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Yeung-Luk BH, Wally A, Swaby C, Jauregui S, Lee E, Zhang R, Chen D, Luk SH, Upadya N, Tieng E, Wilmsen K, Sherman E, Sudhakar D, Luk M, Shrivastav AK, Cao S, Ghosh B, Christenson SA, Huang YJ, Ortega VE, Biswal S, Tang WY, Sidhaye VK. Epigenetic Reprogramming Drives Epithelial Disruption in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2024; 70:165-177. [PMID: 37976469 PMCID: PMC10914773 DOI: 10.1165/rcmb.2023-0147oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/17/2023] [Indexed: 11/19/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) remains a major public health challenge that contributes greatly to mortality and morbidity worldwide. Although it has long been recognized that the epithelium is altered in COPD, there has been little focus on targeting it to modify the disease course. Therefore, mechanisms that disrupt epithelial cell function in patients with COPD are poorly understood. In this study, we sought to determine whether epigenetic reprogramming of the cell-cell adhesion molecule E-cadherin, encoded by the CDH1 gene, disrupts epithelial integrity. By reducing these epigenetic marks, we can restore epithelial integrity and rescue alveolar airspace destruction. We used differentiated normal and COPD-derived primary human airway epithelial cells, genetically manipulated mouse tracheal epithelial cells, and mouse and human precision-cut lung slices to assess the effects of epigenetic reprogramming. We show that the loss of CDH1 in COPD is due to increased DNA methylation site at the CDH1 enhancer D through the downregulation of the ten-eleven translocase methylcytosine dioxygenase (TET) enzyme TET1. Increased DNA methylation at the enhancer D region decreases the enrichment of RNA polymerase II binding. Remarkably, treatment of human precision-cut slices derived from patients with COPD with the DNA demethylation agent 5-aza-2'-deoxycytidine decreased cell damage and reduced air space enlargement in the diseased tissue. Here, we present a novel mechanism that targets epigenetic modifications to reverse the tissue remodeling in human COPD lungs and serves as a proof of concept for developing a disease-modifying target.
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Affiliation(s)
| | - Ara Wally
- Department of Environmental Health and Engineering and
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Carter Swaby
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Sofia Jauregui
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Esther Lee
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Rachel Zhang
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Daniel Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Sean H. Luk
- Department of Environmental Health and Engineering and
| | - Nisha Upadya
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Ethan Tieng
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Kai Wilmsen
- Department of Environmental Health and Engineering and
| | - Ethan Sherman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Dheeksha Sudhakar
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Matthew Luk
- Department of Environmental Health and Engineering and
| | - Abhishek Kumar Shrivastav
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | - Shuo Cao
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | | | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | - Yvonne J. Huang
- Department of Medicine, University of Michigan, Ann Arbor, Michigan; and
| | | | - Shyam Biswal
- Department of Environmental Health and Engineering and
| | - Wan-yee Tang
- Department of Environmental Health and Engineering and
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Venkataramana K. Sidhaye
- Department of Environmental Health and Engineering and
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
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Yang C, Deng L, Bao F, Jiang H, Zhang L. Sevoflurane with Low Concentration Decrease DNA Methylation on Chronic Obstructive Pulmonary Disease (COPD)-Related Gene Promoter in COPD Rat. COPD 2023; 20:348-356. [PMID: 38010369 DOI: 10.1080/15412555.2023.2278282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/28/2023] [Indexed: 11/29/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a difficult-to-cure disease that mainly affects the respiratory system. Inhaled anesthetic drug such as sevoflurane plays a controversial role in COPD by different concentration, but the underlying epigenetic mechanism remains unclear. Here, we prepared lipopolysaccharide (LPS)-induced COPD rat model, and isolated Alveolar type II (ATII) cells. We mainly focused DNA methylation on the promoter of COPD-related genes including Sftpa1, Napsa, Ca2, Sfta2, Lamp3, Wif1, Pgc, and Etv5. We observed COPD rat treated by sevoflurane with low (0.5%) and high (2%) concentrations displayed an opposite DNA methylation pattern. These six genes' promoter were all hypomethylated by 0.5% sevoflurane whereas hypermethylated by 2% sevoflurane, accompanied with the opposite transcriptional activity. We further verified that the DNMT1 binding ability contributed to DNA methylation these six genes' promoter. Moreover, we also captured DNMT1 and identified REC8 meiotic recombination protein (REC8) as the specific binding protein only existed in ATII cells treated with 0.5% sevoflurane rather than 2% and control. The binding ability of REC8 on these target genes' promoter showed highly positive correlation with DNMT1. In summary, we uncovered a potential epigenetic role of sevoflurane with low concentration in ATII cells of COPD that may help us deeply understand the pathogenesis and treatment mechanism of inhaled anesthesia drugs in COPD via a dose-dependent manner.
