1
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Legaki E, Taka S, Papadopoulos NG. The complexity in DNA methylation analysis of allergic diseases. Curr Opin Allergy Clin Immunol 2023; 23:172-178. [PMID: 36752374 DOI: 10.1097/aci.0000000000000895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
PURPOSE OF REVIEW This review aims to report all the recent studies that are implicated in DNA methylation analysis in the field of allergy and to underline the complexity of the study methodologies and results. RECENT FINDINGS Although the growing number of DNA methylation studies have yet to point to a specific mechanism, herein we provide an overview of the majority of pathways considered to be implicated and highlight particular genes, like KNH2 , ATPAF2 and ZNF385A , for their potential as biomarkers. SUMMARY The epigenetic profile of respiratory allergic diseases, and particularly DNA methylation, has been investigated in various populations, so as to gain a better understanding of its role in pathogenesis. Through our analysis, multiple links are presented between differential DNA methylation loci and IgE sensitization, lung functionality and severity of the disease. Additionally, associations of this epigenetic change with maternal asthma, age, sex and environmental factors are described, thus uncovering specific gene families that, after further examination could be used as methylation biomarkers in cases of allergic disease.
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Affiliation(s)
- Evangelia Legaki
- Allergy and Clinical Immunology Unit, Second Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
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2
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Song N, Dong Q, Chen C, Li Q, Mulder H, Plyler E, Easton J, Walker E, Olson S, Neale G, Krull KR, Srivastava DK, Ness KK, Zhang J, Hudson MM, Robison LL, Huang I, Wang Z. Social-epigenetic mediators for racial disparities in pulmonary impairment among childhood cancer survivors. Cancer Commun (Lond) 2022; 43:290-293. [PMID: 36256508 PMCID: PMC9926953 DOI: 10.1002/cac2.12371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/24/2022] [Accepted: 10/08/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Nan Song
- Department of Epidemiology and Cancer ControlSt. Jude Children's Research HospitalMemphisTN38105USA,College of PharmacyChungbuk National UniversityCheongjuChungbuk28160South Korea
| | - Qian Dong
- Department of Epidemiology and Cancer ControlSt. Jude Children's Research HospitalMemphisTN38105USA
| | - Cheng Chen
- Department of Epidemiology and Cancer ControlSt. Jude Children's Research HospitalMemphisTN38105USA,School of Public HealthShanghai Jiaotong UniversityShanghai200025P. R. China
| | - Qian Li
- Department of BiostatisticsSt. Jude Children's Research HospitalMemphisTN38105USA
| | - Heather Mulder
- Department of Computational BiologySt. Jude Children's Research HospitalMemphisTN38105USA
| | - Emily Plyler
- Department of Computational BiologySt. Jude Children's Research HospitalMemphisTN38105USA
| | - John Easton
- Department of Computational BiologySt. Jude Children's Research HospitalMemphisTN38105USA
| | - Emily Walker
- Hartwell CenterSt. Jude Children's Research HospitalMemphisTN38105USA
| | - Scott Olson
- Hartwell CenterSt. Jude Children's Research HospitalMemphisTN38105USA
| | - Geoffrey Neale
- Hartwell CenterSt. Jude Children's Research HospitalMemphisTN38105USA
| | - Kevin R. Krull
- Department of Epidemiology and Cancer ControlSt. Jude Children's Research HospitalMemphisTN38105USA
| | - Deo Kumar Srivastava
- Department of BiostatisticsSt. Jude Children's Research HospitalMemphisTN38105USA
| | - Kirsten K. Ness
- Department of Epidemiology and Cancer ControlSt. Jude Children's Research HospitalMemphisTN38105USA
