1
|
Rakkar K, Pang YL, Rajasekar P, Portelli MA, Hall RJ, Clifford RL, Shaw D, Sayers I. Mepolizumab Induced Changes in Nasal Methylome and Transcriptome to Predict Response in Asthma. Am J Respir Crit Care Med 2024. [PMID: 38386780 DOI: 10.1164/rccm.202308-1477le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/22/2024] [Indexed: 02/24/2024] Open
Affiliation(s)
- Kamini Rakkar
- University of Nottingham, 6123, Nottingham, United Kingdom of Great Britain and Northern Ireland;
| | - Yik L Pang
- University of Nottingham, 6123, Nottingham, United Kingdom of Great Britain and Northern Ireland
| | - Poojitha Rajasekar
- University of Nottingham, 6123, Nottingham, United Kingdom of Great Britain and Northern Ireland
| | - Michael A Portelli
- University of Nottingham, Translational Medical Sciences, Nottingham Biomedical Research Centre, Nottingham, Nottinghamshire, United Kingdom of Great Britain and Northern Ireland
| | - Robert J Hall
- University of Nottingham, 6123, Nottingham, United Kingdom of Great Britain and Northern Ireland
| | - Rachel L Clifford
- University of Nottingham, Nottingham, United Kingdom of Great Britain and Northern Ireland
| | - Dominick Shaw
- University of Nottingham, Respiratory Research Unit, Nottingham, United Kingdom of Great Britain and Northern Ireland
| | - Ian Sayers
- University of Nottingham, Division of Therapeutics & Molecular Medicine, Nottingham, United Kingdom of Great Britain and Northern Ireland
| |
Collapse
|
2
|
Rajasekar P, Hall RJ, Binaya KC, Mahapatra PS, Puppala SP, Thakker D, MacIsaac JL, Lin D, Kobor M, Bolton CE, Sayers I, Hall IP, Clifford RL. Nepalese indoor cookstove smoke extracts alter human airway epithelial gene expression, DNA methylation and hydroxymethylation. Environ Pollut 2023; 337:122561. [PMID: 37742862 DOI: 10.1016/j.envpol.2023.122561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023]
Abstract
Household air pollution caused by inefficient cooking practices causes 4 million deaths a year worldwide. In Nepal, 86% of the rural population use solid fuels for cooking. Over 25% of premature deaths associated with air pollution are respiratory in nature. Here we aimed to identify molecular signatures of different cookstove and fuel type exposures in human airway epithelial cells, to understand the mechanisms mediating cook stove smoke induced lung disease. Primary human airway epithelial cells in submerged culture were exposed to traditional cook stove (TCS), improved cook stove (ICS) and liquefied petroleum gas (LPG) stove smoke extracts. Changes to gene expression, DNA methylation and hydroxymethylation were measured by bulk RNA sequencing and HumanMethylationEPIC BeadChip following oxidative bisulphite conversion, respectively. TCS smoke extract alone reproducibly caused changes in the expression of 52 genes enriched for oxidative stress pathways. TCS, ICS and LPG smoke extract exposures were associated with distinct changes to DNA methylation and hydroxymethylation. A subset of TCS induced genes were associated with differentially methylated and/or hydroxymethylated CpGs sites, and enriched for the ferroptosis pathway and the upstream regulator NFE2L2. DNA methylation and hydroxymethylation changes not associated with a concurrent change in gene expression, were linked to biological processes and molecular pathways important to airway health, including neutrophil function, transforming growth factor beta signalling, GTPase activity, and cell junction organisation. Our data identified differential impacts of TCS, ICS and LPG cook stove smoke on the human airway epithelium transcriptome, DNA methylome and hydroxymethylome and provide further insight into the association between indoor air pollution exposure and chronic lung disease mechanisms.
Collapse
Affiliation(s)
- Poojitha Rajasekar
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Robert J Hall
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - K C Binaya
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Water and Air Theme, Atmosphere Initiative, International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | - Parth S Mahapatra
- Water and Air Theme, Atmosphere Initiative, International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | - Siva P Puppala
- Water and Air Theme, Atmosphere Initiative, International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | - Dhruma Thakker
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Julia L MacIsaac
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Lin
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Kobor
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte E Bolton
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK
| | - Ian Sayers
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Ian P Hall
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Rachel L Clifford
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK.
| |
Collapse
|
3
|
Clifford RL, Jones MJ. Greater Than the Sum of Its Parts: Integrating Multiple Data Sets to Decipher Cigarette Smoking Effects on Airway Epithelium. Am J Respir Cell Mol Biol 2021; 65:335-336. [PMID: 34139135 PMCID: PMC8525203 DOI: 10.1165/rcmb.2021-0207ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Rachel L Clifford
- Centre for Respiratory Medicine University of Nottingham and Nottingham NIHR Biomedical Research Centre Nottingham, United Kingdom
| | - Meaghan J Jones
- Department of Biochemistry and Medical Genetics University of Manitoba Manitoba, Canada and
- Children's Hospital Research Institute of Manitoba Manitoba, Canada
| |
Collapse
|
4
|
Rajasekar P, Patel J, Clifford RL. DNA Methylation of Fibroblast Phenotypes and Contributions to Lung Fibrosis. Cells 2021; 10:cells10081977. [PMID: 34440746 PMCID: PMC8391838 DOI: 10.3390/cells10081977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 11/22/2022] Open
Abstract
Fibroblasts are an integral part of connective tissue and play a crucial role in developing and modulating the structural framework of tissues by acting as the primary source of extracellular matrix (ECM). A precise definition of the fibroblast remains elusive. Lung fibroblasts orchestrate the assembly and turnover of ECM to facilitate gas exchange alongside performing immune functions including the secretion of bioactive molecules and antigen presentation. DNA methylation is the covalent attachment of a methyl group to primarily cytosines within DNA. DNA methylation contributes to diverse cellular phenotypes from the same underlying genetic sequence, with DNA methylation profiles providing a memory of cellular origin. The lung fibroblast population is increasingly viewed as heterogeneous with between 6 and 11 mesenchymal populations identified across health and lung disease to date. DNA methylation has been associated with different lung fibroblast populations in health and with alterations in lung disease, but to varying extents. In this review, we will discuss lung fibroblast heterogeneity and the evidence for a contribution from DNA methylation to defining cell populations and alterations in disease.
