothers
- Bioinformatics Program, Boston University, Section of Computational Biomedicine, Department of Medicine, and Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Marc E. Lenburg
- Bioinformatics Program, Boston University, Section of Computational Biomedicine, Department of Medicine, and Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Avrum Spira
- Bioinformatics Program, Boston University, Section of Computational Biomedicine, Department of Medicine, and Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| |
Collapse
|
34
|
Reynolds HY. Bronchoalveolar lavage and other methods to define the human respiratory tract milieu in health and disease. Lung 2011; 189:87-99. [PMID: 21350888 DOI: 10.1007/s00408-011-9284-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 02/01/2011] [Indexed: 01/19/2023]
Abstract
During fiber-optic bronchoscopy (FOB), surface sampling of the human respiratory airways and alveolar unit can be done with bronchoalveolar lavage (BAL), plus selective sites can be brushed for cells and transbronchial biopsies made in adjacent tissue. This permits analysis of the respiratory tract's milieu in healthy normals, in those with disease, and in control subjects. These combined procedures have been an established approach for obtaining specimens for research and for clinical assessment for over four decades. However, now new less invasive sampling methods are emerging. This review emphasizes BAL and the cellular and noncellular components recovered in fluid that have contributed to improving knowledge of how the respiratory tree's innate immunity can protect, and how airway structures can become deranged and manifest disease. After a discussion of training for FOB and procedural issues, a spectrum of respiratory diseases studied with BAL is presented, including airway illness (asthma and chronic obstructive pulmonary disease), diffuse interstitial lung diseases [idiopathic pulmonary fibrosis, rheumatoid interstitial lung disease (ILD), granulomatous ILDs], lung infections, lung malignancy, and upper and lower tract airway problems. Some recent studies with exhaled breath condensate analyses are given.
Collapse
Affiliation(s)
- Herbert Y Reynolds
- Lung Biology and Disease Branch, Division of Lung Diseases, National Heart, Lung & Blood Institute, 6701 Rockledge Drive, Suite 10042, Two Rockledge Center, MSC 7952, Bethesda, MD 20892-7952, USA.
| |
Collapse
|
35
|
|
36
|
The Human Lung Microbiome. METAGENOMICS OF THE HUMAN BODY 2011. [PMCID: PMC7121966 DOI: 10.1007/978-1-4419-7089-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The human lower respiratory tract is considered sterile in normal healthy individuals (Flanagan et al., 2007; Speert, 2006) despite the fact that every day we breathe in multiple microorganisms present in the air and aspirate thousands of organisms from the mouth and nasopharynx. This apparent sterility is maintained by numerous interrelated components of the lung physical structures such as the mucociliary elevator and components of the innate and adaptive immune systems (discussed below) (reviewed in (Diamond et al., 2000; Gerritsen, 2000)). However, it is possible that the observed sterility might be a result of the laboratory practices applied to study the flora of the lungs. Historically, researchers faced with a set of diseases characterized by a changing and largely cryptic lung microbiome have lacked tools to study lung ecology as a whole and have concentrated on familiar, cultivatable candidate pathogens.
Collapse
|
37
|
Wang R, Wang G, Ricard MJ, Ferris B, Strulovici-Barel Y, Salit J, Hackett NR, Gudas LJ, Crystal RG. Smoking-induced upregulation of AKR1B10 expression in the airway epithelium of healthy individuals. Chest 2010; 138:1402-10. [PMID: 20705797 DOI: 10.1378/chest.09-2634] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The aldo-keto reductase (AKR) gene superfamily codes for monomeric, soluble reduced nicotinamide adenine dinucleotide phosphate-dependent oxidoreductases that mediate elimination reactions. AKR1B10, an AKR that eliminates retinals, has been observed as upregulated in squamous metaplasia and non-small cell lung cancer and has been suggested as a diagnostic marker specific to tobacco-related carcinogenesis. We hypothesized that upregulation of AKR1B10 expression may be initiated in healthy smokers prior to the development of evidence of lung cancer. METHODS Expression of AKR1B10 was assessed at the mRNA level using microarrays with TaqMan confirmation in the large airway epithelium (21 healthy nonsmokers, 31 healthy smokers) and small airway epithelium (51 healthy nonsmokers, 58 healthy smokers) obtained by fiberoptic bronchoscopy and brushing. RESULTS Compared with healthy nonsmokers, AKR1B10 mRNA levels were significantly upregulated in both large and small airway epithelia of healthy smokers. Consistent with the mRNA data, AKR1B10 protein was significantly upregulated in the airway epithelium of healthy smokers as assessed by Western blot analysis and immunohistochemistry, with AKR1B10 expressed in both differentiated and basal cells. Finally, cigarette smoke extract mediated upregulation of AKR1B10 in airway epithelial cells in vitro, and transfection of AKR1B10 into airway epithelial cells enhanced the conversion of retinal to retinol. CONCLUSIONS Smoking per se mediates upregulation of AKR1B10 expression in the airway epithelia of healthy smokers with no evidence of lung cancer. In the context of these observations and the link of AKR1B10 to the metabolism of retinals and to lung cancer, the smoking-induced upregulation of AKR1B10 may be an early process in the multiple events leading to lung cancer.