| | - Jinghui Zhang
- Department of Computational BiologySt. Jude Children's Research HospitalMemphisTN38105USA
| | - Melissa M. Hudson
- Department of Epidemiology and Cancer ControlSt. Jude Children's Research HospitalMemphisTN38105USA,Department of OncologySt. Jude Children's Research HospitalMemphisTN38105USA
| | - Leslie L. Robison
- Department of Epidemiology and Cancer ControlSt. Jude Children's Research HospitalMemphisTN38105USA
| | - I‐Chan Huang
- Department of Epidemiology and Cancer ControlSt. Jude Children's Research HospitalMemphisTN38105USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer ControlSt. Jude Children's Research HospitalMemphisTN38105USA,Department of BiostatisticsSt. Jude Children's Research HospitalMemphisTN38105USA
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3
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Lee M, Huan T, McCartney DL, Chittoor G, de Vries M, Lahousse L, Nguyen JN, Brody JA, Castillo-Fernandez J, Terzikhan N, Qi C, Joehanes R, Min JL, Smilnak GJ, Shaw JR, Yang CX, Colicino E, Hoang TT, Bermingham ML, Xu H, Justice AE, Xu CJ, Rich SS, Cox SR, Vonk JM, Prokić I, Sotoodehnia N, Tsai PC, Schwartz JD, Leung JM, Sikdar S, Walker RM, Harris SE, van der Plaat DA, Van Den Berg DJ, Bartz TM, Spector TD, Vokonas PS, Marioni RE, Taylor AM, Liu Y, Barr RG, Lange LA, Baccarelli AA, Obeidat M, Fornage M, Wang T, Ward JM, Motsinger-Reif AA, Hemani G, Koppelman GH, Bell JT, Gharib SA, Brusselle G, Boezen HM, North KE, Levy D, Evans KL, Dupuis J, Breeze CE, Manichaikul A, London SJ. Pulmonary Function and Blood DNA Methylation: A Multiancestry Epigenome-Wide Association Meta-analysis. Am J Respir Crit Care Med 2022; 206:321-336. [PMID: 35536696 PMCID: PMC9890261 DOI: 10.1164/rccm.202108-1907oc] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Rationale: Methylation integrates factors present at birth and modifiable across the lifespan that can influence pulmonary function. Studies are limited in scope and replication. Objectives: To conduct large-scale epigenome-wide meta-analyses of blood DNA methylation and pulmonary function. Methods: Twelve cohorts analyzed associations of methylation at cytosine-phosphate-guanine probes (CpGs), using Illumina 450K or EPIC/850K arrays, with FEV1, FVC, and FEV1/FVC. We performed multiancestry epigenome-wide meta-analyses (total of 17,503 individuals; 14,761 European, 2,549 African, and 193 Hispanic/Latino ancestries) and interpreted results using integrative epigenomics. Measurements and Main Results: We identified 1,267 CpGs (1,042 genes) differentially methylated (false discovery rate, <0.025) in relation to FEV1, FVC, or FEV1/FVC, including 1,240 novel and 73 also related to chronic obstructive pulmonary disease (1,787 cases). We found 294 CpGs unique to European or African ancestry and 395 CpGs unique to never or ever smokers. The majority of significant CpGs correlated with nearby gene expression in blood. Findings were enriched in key regulatory elements for gene function, including accessible chromatin elements, in both blood and lung. Sixty-nine implicated genes are targets of investigational or approved drugs. One example novel gene highlighted by integrative epigenomic and druggable target analysis is TNFRSF4. Mendelian randomization and colocalization analyses suggest that epigenome-wide association study signals capture causal regulatory genomic loci. Conclusions: We identified numerous novel loci differentially methylated in relation to pulmonary function; few were detected in large genome-wide association studies. Integrative analyses highlight functional relevance and potential therapeutic targets. This comprehensive discovery of potentially modifiable, novel lung function loci expands knowledge gained from genetic studies, providing insights into lung pathogenesis.