Collapse
|
5
|
Li H, Ryu MH, Rider CF, Tse W, Clifford RL, Aristizabal MJ, Wen W, Carlsten C. Predominant DNMT and TET mediate effects of allergen on the human bronchial epithelium in a controlled air pollution exposure study. J Allergy Clin Immunol 2020; 147:1671-1682. [PMID: 33069714 DOI: 10.1016/j.jaci.2020.08.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/29/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Epidemiological data show that traffic-related air pollution contributes to the increasing prevalence and severity of asthma. DNA methylation (DNAm) changes may elucidate adverse health effects of environmental exposures. OBJECTIVES We sought to assess the effects of allergen and diesel exhaust (DE) exposures on global DNAm and its regulation enzymes in human airway epithelium. METHODS A total of 11 participants, including 7 with and 4 without airway hyperresponsiveness, were recruited for a randomized, double-blind crossover study. Each participant had 3 exposures: filtered air + saline, filtered air + allergen, and DE + allergen. Forty-eight hours postexposure, endobronchial biopsies and bronchoalveolar lavages were collected. Levels of DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) enzymes, 5-methylcytosine, and 5-hydroxymethylcytosine were determined by immunohistochemistry. Cytokines and chemokines in bronchoalveolar lavages were measured by electrochemiluminescence multiplex assays. RESULTS Predominant DNMT (the most abundant among DNMT1, DNMT3A, and DNMT3B) and predominant TET (the most abundant among TET1, TET2, and TET3) were participant-dependent. 5-Methylcytosine and its regulation enzymes differed between participants with and without airway hyperresponsiveness at baseline (filtered air + saline) and in response to allergen challenge (regardless of DE exposure). Predominant DNMT and predominant TET correlated with lung function. Allergen challenge effect on IL-8 in bronchoalveolar lavages was modified by TET2 baseline levels in the epithelium. CONCLUSIONS Response to allergen challenge is associated with key DNAm regulation enzymes. This relationship is generally unaltered by DE coexposure but is rather dependent on airway hyperresponsiveness status. These enzymes therefore warranted further inquiry regarding their potential in diagnosis, prognosis, and treatment of asthma.
Collapse
Affiliation(s)
- Hang Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Air Pollution Exposure Laboratory, Department of Medicine, Division of Respiratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Min Hyung Ryu
- Air Pollution Exposure Laboratory, Department of Medicine, Division of Respiratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher F Rider
- Air Pollution Exposure Laboratory, Department of Medicine, Division of Respiratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Wayne Tse
- Air Pollution Exposure Laboratory, Department of Medicine, Division of Respiratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rachel L Clifford
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, United Kingdom
| | - Maria J Aristizabal
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada; Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada
| | - Weiping Wen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Chris Carlsten
- Air Pollution Exposure Laboratory, Department of Medicine, Division of Respiratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
6
|
Clifford RL, Yang CX, Fishbane N, Patel J, MacIsaac JL, McEwen LM, May ST, Castellanos-Uribe M, Nair P, Obeidat M, Kobor MS, Knox AJ, Hackett TL. TWIST1 DNA methylation is a cell marker of airway and parenchymal lung fibroblasts that are differentially methylated in asthma. Clin Epigenetics 2020; 12:145. [PMID: 33008450 PMCID: PMC7531162 DOI: 10.1186/s13148-020-00931-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/01/2020] [Indexed: 12/21/2022] Open
Abstract
Background Mesenchymal fibroblasts are ubiquitous cells that maintain the extracellular matrix of organs. Within the lung, airway and parenchymal fibroblasts are crucial for lung development and are altered with disease, but it has been difficult to understand their roles due to the lack of distinct molecular markers. We studied genome-wide DNA methylation and gene expression in airway and parenchymal lung fibroblasts from healthy and asthmatic donors, to identify a robust cell marker and to determine if these cells are molecularly distinct in asthma. Results Airway (N = 8) and parenchymal (N = 15) lung fibroblasts from healthy individuals differed in the expression of 158 genes, and DNA methylation of 3936 CpGs (Bonferroni adjusted p value < 0.05). Differential DNA methylation between cell types was associated with differential expression of 42 genes, but no single DNA methylation CpG feature (location, effect size, number) defined the interaction. Replication of gene expression and DNA methylation in a second cohort identified TWIST1 gene expression, DNA methylation and protein expression as a cell marker of airway and parenchymal lung fibroblasts, with DNA methylation having 100% predictive discriminatory power. DNA methylation was differentially altered in parenchymal (112 regions) and airway fibroblasts (17 regions) with asthmatic status, with no overlap between regions. Conclusions Differential methylation of TWIST1 is a robust cell marker of airway and parenchymal lung fibroblasts. Airway and parenchymal fibroblast DNA methylation are differentially altered in individuals with asthma, and the role of both cell types should be considered in the pathogenesis of asthma.