Collapse
Affiliation(s)
- Rui Wang
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Fu XW, Wood K, Spindel ER. Prenatal nicotine exposure increases GABA signaling and mucin expression in airway epithelium. Am J Respir Cell Mol Biol 2010; 44:222-9. [PMID: 20448051 DOI: 10.1165/rcmb.2010-0109oc] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Maternal smoking during pregnancy increases the risk of respiratory disease in offspring, but surprisingly little is known about the underlying mechanisms. Nicotinic acetylcholine receptors (nAChRs) expressed in bronchial epithelial cells (BECs) mediate the effects of nicotine on lung development and function. Recently, BECs were also shown to express a GABAergic paracrine loop that was implicated in mucus overproduction in asthma. We therefore investigated the interactions between cholinergic and GABAergic signaling in rhesus macaque BECs, and found that nicotine upregulated GABA signaling in BECs through the sequential activation of BEC nAChR and GABA receptors. The incubation of primary cultures of rhesus BECs increased concentrations of GAD, GABA(A) receptors, and mucin mRNA. The nicotine-induced increase in glutamatic acid decarboxylase (GAD) and GABA(A) receptor mRNA resulted in increased GABA-induced currents and increased expression of mucin. The ability of nicotine to increase mucin expression was blocked by nicotinic and GABA(A) antagonists. These results implicate GABA signaling as a middleman in nicotine's effects on mucus overproduction. Similar effects of nicotine on GABA signaling and the expression of mucin were seen in vivo after chronic exposure of rhesus monkeys to nicotine. These data provide a new mechanism linking smoking with the increased mucin seen in asthma and chronic obstructive pulmonary disorder, and suggest a new paradigm of communication between non-neuronal transmitter systems in BECs. The existence of neural-like transmitter interactions in BECs suggests that some drugs active in the central nervous system may possess previously unexpected utility in respiratory diseases.
Collapse
Affiliation(s)
- Xiao Wen Fu
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, 97006, USA
| | | | | |
Collapse
|
39
|
López-Boado YS, Li JU, Clayton CL, Wright JL, Churg A. Modification of the rat airway explant transcriptome by cigarette smoke. Inhal Toxicol 2010; 22:234-44. [PMID: 19883206 DOI: 10.3109/08958370903191437] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Although a number of animal model studies have addressed changes in gene expression in the parenchyma and their relationship to emphysema, much less is known about the pathogenesis of cigarette smoke-induced small airway remodeling. In this study the authors exposed rat tracheal explants, a model of the airway wall, to whole smoke for 15 min, and then cultured the explants in air. The airway transcriptome was evaluated using RAE 230_2 gene chips. By 2 h after starting smoke exposure, expression levels of 502 genes were differentially expressed by more than 1.5 times (p < .01 or less) and by 24 h 1870 genes were significantly changed up or down. These included genes involved in antioxidant protection, epithelial defense and remodeling, inflammatory mediators and transcription factors, and a number of unexpected genes, including the matrix metalloproteinase (MMP)-12 inducer, tachykinin-1 (substance P). Pretreatment of the explants with 1 x 10(-7) M dexamethasone reduced the number of significantly changed genes by approximately 47% at 2 h and 68% at 24 h and in almost all instances reduced the magnitude of the smoke-induced changes. The authors conclude that even a very brief exposure to cigarette smoke can lead to rapid changes in the expression of a large number of genes in rat tracheal explants, and that these effects are directly mediated by smoke, without a need for exogenous inflammatory cells. Steroids, contrary to the usual belief, are able to ameliorate many of these changes, at least in this very acute model.