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Affiliation(s)
- Chuanxin Yang
- Department of Anesthesiology, Qingpu Branch of Zhongshan, Fudan University, Shanghai, China
| | - Libing Deng
- Department of Anesthesiology, Qingpu Branch of Zhongshan, Fudan University, Shanghai, China
| | - Fang Bao
- Department of Anesthesiology, Qingpu Branch of Zhongshan, Fudan University, Shanghai, China
| | - Hui Jiang
- Department of Anesthesiology, Qingpu Branch of Zhongshan, Fudan University, Shanghai, China
| | - Long Zhang
- Department of Anesthesiology, Qingpu Branch of Zhongshan, Fudan University, Shanghai, China
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3
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Cai X, Yang R, Shi W, Cai Y, Ma Z. Exploration of the common pathogenic link between COVID-19 and diabetic foot ulcers: An in silico approach. Health Sci Rep 2023; 6:e1686. [PMID: 37936615 PMCID: PMC10626003 DOI: 10.1002/hsr2.1686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/09/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Background and Aims The Coronavirus Disease-19 (COVID-19) is posing an ongoing threat to human health. Patients of diabetic foot ulcer (DFU) are susceptible to COVID-19-induced adverse outcomes. Nevertheless, investigations into their mutual molecular mechanisms have been limited to date. In the present work, we tried to uncover the shared pathogenesis and regulatory gene targets of COVID-19 and DFU. Methods In this study, we chose GSE161281 as the COVID-19 data set, which contained severe acute respiratory syndrome coronavirus 2 infected human induced embryonic stem cell-derived peripheral neurons (n = 2) with uninfected controls (n = 2). The GSE134431 designated as the DFU data set, comprising full-thickness DFU (n = 13) and diabetic foot skin (n = 8) samples from diabetic patients. The differential expressed genes (DEGs) were identified from GSE161281 and GSE134431, and the common DEGs between COVID-19 and DFU were extracted. Multifactor regulatory network and co-expression network of the common DEGs were analyzed, along with candidate drug prediction. Results Altogether, six common DEGs (dickkopf-related protein 1 [DKK1], serine proteinase inhibitor A3 [SERPINA3], ras homolog family member D [RHOD], myelin protein zero like 3 [MPZL3], Claudin-11 [CLDN11], and epidermal growth factor receptor pathway substrate 8-like 1 [EPS8L1]) were found between COVID-19 and DFU. Functional analyses indicated that pathways of apoptotic and Wnt signaling may contribute to progression of COVID-19. Gene co-expression network implied the shared pathways of immune regulation and cytokine response participated collectively in the development of DFU and COVID-19. A multifactor regulatory network was constructed integrating the corresponding microRNAs (miRNAs) and transcription factors. Additionally, we proposed potential drug objects for the combined therapy. Conclusion Our study revealed the shared molecular mechanisms underlying COVID-19 and DFU. The identified pivotal targets and common pathways can provide new perspectives for further research and assist the development of management strategies in patients of DFU complicated with COVID-19.