Collapse
Affiliation(s)
- Rachel L Clifford
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK. .,BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Nick Fishbane
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Jamie Patel
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Julia L MacIsaac
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa M McEwen
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean T May
- Nottingham Arabidopsis Stock Centre, Plant Sciences Building, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Marcos Castellanos-Uribe
- Nottingham Arabidopsis Stock Centre, Plant Sciences Building, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Parameswaran Nair
- Firestone Institute for Respiratory Health, St Joseph's Healthcare and Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Ma'en Obeidat
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada.,Department of Anaesthesiology, Pharmacology & Therapeutics, University of British Columbia, Vancouver, Canada
| | - Michael S Kobor
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alan J Knox
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Tillie-Louise Hackett
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada.,Department of Anaesthesiology, Pharmacology & Therapeutics, University of British Columbia, Vancouver, Canada
| |
Collapse
|
7
|
Clifford RL, Patel J, MacIsaac JL, McEwen LM, Johnson SR, Shaw D, Knox AJ, Hackett TL, Kobor MS. Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation. Sci Rep 2019; 9:14409. [PMID: 31595000 PMCID: PMC6783553 DOI: 10.1038/s41598-019-50873-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/15/2019] [Indexed: 12/14/2022] Open
Abstract
The airway epithelium forms the interface between the inhaled environment and the lung. The airway epithelium is dysfunctional in asthma and epigenetic mechanisms are considered a contributory factor. We hypothesised that the DNA methylation profiles of cultured primary airway epithelial cells (AECs) would differ between cells isolated from individuals with asthma (n = 17) versus those without asthma (n = 16). AECs were isolated from patients by two different isolation techniques; pronase digestion (9 non-asthmatic, 8 asthmatic) and bronchial brushings (7 non-asthmatic and 9 asthmatic). DNA methylation was assessed using an Illumina Infinium HumanMethylation450 BeadChip array. DNA methylation of AECs clustered by isolation technique and linear regression identified 111 CpG sites differentially methylated between isolation techniques in healthy individuals. As a consequence, the effect of asthmatic status on DNA methylation was assessed within AEC samples isolated using the same technique. In pronase isolated AECs, 15 DNA regions were differentially methylated between asthmatics and non-asthmatics. In bronchial brush isolated AECs, 849 differentially methylated DNA regions were identified with no overlap to pronase regions. In conclusion, regardless of cell isolation technique, differential DNA methylation was associated with asthmatic status in AECs, providing further evidence for aberrant DNA methylation as a signature of epithelial dysfunction in asthma.
Collapse
Affiliation(s)
- Rachel L Clifford
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham, UK. .,Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Jamie Patel
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa M McEwen
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simon R Johnson
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Dominick Shaw
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Alan J Knox
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Tillie-Louise Hackett
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada.,Department of Anaesthesiology, Pharmacology & Therapeutics, University of British Columbia, Vancouver, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
8
|
Kaczmarek KA, Clifford RL, Knox AJ. Epigenetic Changes in Airway Smooth Muscle as a Driver of Airway Inflammation and Remodeling in Asthma. Chest 2018; 155:816-824. [PMID: 30414795 DOI: 10.1016/j.chest.2018.10.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/10/2018] [Accepted: 10/29/2018] [Indexed: 12/18/2022] Open
Abstract
Epigenetic changes are heritable changes in gene expression, without changing the DNA sequence. Epigenetic processes provide a critical link between environmental insults to the airway and functional changes that determine how airway cells respond to future stimuli. There are three primary epigenetic processes: histone modifications, DNA modification, and noncoding RNAs. Airway smooth muscle has several important roles in the development and maintenance of the pathologic processes occurring in asthma, including inflammation, remodeling, and contraction/hyperresponsiveness. In this review, we describe the evidence for the role of epigenetic changes in driving these processes in airway smooth muscle cells in asthma, with a particular focus on histone modifications. We also discuss how existing therapies may target some of these changes and how epigenetic processes provide targets for the development of novel asthma therapeutics. Epigenetic marks may also provide a biomarker to assess phenotype and treatment responses.
Collapse
Affiliation(s)
- Klaudia A Kaczmarek
- Division of Respiratory Medicine, Nottingham University Hospitals NHS Trust (City Hospital Campus); and the Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node
| | - Rachel L Clifford
- Division of Respiratory Medicine, Nottingham University Hospitals NHS Trust (City Hospital Campus); and the Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node
| | - Alan J Knox
- Division of Respiratory Medicine, Nottingham University Hospitals NHS Trust (City Hospital Campus); and the Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node.
| |
Collapse
|
9
|
Clifford RL, Fishbane N, Patel J, MacIsaac JL, McEwen LM, Fisher AJ, Brandsma CA, Nair P, Kobor MS, Hackett TL, Knox AJ. Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD. Clin Epigenetics 2018; 10:32. [PMID: 29527240 PMCID: PMC5838860 DOI: 10.1186/s13148-018-0464-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 02/25/2018] [Indexed: 11/10/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease of the lungs that is currently the fourth leading cause of death worldwide. Genetic factors account for only a small amount of COPD risk, but epigenetic mechanisms, including DNA methylation, have the potential to mediate the interactions between an individual's genetics and environmental exposure. DNA methylation is highly cell type-specific, and individual cell type studies of DNA methylation in COPD are sparse. Fibroblasts are present within the airway and parenchyma of the lung and contribute to the aberrant deposition of extracellular matrix in COPD. No assessment or comparison of genome-wide DNA methylation profiles in the airway and parenchymal fibroblasts from individuals with and without COPD has been undertaken. These data provide valuable insight into the molecular mechanisms contributing to COPD and the differing pathologies of small airways disease and emphysema in COPD. Methods Genome-wide DNA methylation was evaluated at over 485,000 CpG sites using the Illumina Infinium HumanMethylation450 BeadChip array in the airway (non-COPD n = 8, COPD n = 7) and parenchymal fibroblasts (non-COPD n = 17, COPD n = 29) isolated from individuals with and without COPD. Targeted gene expression was assessed by qPCR in matched RNA samples. Results Differentially methylated DNA regions were identified between cells isolated from individuals with and without COPD in both airway and parenchymal fibroblasts. Only in parenchymal fibroblasts was differential DNA methylation associated with differential gene expression. A second analysis of differential DNA methylation variability identified 359 individual differentially variable CpG sites in parenchymal fibroblasts. No differentially variable CpG sites were identified in the airway fibroblasts. Five differentially variable-methylated CpG sites, associated with three genes, were subsequently assessed for gene expression differences. Two genes (OAT and GRIK2) displayed significantly increased gene expression in cells isolated from individuals with COPD. Conclusions Differential and variable DNA methylation was associated with COPD status in the parenchymal fibroblasts but not airway fibroblasts. Aberrant DNA methylation was associated with altered gene expression imparting biological function to DNA methylation changes. Changes in DNA methylation are therefore implicated in the molecular mechanisms underlying COPD pathogenesis and may represent novel therapeutic targets.