Collapse
|
40
|
Mineo D, Ambrogi V, Cufari ME, Gambardella S, Pignotti L, Pompeo E, Mineo TC. Variations of inflammatory mediators and alpha1-antitrypsin levels after lung volume reduction surgery for emphysema. Am J Respir Crit Care Med 2010; 181:806-14. [PMID: 20056899 DOI: 10.1164/rccm.200910-1476oc] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE In emphysema, chronic inflammation, including protease-antiprotease imbalance, is responsible for declining pulmonary function and progressive cachexia. OBJECTIVES To evaluate variations of inflammatory mediators and alpha(1)-antitrypsin levels after lung volume reduction surgery (LVRS) compared with respiratory rehabilitation. METHODS A total of 28 patients with moderate to severe emphysema, who underwent video-assisted thoracoscopic LVRS, were compared with 26 similar patients, who refused operation and followed a standardized rehabilitation program, and to a matched healthy group. Respiratory function, body composition, circulating inflammatory mediators, and alpha(1)-antitrypsin levels were evaluated before and 12 months after treatment. Gene expression levels of inflammatory mediators and protease-antiprotease were assessed in emphysematous specimens from 17 operated patients by matching to normal tissue from resection margins. MEASUREMENTS AND MAIN RESULTS Significant improvements were only obtained after surgery in respiratory function (FEV(1), +25.2%, P < 0.0001; residual volume [RV], -19.5%, P < 0.0001; diffusing lung capacity for carbon monoxide, +3.3%, P < 0.05) and body composition (fat-free mass, +6.5%, P < 0.01; fat mass, +11.9%, P < 0.01), with decrement of circulating inflammatory mediators (TNF-alpha, -22.2%, P < 0.001; IL-6, -24.5%, P < 0.001; IL-8, -20.0%, P < 0.001) and increment of antiprotease levels (alpha(1)-antitrypsin, +27.0%, P < 0.001). Supportive gene expression analysis demonstrated active inflammation and protease hyperactivity in the resected emphysematous tissue. Reduction of TNF-alpha and IL-6 and increment of alpha(1)-antitrypsin levels significantly correlated with reduction of RV (P = 0.03, P = 0.009, and P = 0.001, respectively), and partially with increment of fat-free mass (P = 0.03, P = 0.02, and P = 0.09, respectively). CONCLUSIONS LVRS significantly reduced circulating inflammatory mediators and increased antiprotease levels over respiratory rehabilitation, also improving respiratory function and nutritional status. Correlations of inflammatory mediators and antiprotease levels with RV and, partly, with body composition suggest that elimination of inflammatory emphysematous tissue may explain clinical improvements after surgery.
Collapse
Affiliation(s)
- Davide Mineo
- Division of Thoracic Surgery, Tor Vergata University of Rome and Policlinic, 00133 Rome, Italy.
| | | | | | | | | | | | | |
Collapse
|
41
|
Ocak S, Sos ML, Thomas RK, Massion PP. High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications. Eur Respir J 2009; 34:489-506. [PMID: 19648524 DOI: 10.1183/09031936.00042409] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
During the last decade, high-throughput technologies including genomic, epigenomic, transcriptomic and proteomic have been applied to further our understanding of the molecular pathogenesis of this heterogeneous disease, and to develop strategies that aim to improve the management of patients with lung cancer. Ultimately, these approaches should lead to sensitive, specific and noninvasive methods for early diagnosis, and facilitate the prediction of response to therapy and outcome, as well as the identification of potential novel therapeutic targets. Genomic studies were the first to move this field forward by providing novel insights into the molecular biology of lung cancer and by generating candidate biomarkers of disease progression. Lung carcinogenesis is driven by genetic and epigenetic alterations that cause aberrant gene function; however, the challenge remains to pinpoint the key regulatory control mechanisms and to distinguish driver from passenger alterations that may have a small but additive effect on cancer development. Epigenetic regulation by DNA methylation and histone modifications modulate chromatin structure and, in turn, either activate or silence gene expression. Proteomic approaches critically complement these molecular studies, as the phenotype of a cancer cell is determined by proteins and cannot be predicted by genomics or transcriptomics alone. The present article focuses on the technological platforms available and some proposed clinical applications. We illustrate herein how the "-omics" have revolutionised our approach to lung cancer biology and hold promise for personalised management of lung cancer.