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Affiliation(s)
- Xueyao Cai
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
| | - Ruijin Yang
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
| | - Wenjun Shi
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuchen Cai
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zhengzheng Ma
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
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Chen Q, Nwozor KO, van den Berge M, Slebos DJ, Faiz A, Jonker MR, Boezen HM, Heijink IH, de Vries M. From Differential DNA Methylation in COPD to Mitochondria: Regulation of AHRR Expression Affects Airway Epithelial Response to Cigarette Smoke. Cells 2022; 11:3423. [PMID: 36359818 PMCID: PMC9656229 DOI: 10.3390/cells11213423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 08/01/2023] Open
Abstract
Cigarette smoking causes hypomethylation of the gene Aryl Hydrocarbon Receptor Repressor (AHRR), which regulates detoxification and oxidative stress-responses. We investigated whether AHRR DNA methylation is related to chronic obstructive pulmonary disease (COPD) and studied its function in airway epithelial cells (AECs). The association with COPD was assessed in blood from never and current smokers with/without COPD, and in AECs from ex-smoking non-COPD controls and GOLD stage II-IV COPD patients cultured with/without cigarette smoke extract (CSE). The effect of CRISPR/Cas9-induced AHRR knockout on proliferation, CSE-induced mitochondrial membrane potential and apoptosis/necrosis in human bronchial epithelial 16HBE cells was studied. In blood, DNA methylation of AHRR at cg05575921 and cg21161138 was lower in smoking COPD subjects than smoking controls. In vitro, AHRR DNA methylation at these CpG-sites was lower in COPD-derived than control-derived AECs only upon CSE exposure. Upon AHRR knockout, we found a lower proliferation rate at baseline, stronger CSE-induced decrease in mitochondrial membrane potential, and higher CSE-induced late apoptosis/necroptosis. Together, our results show lower DNA methylation of AHRR upon smoking in COPD patients compared to non-COPD controls. Our data suggest that higher airway epithelial AHRR expression may lead to impaired cigarette smoke-induced mitochondrial dysfunction and apoptosis/necroptosis, potentially promoting unprogrammed/immunogenic cell death.
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Affiliation(s)
- Qing Chen
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, 9713 GZ Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands
| | - Kingsley Okechukwu Nwozor
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, 9713 GZ Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands
- Centre for Heart Lung Innovation, Department of Anesthesiology, Pharmacology & Therapeutics, The University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonology Disease, 9713 GZ Groningen, The Netherlands
| | - Dirk-Jan Slebos
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonology Disease, 9713 GZ Groningen, The Netherlands
| | - Alen Faiz
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonology Disease, 9713 GZ Groningen, The Netherlands
- Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Marnix R. Jonker
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, 9713 GZ Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands
| | - H. Marike Boezen
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, 9713 GZ Groningen, The Netherlands
| | - Irene H. Heijink
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, 9713 GZ Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonology Disease, 9713 GZ Groningen, The Netherlands
| | - Maaike de Vries
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, 9713 GZ Groningen, The Netherlands
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Alfahad AJ, Alzaydi MM, Aldossary AM, Alshehri AA, Almughem FA, Zaidan NM, Tawfik EA. Current views in chronic obstructive pulmonary disease pathogenesis and management. Saudi Pharm J 2022; 29:1361-1373. [PMID: 35002373 PMCID: PMC8720819 DOI: 10.1016/j.jsps.2021.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/22/2021] [Indexed: 01/11/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a progressive lung dysfunction caused mainly by inhaling toxic particles and cigarette smoking (CS). The continuous exposure to ruinous molecules can lead to abnormal inflammatory responses, permanent damages to the respiratory system, and irreversible pathological changes. Other factors, such as genetics and aging, influence the development of COPD. In the last decade, accumulating evidence suggested that mitochondrial alteration, including mitochondrial DNA damage, increased mitochondrial reactive oxygen species (ROS), abnormal autophagy, and apoptosis, have been implicated in the pathogenesis of COPD. The alteration can also extend to epigenetics, namely DNA methylation, histone modification, and non-coding RNA. This review will discuss the recent progressions in COPD pathology, pathophysiology, and molecular pathways. More focus will be shed on mitochondrial and epigenetic variations related to COPD development and the role of nanomedicine as a potential tool for the prevention and treatment of this disease.