Collapse
Affiliation(s)
- Rachel L. Clifford
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Nick Fishbane
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Jamie Patel
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Julia L. MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Lisa M. McEwen
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Andrew J. Fisher
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, Groningen, The Netherlands
- GRIAC (Groningen Research Institute of Asthma and COPD), University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Parameswaran Nair
- Firestone Institute for Respiratory Health, St Joseph’s Healthcare and Department of Medicine, McMaster University, Hamilton, Ontario Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Tillie-Louise Hackett
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
- Department of Anaesthesiology, Pharmacology, & Therapeutics, University of British Columbia, Vancouver, Canada
| | - Alan J. Knox
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| |
Collapse
|
10
|
Clifford RL, Fishbane N, Rajasekar P, Fisher AJ, Kobor MS, Knox AJ, Hackett TL. S133 Investigating genome wide dna methylation in airway and parenchymal fibroblasts from healthy individuals and individuals with copd. Thorax 2016. [DOI: 10.1136/thoraxjnl-2016-209333.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
11
|
Kaczmarek KA, Clifford RL, Patel JK, Shaw DE, Dowden J, Knox AJ. P236 The role of histone arginine methylation in gene expression of airway smooth muscle cells in asthma. Thorax 2016. [DOI: 10.1136/thoraxjnl-2016-209333.379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
12
|
Clifford RL, Patel JK, Shaw DE, Knox AJ, Kobor MS. P238 Investigating genome wide dna methylation in airway smooth muscle cells from asthmatic and non-asthmatic donors. Thorax 2016. [DOI: 10.1136/thoraxjnl-2016-209333.381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
13
|
Tatler AL, Goodwin AT, Gbolahan O, Saini G, Porte J, John AE, Clifford RL, Violette SM, Weinreb PH, Parfrey H, Wolters PJ, Gauldie J, Kolb M, Jenkins G. Amplification of TGFβ Induced ITGB6 Gene Transcription May Promote Pulmonary Fibrosis. PLoS One 2016; 11:e0158047. [PMID: 27494713 PMCID: PMC4975449 DOI: 10.1371/journal.pone.0158047] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/09/2016] [Indexed: 01/13/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a devastating, progressive disease with poor survival rates and limited treatment options. Upregulation of αvβ6 integrins within the alveolar epithelial cells is a characteristic feature of IPF and correlates with poor patient survival. The pro-fibrotic cytokine TGFβ1 can upregulate αvβ6 integrin expression but the molecular mechanisms driving this effect have not previously been elucidated. We confirm that stimulation with exogenous TGFβ1 increases expression of the integrin β6 subunit gene (ITGB6) and αvβ6 integrin cell surface expression in a time- and concentration-dependent manner. TGFβ1-induced ITGB6 expression occurs via transcriptional activation of the ITGB6 gene, but does not result from effects on ITGB6 mRNA stability. Basal expression of ITGB6 in, and αvβ6 integrins on, lung epithelial cells occurs via homeostatic αvβ6-mediated TGFβ1 activation in the absence of exogenous stimulation, and can be amplified by TGFβ1 activation. Fundamentally, we show for the first time that TGFβ1-induced ITGB6 expression occurs via canonical Smad signalling since dominant negative constructs directed against Smad3 and 4 inhibit ITGB6 transcriptional activity. Furthermore, disruption of a Smad binding site at -798 in the ITGB6 promoter abolishes TGFβ1-induced ITGB6 transcriptional activity. Using chromatin immunoprecipitation we demonstrate that TGFβ1 stimulation of lung epithelial cells results in direct binding of Smad3, and Smad4, to the ITGB6 gene promoter within this region. Finally, using an adenoviral TGFβ1 over-expression model of pulmonary fibrosis we demonstrate that Smad3 is crucial for TGFβ1-induced αvβ6 integrin expression within the alveolar epithelium in vivo. Together, these data confirm that a homeostatic, autocrine loop of αvβ6 integrin activated TGFβ1-induced ITGB6 gene expression regulates epithelial basal αvβ6 integrin expression, and demonstrates that this occurs via Smad-dependent transcriptional regulation at a single Smad binding site in the promoter of the β6 subunit gene. Active TGFβ1 amplifies this pathway both in vitro and in vivo, which may promote fibrosis.