Collapse
Affiliation(s)
- S Ocak
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232-6838, USA
| | | | | | | |
Collapse
|
42
|
Quality control in microarray assessment of gene expression in human airway epithelium. BMC Genomics 2009; 10:493. [PMID: 19852842 PMCID: PMC2774870 DOI: 10.1186/1471-2164-10-493] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 10/24/2009] [Indexed: 11/16/2022] Open
Abstract
Background Microarray technology provides a powerful tool for defining gene expression profiles of airway epithelium that lend insight into the pathogenesis of human airway disorders. The focus of this study was to establish rigorous quality control parameters to ensure that microarray assessment of the airway epithelium is not confounded by experimental artifact. Samples (total n = 223) of trachea, large and small airway epithelium were collected by fiberoptic bronchoscopy of 144 individuals and hybridized to Affymetrix microarrays. The pre- and post-chip quality control (QC) criteria established, included: (1) RNA quality, assessed by RNA Integrity Number (RIN) ≥ 7.0; (2) cRNA transcript integrity, assessed by signal intensity ratio of GAPDH 3' to 5' probe sets ≤ 3.0; and (3) the multi-chip normalization scaling factor ≤ 10.0. Results Of the 223 samples, all three criteria were assessed in 191; of these 184 (96.3%) passed all three criteria. For the remaining 32 samples, the RIN was not available, and only the other two criteria were used; of these 29 (90.6%) passed these two criteria. Correlation coefficients for pairwise comparisons of expression levels for 100 maintenance genes in which at least one array failed the QC criteria (average Pearson r = 0.90 ± 0.04) were significantly lower (p < 0.0001) than correlation coefficients for pairwise comparisons between arrays that passed the QC criteria (average Pearson r = 0.97 ± 0.01). Inter-array variability was significantly decreased (p < 0.0001) among samples passing the QC criteria compared with samples failing the QC criteria. Conclusion Based on the aberrant maintenance gene data generated from samples failing the established QC criteria, we propose that the QC criteria outlined in this study can accurately distinguish high quality from low quality data, and can be used to delete poor quality microarray samples before proceeding to higher-order biological analyses and interpretation.
Collapse
|
43
|
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.
Collapse
Affiliation(s)
- Meredith L Turetz
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College New York, New York, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Hübner RH, Schwartz JD, De Bishnu P, Ferris B, Omberg L, Mezey JG, Hackett NR, Crystal RG. Coordinate control of expression of Nrf2-modulated genes in the human small airway epithelium is highly responsive to cigarette smoking. Mol Med 2009; 15:203-19. [PMID: 19593404 DOI: 10.2119/molmed.2008.00130] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Accepted: 03/20/2009] [Indexed: 12/30/2022] Open
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) is an oxidant-responsive transcription factor known to induce detoxifying and antioxidant genes. Cigarette smoke, with its large oxidant content, is a major stress on the cells of small airway epithelium, which are vulnerable to oxidant damage. We assessed the role of cigarette smoke in activation of Nrf2 in the human small airway epithelium in vivo. Fiberoptic bronchoscopy was used to sample the small airway epithelium in healthy-nonsmoker and healthy-smoker, and gene expression was assessed using microarrays. Relative to nonsmokers, Nrf2 protein in the small airway epithelium of smokers was activated and localized in the nucleus. The human homologs of 201 known murine Nrf2-modulated genes were identified, and 13 highly smoking-responsive Nrf2-modulated genes were identified. Construction of an Nrf2 index to assess the expression levels of these 13 genes in the airway epithelium of smokers showed coordinate control, an observation confirmed by quantitative PCR. This coordinate level of expression of the 13 Nrf2-modulated genes was independent of smoking history or demographic parameters. The Nrf2 index was used to identify two novel Nrf2-modulated, smoking-responsive genes, pirin (PIR) and UDP glucuronosyltransferase 1-family polypeptide A4 (UGT1A4). Both genes were demonstrated to contain functional antioxidant response elements in the promoter region. These observations suggest that Nrf2 plays an important role in regulating cellular defenses against smoking in the highly vulnerable small airway epithelium cells, and that there is variability within the human population in the Nrf2 responsiveness to oxidant burden.
Collapse
Affiliation(s)
- Ralf-Harto Hübner
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, United States of America
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Abstract
Worldwide over 1 million people die due to lung cancer each year. It is estimated that cigarette smoking explains almost 90% of lung cancer risk in men and 70 to 80% in women. Clinically evident lung cancers have multiple genetic and epigenetic abnormalities. These abnormalities may result in activation of oncogenes and inactivation of tumor-suppressor genes. Chronic inflammation, which is known to promote cancer, may result both from smoking and from genetic abnormalities. These mediators in turn may be responsible for increased macrophage recruitment, delayed neutrophil clearance, and increase in reactive oxygen species (ROS). Thus, the pulmonary environment presents a unique milieu in which lung carcinogenesis proceeds in complicity with the host cellular network. The pulmonary diseases that are associated with the greatest risk for lung cancer are characterized by abundant and deregulated inflammation. Pulmonary disorders such as chronic obstructive pulmonary disease (COPD)/emphysema are characterized by profound abnormalities in inflammatory and fibrotic pathways. The cytokines and growth factors aberrantly produced in COPD and the developing tumor microenvironment have been found to have deleterious properties that simultaneously pave the way for both epithelial-mesenchymal transition (EMT) and destruction of specific host cell-mediated immune responses. Full definition of these pathways will afford the opportunity to intervene in specific inflammatory events mediating lung tumorigenesis and resistance to therapy.
Collapse
|
46
|
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.
Collapse
|