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Affiliation(s)
- Ahmed J Alfahad
- National Center of Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Mai M Alzaydi
- National Center of Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Ahmad M Aldossary
- National Center of Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Abdullah A Alshehri
- National Center of Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Fahad A Almughem
- National Center of Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Nada M Zaidan
- Center of Excellence in Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Essam A Tawfik
- National Center of Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia.,Center of Excellence in Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
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6
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de Vries M, Nedeljkovic I, van der Plaat DA, Zhernakova A, Lahousse L, Brusselle GG, Amin N, van Duijn CM, Vonk JM, Boezen HM. DNA methylation is associated with lung function in never smokers. Respir Res 2019; 20:268. [PMID: 31791327 PMCID: PMC6889726 DOI: 10.1186/s12931-019-1222-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/22/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Active smoking is the main risk factor for COPD. Here, epigenetic mechanisms may play a role, since cigarette smoking is associated with differential DNA methylation in whole blood. So far, it is unclear whether epigenetics also play a role in subjects with COPD who never smoked. Therefore, we aimed to identify differential DNA methylation associated with lung function in never smokers. METHODS We determined epigenome-wide DNA methylation levels of 396,243 CpG-sites (Illumina 450 K) in blood of never smokers in four independent cohorts, LifeLines COPD&C (N = 903), LifeLines DEEP (N = 166), Rotterdam Study (RS)-III (N = 150) and RS-BIOS (N = 206). We meta-analyzed the cohort-specific methylation results to identify differentially methylated CpG-sites with FEV1/FVC. Expression Quantitative Trait Methylation (eQTM) analysis was performed in the Biobank-based Integrative Omics Studies (BIOS). RESULTS A total of 36 CpG-sites were associated with FEV1/FVC in never smokers at p-value< 0.0001, but the meta-analysis did not reveal any epigenome-wide significant CpG-sites. Of interest, 35 of these 36 CpG-sites have not been associated with lung function before in studies including subjects irrespective of smoking history. Among the top hits were cg10012512, cg02885771, annotated to the gene LTV1 Ribosome Biogenesis factor (LTV1), and cg25105536, annotated to Kelch Like Family Member 32 (KLHL32). Moreover, a total of 11 eQTMS were identified. CONCLUSIONS With the identification of 35 CpG-sites that are unique for never smokers, our study shows that DNA methylation is also associated with FEV1/FVC in subjects that never smoked and therefore not merely related to smoking.
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Affiliation(s)
- Maaike de Vries
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands. .,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.
| | - Ivana Nedeljkovic
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Diana A van der Plaat
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Bioanalysis, FFW, Ghent University, Ghent, Belgium
| | - Guy G Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.,Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
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Kaur G, Begum R, Thota S, Batra S. A systematic review of smoking-related epigenetic alterations. Arch Toxicol 2019; 93:2715-2740. [PMID: 31555878 DOI: 10.1007/s00204-019-02562-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023]
Abstract
The aim of this study is to provide a systematic review of the known epigenetic alterations caused by cigarette smoke; establish an evidence-based perspective of their clinical value for screening, diagnosis, and treatment of smoke-related disorders; and discuss the challenges and ethical concerns associated with epigenetic studies. A well-defined, reproducible search strategy was employed to identify relevant literature (clinical, cellular, and animal-based) between 2000 and 2019 based on AMSTAR guidelines. A total of 80 studies were identified that reported alterations in DNA methylation, histone modifications, and miRNA expression following exposure to cigarette smoke. Changes in DNA methylation were most extensively documented for genes including AHRR, F2RL3, DAPK, and p16 after exposure to cigarette smoke. Likewise, miR16, miR21, miR146, and miR222 were identified to be differentially expressed in smokers and exhibit potential as biomarkers for determining susceptibility to COPD. We also identified 22 studies highlighting the transgenerational effects of maternal and paternal smoking on offspring. This systematic review lists the epigenetic events/alterations known to occur in response to cigarette smoke exposure and identifies the major genes and miRNAs that are potential targets for translational research in associated pathologies. Importantly, the limitations and ethical concerns related to epigenetic studies are also highlighted, as are the effects on the ability to address specific questions associated with exposure to tobacco/cigarette smoke. In the future, improved interpretation of epigenetic signatures will lead to their increased use as biomarkers and/or in drug development.