Collapse
Affiliation(s)
- Amanda L. Tatler
- Division of Respiratory Medicine–City, University of Nottingham, Nottingham, United Kingdom
- * E-mail:
| | - Amanda T. Goodwin
- Division of Respiratory Medicine–City, University of Nottingham, Nottingham, United Kingdom
| | - Olumide Gbolahan
- Division of Respiratory Medicine–City, University of Nottingham, Nottingham, United Kingdom
| | - Gauri Saini
- Division of Respiratory Medicine–City, University of Nottingham, Nottingham, United Kingdom
| | - Joanne Porte
- Division of Respiratory Medicine–City, University of Nottingham, Nottingham, United Kingdom
| | - Alison E. John
- Division of Respiratory Medicine–City, University of Nottingham, Nottingham, United Kingdom
| | - Rachel L. Clifford
- Division of Respiratory Medicine–City, University of Nottingham, Nottingham, United Kingdom
| | | | | | - Helen Parfrey
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Paul J. Wolters
- School of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jack Gauldie
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Martin Kolb
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Gisli Jenkins
- Division of Respiratory Medicine–City, University of Nottingham, Nottingham, United Kingdom
| |
Collapse
|
14
|
Poghosyan A, Patel JK, Clifford RL, Knox AJ. Epigenetic dysregulation of interleukin 8 (CXCL8) hypersecretion in cystic fibrosis airway epithelial cells. Biochem Biophys Res Commun 2016; 476:431-437. [PMID: 27240956 DOI: 10.1016/j.bbrc.2016.05.140] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
Airway epithelial cells in cystic fibrosis (CF) overexpress Interleukin 8 (CXCL8) through poorly defined mechanisms. CXCL8 transcription is dependent on coordinated binding of CCAAT/enhancer binding protein (C/EBP)β, nuclear factor (NF)-κB, and activator protein (AP)-1 to the promoter. Here we show abnormal epigenetic regulation is responsible for CXCL8 overexpression in CF cells. Under basal conditions CF cells had increased bromodomain (Brd)3 and Brd4 recruitment and enhanced NF-κB and C/EBPβ binding to the CXCL8 promoter compared to non-CF cells due to trimethylation of histone H3 at lysine 4 (H3K4me3) and DNA hypomethylation at CpG6. IL-1β increased NF-κB, C/EBPβ and Brd4 binding. Furthermore, inhibitors of bromodomain and extra-terminal domain family (BET) proteins reduced CXCL8 production in CF cells suggesting a therapeutic target for the BET pathway.
Collapse
Affiliation(s)
- Anna Poghosyan
- Division of Respiratory Medicine, Nottingham Respiratory Research Unit, University of Nottingham, Clinical Sciences Building, City Hospital, Nottingham, NG5 1PB, United Kingdom.
| | - Jamie K Patel
- Division of Respiratory Medicine, Nottingham Respiratory Research Unit, University of Nottingham, Clinical Sciences Building, City Hospital, Nottingham, NG5 1PB, United Kingdom
| | - Rachel L Clifford
- Division of Respiratory Medicine, Nottingham Respiratory Research Unit, University of Nottingham, Clinical Sciences Building, City Hospital, Nottingham, NG5 1PB, United Kingdom
| | - Alan J Knox
- Division of Respiratory Medicine, Nottingham Respiratory Research Unit, University of Nottingham, Clinical Sciences Building, City Hospital, Nottingham, NG5 1PB, United Kingdom.
| |
Collapse
|
15
|
Clifford RL, Jones MJ, MacIsaac JL, McEwen LM, Goodman SJ, Mostafavi S, Kobor MS, Carlsten C. Inhalation of diesel exhaust and allergen alters human bronchial epithelium DNA methylation. J Allergy Clin Immunol 2016; 139:112-121. [PMID: 27321436 DOI: 10.1016/j.jaci.2016.03.046] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/15/2016] [Accepted: 03/22/2016] [Indexed: 01/24/2023]
Abstract
BACKGROUND Allergic disease affects 30% to 40% of the world's population, and its development is determined by the interplay between environmental and inherited factors. Air pollution, primarily consisting of diesel exhaust emissions, has increased at a similar rate to allergic disease. Exposure to diesel exhaust may play a role in the development and progression of allergic disease, in particular allergic respiratory disease. One potential mechanism underlying the connection between air pollution and increased allergic disease incidence is DNA methylation, an epigenetic process with the capacity to integrate gene-environment interactions. OBJECTIVE We sought to investigate the effect of allergen and diesel exhaust exposure on bronchial epithelial DNA methylation. METHODS We performed a randomized crossover-controlled exposure study to allergen and diesel exhaust in humans, and measured single-site (CpG) resolution global DNA methylation in bronchial epithelial cells. RESULTS Exposure to allergen alone, diesel exhaust alone, or allergen and diesel exhaust together (coexposure) led to significant changes in 7 CpG sites at 48 hours. However, when the same lung was exposed to allergen and diesel exhaust but separated by approximately 4 weeks, significant changes in more than 500 sites were observed. Furthermore, sites of differential methylation differed depending on which exposure was experienced first. Functional analysis of differentially methylated CpG sites found genes involved in transcription factor activity, protein metabolism, cell adhesion, and vascular development, among others. CONCLUSIONS These findings suggest that specific exposures can prime the lung for changes in DNA methylation induced by a subsequent insult.
Collapse
Affiliation(s)
- Rachel L Clifford
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Meaghan J Jones
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa M McEwen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah J Goodman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sara Mostafavi
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada; Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Canadian Institute for Advanced Research, Toronto, Ontario, Canada; Human Early Learning Partnership, School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chris Carlsten
- Air Pollution Exposure Laboratory, Chan-Yeung Centre for Occupational and Environmental Lung Disease, Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
16
|
Clifford RL, Patel JK, John AE, Tatler AL, Mazengarb L, Brightling CE, Knox AJ. CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: regulation by BET. Am J Physiol Lung Cell Mol Physiol 2015; 308:L962-72. [PMID: 25713319 PMCID: PMC4421784 DOI: 10.1152/ajplung.00021.2015] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 02/13/2015] [Indexed: 01/03/2023] Open
Abstract
Asthma is characterized by airway inflammation and remodeling and CXCL8 is a CXC chemokine that drives steroid-resistant neutrophilic airway inflammation. We have shown that airway smooth muscle (ASM) cells isolated from asthmatic individuals secrete more CXCL8 than cells from nonasthmatic individuals. Here we investigated chromatin modifications at the CXCL8 promoter in ASM cells from nonasthmatic and asthmatic donors to further understand how CXCL8 is dysregulated in asthma. ASM cells from asthmatic donors had increased histone H3 acetylation, specifically histone H3K18 acetylation, and increased binding of histone acetyltransferase p300 compared with nonasthmatic donors but no differences in CXCL8 DNA methylation. The acetylation reader proteins Brd3 and Brd4 were bound to the CXCL8 promoter and Brd inhibitors inhibited CXCL8 secretion from ASM cells by disrupting Brd4 and RNA polymerase II binding to the CXCL8 promoter. Our results show a novel dysregulation of CXCL8 transcriptional regulation in asthma characterized by a promoter complex that is abnormal in ASM cells isolated from asthmatic donors and can be modulated by Brd inhibitors. Brd inhibitors may provide a new therapeutic strategy for steroid-resistant inflammation.
Collapse
Affiliation(s)
- Rachel L Clifford
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| | - Jamie K Patel
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| | - Alison E John
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| | - Amanda L Tatler
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| | - Lisa Mazengarb
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| | - Christopher E Brightling
- Institute for Lung Health, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Alan J Knox
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| |
Collapse
|
17
|
Xia YC, Redhu NS, Moir LM, Koziol-White C, Ammit AJ, Al-Alwan L, Camoretti-Mercado B, Clifford RL. Pro-inflammatory and immunomodulatory functions of airway smooth muscle: Emerging concepts. Pulm Pharmacol Ther 2013; 26:64-74. [DOI: 10.1016/j.pupt.2012.05.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/08/2012] [Accepted: 05/09/2012] [Indexed: 12/22/2022]
|
18
|
Tatler AL, Saini G, Goodwin A, Gbolohan O, Clifford RL, Al’Hourani M, Porte J, Violette S, Weinreb P, Knox A, Laurent G, Wolters P, Gauldie J, Kolb M, Jenkins G. S69 Transcriptional Mechanisms Regulating Expression of the Avb6 Integrin in IPF. Thorax 2012. [DOI: 10.1136/thoraxjnl-2012-202678.075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
19
|
Abstract
Maintenance of airway tone, prevention of airway obstruction, and acute relief from bronchospasm are key targets of asthma therapy. This role is currently performed by β-agonists. However, chronic use of β-agonists to treat asthma is associated with desensitization of β-agonist signaling and a resultant loss of bronchodilator effect, worsening of airway hyperreactivity, and increased incidence of asthma-related morbidity and mortality. There have been several attempts to identify novel non-β-agonist bronchodilators including ATP-sensitive potassium channel (K(ATP)) agonists such as cromakalim and its active enantiomer BRL-38227 and the cGMP activators atrial natriuretic peptide (ANP) and BAY 41-22722. However, these either have not made it to clinical trial, required high doses, had little effect in patients, or had a high incidence of side effects. Recent data suggests that a novel bronchodilator target exists, the bitter taste receptor TAS2R. Two recent studies [An SS, Wang WC, Koziol-White CJ, Ahn K, Lee DY, Kurten RC, Panettieri RA Jr, Liggett SB. Am J Physiol Lung Cell Mol Physiol 303: L304-L311, 2012; Pulkkinen V, Manson ML, Säfholm J, Adner M, Dahlén SE. Am J Physiol Lung Cell Mol Physiol. doi:10.1152/ajplung.00205.2012.] provide new understanding of the signaling pathways utilized by TAS2Rs to mediate their bronchodilatory effects and how TAS2R-mediated bronchodilation is affected by β-agonist signaling desensitization. As our understanding of TAS2Rs and their agonists increases, they move closer to a viable therapeutic option; however, further definition is still required and questions remain to be answered. This editorial focus discusses these studies within the context of existing literature and raises questions and challenges for the future development of bitter (better?) therapies for asthma.
Collapse
|
20
|
Clifford RL, Singer CA, John AE. Epigenetics and miRNA emerge as key regulators of smooth muscle cell phenotype and function. Pulm Pharmacol Ther 2012; 26:75-85. [PMID: 22800879 DOI: 10.1016/j.pupt.2012.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 07/02/2012] [Accepted: 07/04/2012] [Indexed: 10/28/2022]
Abstract
Regulation of phenotypic plasticity in smooth muscle requires an understanding of the mechanisms regulating phenotype-specific genes and the processes dysregulated during pathogenesis. Decades of study in airway smooth muscle has provided extensive knowledge of the gene expression patterns and signaling pathways necessary to maintain and alter smooth muscle cell phenotype. With this solid foundation, the importance and complexity of inheritable epigenetic modifications and mechanisms silencing gene expression have now emerged as fundamental components regulating aspects of inflammation, proliferation and remodeling.