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Affiliation(s)
- Gagandeep Kaur
- Laboratory of Pulmonary Immuno-toxicology, Department of Environmental Toxicology, 129 Health Research Centre, Southern University and A&M College, Baton Rouge, LA, 70813, USA
| | - Rizwana Begum
- Laboratory of Pulmonary Immuno-toxicology, Department of Environmental Toxicology, 129 Health Research Centre, Southern University and A&M College, Baton Rouge, LA, 70813, USA
| | - Shilpa Thota
- Laboratory of Pulmonary Immuno-toxicology, Department of Environmental Toxicology, 129 Health Research Centre, Southern University and A&M College, Baton Rouge, LA, 70813, USA
| | - Sanjay Batra
- Laboratory of Pulmonary Immuno-toxicology, Department of Environmental Toxicology, 129 Health Research Centre, Southern University and A&M College, Baton Rouge, LA, 70813, USA.
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8
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Lahousse L. Epigenetic targets for lung diseases. EBioMedicine 2019; 43:24-25. [PMID: 30981649 PMCID: PMC6557802 DOI: 10.1016/j.ebiom.2019.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 04/05/2019] [Indexed: 02/06/2023] Open
Affiliation(s)
- Lies Lahousse
- Department of Bioanalysis, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
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9
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Bermingham ML, Walker RM, Marioni RE, Morris SW, Rawlik K, Zeng Y, Campbell A, Redmond P, Whalley HC, Adams MJ, Hayward C, Deary IJ, Porteous DJ, McIntosh AM, Evans KL. Identification of novel differentially methylated sites with potential as clinical predictors of impaired respiratory function and COPD. EBioMedicine 2019; 43:576-586. [PMID: 30935889 PMCID: PMC6557748 DOI: 10.1016/j.ebiom.2019.03.072] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 12/22/2022] Open
Abstract
Background The causes of poor respiratory function and COPD are incompletely understood, but it is clear that genes and the environment play a role. As DNA methylation is under both genetic and environmental control, we hypothesised that investigation of differential methylation associated with these phenotypes would permit mechanistic insights, and improve prediction of COPD. We investigated genome-wide differential DNA methylation patterns using the recently released 850 K Illumina EPIC array. This is the largest single population, whole-genome epigenetic study to date. Methods Epigenome-wide association studies (EWASs) of respiratory function and COPD were performed in peripheral blood samples from the Generation Scotland: Scottish Family Health Study (GS:SFHS) cohort (n = 3781; 274 COPD cases and 2919 controls). In independent COPD incidence data (n = 149), significantly differentially methylated sites (DMSs; p < 3.6 × 10−8) were evaluated for their added predictive power when added to a model including clinical variables, age, sex, height and smoking history using receiver operating characteristic analysis. The Lothian Birth Cohort 1936 (LBC1936) was used to replicate association (n = 895) and prediction (n = 178) results. Findings We identified 28 respiratory function and/or COPD associated DMSs, which mapped to genes involved in alternative splicing, JAK-STAT signalling, and axon guidance. In prediction analyses, we observed significant improvement in discrimination between COPD cases and controls (p < .05) in independent GS:SFHS (p = .016) and LBC1936 (p = .010) datasets by adding DMSs to a clinical model. Interpretation Identification of novel DMSs has provided insight into the molecular mechanisms regulating respiratory function and aided prediction of COPD risk. Further studies are needed to assess the causality and clinical utility of identified associations. Fund Wellcome Trust Strategic Award 10436/Z/14/Z.
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Affiliation(s)
- Mairead L Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, UK
| | - Yanni Zeng
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Heather C Whalley
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK; Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK; Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
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