Collapse
Affiliation(s)
- Rachel L Clifford
- University of Nottingham, Division of Respiratory Medicine and Nottingham Respiratory Research Unit, Clinical Sciences Building, City Hospital, Hucknall Road, Nottingham NG5 1PB, England, UK.
| | | | | |
Collapse
|
21
|
Clifford RL, John AE, Brightling CE, Knox AJ. Abnormal histone methylation is responsible for increased vascular endothelial growth factor 165a secretion from airway smooth muscle cells in asthma. J Immunol 2012; 189:819-31. [PMID: 22689881 DOI: 10.4049/jimmunol.1103641] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Vascular endothelial growth factor (VEGF), a key angiogenic molecule, is aberrantly expressed in several diseases including asthma where it contributes to bronchial vascular remodeling and chronic inflammation. Asthmatic human airway smooth muscle cells hypersecrete VEGF, but the mechanism is unclear. In this study, we defined the mechanism in human airway smooth muscle cells from nonasthmatic and asthmatic patients. We found that asthmatic cells lacked a repression complex at the VEGF promoter, which was present in nonasthmatic cells. Recruitment of G9A, trimethylation of histone H3 at lysine 9 (H3K9me3), and a resultant decrease in RNA polymerase II at the VEGF promoter was critical to repression of VEGF secretion in nonasthmatic cells. At the asthmatic promoter, H3K9me3 was absent because of failed recruitment of G9a; RNA polymerase II binding, in association with TATA-binding protein-associated factor 1, was increased; H3K4me3 was present; and Sp1 binding was exaggerated and sustained. In contrast, DNA methylation and histone acetylation were similar in asthmatic and nonasthmatic cells. This is the first study, to our knowledge, to show that airway cells in asthma have altered epigenetic regulation of remodeling gene(s). Histone methylation at genes such as VEGF may be an important new therapeutic target.
Collapse
|
22
|
Clifford RL, Coward WR, Knox AJ, John AE. Transcriptional regulation of inflammatory genes associated with severe asthma. Curr Pharm Des 2012; 17:653-66. [PMID: 21406061 DOI: 10.2174/138161211795429000] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 02/24/2011] [Indexed: 11/22/2022]
Abstract
The 10% of patients with the most severe asthma are responsible for a large part of healthcare expenditure and morbidity. Understanding the processes involved is key if new therapeutic approaches are to be developed. Evidence is accumulating that chronic diseases such as asthma are associated with temporal and spatial alterations in the pattern of inflammatory gene expression within the airways. Expression of these genes can be regulated by transcriptional, posttranscriptional, translational and epigenetic mechanisms. It is well established that binding of activated transcription factors to specific inducible gene promoter sites is tightly controlled by chromatin state as a result of histone modifications, particularly the balance between histone acetylation and deacetylation [1]. The interaction between transcription factors and the promoter is key to the diversification of gene expression in a time dependent manner leading to altered gene expression profiles. Alterations of the accessibility of transcription factors to the DNA can have residing effects upon gene transcription. This review will focus on the regulation of several groups of key genes which are involved in chronic airway inflammation and remodelling in asthma drawing mainly from our experience of studying these processes in airway smooth muscle cells. An overview is shown in figure 1.
Collapse
Affiliation(s)
- Rachel L Clifford
- Division of Respiratory Medicine and Nottingham Biomedical Research Unit, City hospital, England, UK
| | | | | | | |
Collapse
|
23
|
Patel JK, Clifford RL, Deacon K, Knox AJ. Ciclesonide inhibits TNFα- and IL-1β-induced monocyte chemotactic protein-1 (MCP-1/CCL2) secretion from human airway smooth muscle cells. Am J Physiol Lung Cell Mol Physiol 2012; 302:L785-92. [PMID: 22246000 PMCID: PMC3331580 DOI: 10.1152/ajplung.00257.2011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Monocyte chemotactic protein-1 (MCP-1) is a member of the CC family of cytokines. It has monocyte and lymphocyte chemotactic activity and stimulates histamine release from basophils. MCP-1 is implicated in the pathogenesis of inflammatory diseases, including asthma. The airway smooth muscle (ASM) layer is thickened in asthma, and the growth factors and cytokines secreted by ASM cells play a role in the inflammatory response of the bronchial wall. Glucocorticoids and β2-agonists are first-line drug treatments for asthma. Little is known about the effect of asthma treatments on MCP-1 production from human ASM cells. Here, we determined the effect of ciclesonide (a glucocorticoid) and formoterol (a β2-agonist) on MCP-1 production from human ASM cells. TNFα and IL-1β induced MCP-1 secretion from human ASM cells. Formoterol had no effect on MCP-1 expression, while ciclesonide significantly inhibited IL-1β- and TNFα-induced MCP-1. Furthermore, ciclesonide inhibited IL-1β- and TNFα-induced MCP-1 mRNA and IL-1β- and TNFα-induced MCP-1 promoter and enhancer luciferase reporters. Western blots showed that ciclesonide had no effect on IκB degradation. Finally, ciclesonide inhibited an NF-κB luciferase reporter. Our data show that ciclesonide inhibits IL-1β- and TNFα-induced MCP-1 production from human ASM cells via a transcriptional mechanism involving inhibition of NF-κB binding.
Collapse
Affiliation(s)
- Jamie K Patel
- Division of Respiratory Medicine, Nottingham Respiratory Biomedical Research Unit, University of Nottingham, United Kingdom
| | | | | | | |
Collapse
|
24
|
Clarke DL, Clifford RL, Jindarat S, Proud D, Pang L, Belvisi M, Knox AJ. TNFα and IFNγ synergistically enhance transcriptional activation of CXCL10 in human airway smooth muscle cells via STAT-1, NF-κB, and the transcriptional coactivator CREB-binding protein. J Biol Chem 2010; 285:29101-10. [PMID: 20833730 DOI: 10.1074/jbc.m109.0999952] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Asthmatic airway smooth muscle (ASM) expresses interferon-γ-inducible protein-10 (CXCL10), a chemokine known to mediate mast cell migration into ASM bundles that has been reported in the airways of asthmatic patients. CXCL10 is elevated in patients suffering from viral exacerbations of asthma and in patients with chronic obstructive pulmonary disease (COPD), diseases in which corticosteroids are largely ineffective. IFNγ and TNFα synergistically induce CXCL10 release from human ASM cells in a steroid-insensitive manner, via an as yet undefined mechanism. We report that TNFα activates the classical NF-κB (nuclear factor κB) pathway, whereas IFNγ activates JAK2/STAT-1α and that inhibition of the JAK/STAT pathway is more effective in abrogating CXCL10 release than the steroid fluticasone. The synergy observed with TNFα and IFNγ together, however, did not lie at the level of NF-κB activation, STAT-1α phosphorylation, or in vivo binding of these transcription factors to the CXCL10 promoter. Stimulation of human ASM cells with TNFα and IFNγ induced histone H4 but not histone H3 acetylation at the CXCL10 promoter, although no synergism was observed when both cytokines were combined. We show, however, that TNFα and IFNγ exert a synergistic effect on the recruitment of CREB-binding protein (CBP) to the CXCL10, which is accompanied by increased RNA polymerase II. Our results provide evidence that synergism between TNFα and IFNγ lies at the level of coactivator recruitment in human ASM and suggest that inhibition of JAK/STAT signaling may be of therapeutic benefit in steroid-resistant airway disease.
Collapse
Affiliation(s)
- Deborah L Clarke
- Nottingham Respiratory Biomedical Research Unit, City Hospital, University of Nottingham, Nottingham NG5 1PB, United Kingdom.
| | | | | | | | | | | | | |
Collapse
|
25
|
Clarke DL, Clifford RL, Jindarat S, Proud D, Pang L, Belvisi M, Knox AJ. TNFα and IFNγ Synergistically Enhance Transcriptional Activation of CXCL10 in Human Airway Smooth Muscle Cells via STAT-1, NF-κB, and the Transcriptional Coactivator CREB-binding Protein. J Biol Chem 2010. [DOI: 10.1074/jbc.m109.099952] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
26
|
Abstract
Increased airway smooth muscle (ASM) mass plays a critical role in chronic asthmatic airway remodelling. ASM cell hypertrophy and hyperplasia are likely to contribute to increased ASM mass and a variety of mitogens induce ASM proliferation in cell culture. Recent recognition of widespread vitamin D deficiency and identification of the vitamin D receptor on many cells has implicated vitamin D as a potential therapeutic target for many disorders including cancer, infection and asthma. In this issue of British Journal of Pharmacology, Damera et al. show that calcitriol, a secosteroidal modulator of vitamin D receptors, inhibited thrombin and platelet-derived growth factor-induced ASM cell proliferation. They also, perhaps surprisingly, show the glucocorticoid dexamethasone to potentiate mitogen-induced ASM proliferation. Their results begin to elucidate the molecular mechanism(s) utilized by calcitriol to inhibit cell proliferation and suggest hyperphosphorylation of retinoblastoma protein and activation of checkpoint kinase 1 (Chk1) as critical to this process. This study identifies inhibition of ASM proliferation as a cellular effect of vitamin D and supports the hypothesis that vitamin D is a potential treatment for airway remodelling in asthma.
Collapse
|
27
|
Clifford RL, Deacon K, Knox AJ. Novel regulation of vascular endothelial growth factor-A (VEGF-A) by transforming growth factor (beta)1: requirement for Smads, (beta)-CATENIN, AND GSK3(beta). J Biol Chem 2008; 283:35337-53. [PMID: 18952601 DOI: 10.1074/jbc.m803342200] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vascular endothelial growth factor (VEGF) is a vital angiogenic effector, regulating key angiogenic processes. Vascular development relies on numerous signaling pathways, of which those induced by transforming growth factor-beta (TGFbeta) are critical. The Wnt/beta-catenin signaling pathway is emerging as necessary for vascular development. Although VEGF, TGFbeta, and Wnt signal transductions are well studied individually, it has not been demonstrated previously that all three can interact or be dependent on each other. We show that regulation of VEGF by TGFbeta(1), in human pulmonary artery smooth muscle cells (PASMCs), depends on a direct interaction between TGFbeta signaling proteins, Smads, and members of the Wnt/beta-catenin signaling family. VEGF promoter reporter constructs identified a region of the VEGF promoter containing two T cell factor (TCF)-binding sites as necessary for TGFbeta(1)-induced VEGF transcription. Mutation of TCF sites and expression of dominant negative TCF4 abolished TGFbeta(1)-induced VEGF promoter activity. Studies in Smad2 and Smad3 knock-out mouse embryonic fibroblasts demonstrated that one or both are required for VEGF regulation by TGFbeta(1), with transfection of dominant negative Smad2 or Smad3 into PASMCs confirming this. Chromatin immunoprecipitation assays showed in cell interactions of Smad2 and Smad3 with TCF4 and beta-catenin at the VEGF promoter, whereas co-immunoprecipitation showed a direct physical interaction between Smad2 and beta-catenin in the nucleus of PASMCs. Finally, we demonstrate that TGFbeta(1) regulates TCF by modifying beta-catenin phosphorylation via regulation of glycogen synthase kinase 3beta. These results provide new insight into the molecular regulation of VEGF by two interacting pathways necessary for vascular development, maintenance, and disease.
Collapse
Affiliation(s)
- Rachel L Clifford
- Centre for Respiratory Research, Clinical Sciences Building, University of Nottingham, Nottingham NG5 1PB, United Kingdom
| | | | | |
Collapse
|