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Affiliation(s)
| | - Tianxiao Huan
- Department of Ophthalmology, University of Massachusetts Medical School, Worcester, Massachusetts.,Framingham Heart Study, National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services, Framingham, Massachusetts
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer and
| | - Geetha Chittoor
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania.,Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Maaike de Vries
- Department of Epidemiology.,Groningen Research Institute for Asthma and COPD, and
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ghent, Belgium.,Department of Epidemiology and
| | - Jennifer N Nguyen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Division of Cardiology, Department of Medicine
| | - Juan Castillo-Fernandez
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | | | - Cancan Qi
- Groningen Research Institute for Asthma and COPD, and.,Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Roby Joehanes
- Framingham Heart Study, National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services, Framingham, Massachusetts
| | - Josine L Min
- Medical Research Council Integrative Epidemiology Unit and.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | | | - Jessica R Shaw
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, and
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Mairead L Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer and
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Anne E Justice
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania.,Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine, a joint venture between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Research Group Bioinformatics and Computational Genomics, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Simon R Cox
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Judith M Vonk
- Department of Epidemiology.,Groningen Research Institute for Asthma and COPD, and
| | | | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Department of Epidemiology
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom.,Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Joel D Schwartz
- Department of Environmental Health and.,Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts.,Channing Laboratory, Harvard Medical School, Boston, Massachusetts
| | - Janice M Leung
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sinjini Sikdar
- Epidemiology Branch.,Department of Mathematics and Statistics, Old Dominion University, Norfolk, Virginia
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer and
| | - Sarah E Harris
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Diana A van der Plaat
- Department of Epidemiology.,National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - David J Van Den Berg
- Department of Preventive Medicine and.,Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Biostatistics
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Pantel S Vokonas
- Veterans Affairs Boston Healthcare System, School of Medicine and School of Public Health, Boston University, Boston, Massachusetts
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer and
| | - Adele M Taylor
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina
| | - R Graham Barr
- Department of Medicine and.,Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, and.,Department of Epidemiology, University of Colorado, Aurora, Colorado
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Ma'en Obeidat
- Centre for Heart Lung Innovation, The University of British Columbia, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, and.,Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas
| | | | | | - Alison A Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit and.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Gerard H Koppelman
- Groningen Research Institute for Asthma and COPD, and.,Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Division of Cardiology, Department of Medicine.,Computational Medicine Core, Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington
| | - Guy Brusselle
- Department of Epidemiology and.,Department of Respiratory Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium; and
| | - H Marike Boezen
- Department of Epidemiology.,Groningen Research Institute for Asthma and COPD, and
| | - Kari E North
- Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Daniel Levy
- Framingham Heart Study, National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services, Framingham, Massachusetts
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer and
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
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4
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Ye Z, Jiang L, Zhao M, Liu J, Dai H, Hou Y, Wang Z. Epigenome-wide screening of CpG markers to develop a multiplex methylation SNaPshot assay for age prediction. Leg Med (Tokyo) 2022; 59:102115. [PMID: 35810521 DOI: 10.1016/j.legalmed.2022.102115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/05/2022] [Accepted: 07/02/2022] [Indexed: 11/30/2022]
Abstract
Age prediction can provide important information about the contributors of biological evidence left at crime scenes. DNA methylation has been regarded as the most promising age-predictive biomarker. Measuring themethylation level at the genome-wide scaleis an important step to screen specific markers for forensic age prediction. In present study, we screened out five age-related CpG sites from the public EPIC BeadChip data and evaluated them in a training set (115 blood) by multiplex methylation SNaPshot assay. Through full subset regression, the five markers were narrowed down to three, namely cg10501210 (C1orf132), cg16867657 (ELOVL2), and cg13108341 (DNAH9), of which the last one was a newly discovered age-related CpG site. An age prediction model was built based on these three markers, explaining 86.8% of the variation of age with a mean absolute deviation (MAD) of 4.038 years. Then, the multiplex methylation SNaPshot assay was adjusted according to the age prediction model. Considering that bloodstains are one of the most common biological samples in practical cases, three validation sets composed of 30 blood, 30 fresh bloodstains and 30 aged bloodstains were used for evaluation of the age prediction model. The MAD of each set was estimated as 4.734, 4.490, and 5.431 years, respectively, suggesting that our age prediction model was applicable for age prediction for blood and bloodstains in Chinese Han population of 11-71 age. In general, this study describes a workflow of screening CpG markers from public chip data and presents a 3-CpG markers model for forensic age prediction.
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Affiliation(s)
- Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Mengyao Zhao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hao Dai
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, China.
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5
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Silva TD, Voisey J, Hopkins P, Apte S, Chambers D, O'Sullivan B. Markers of rejection of a lung allograft: state of the art. Biomark Med 2022; 16:483-498. [PMID: 35315284 DOI: 10.2217/bmm-2021-1013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chronic lung allograft dysfunction (CLAD) affects approximately 50% of all lung transplant recipients by 5 post-operative years and is the leading cause of death in lung transplant recipients. Early CLAD diagnosis or ideally prediction of CLAD is essential to enable early intervention before significant lung injury occurs. New technologies have emerged to facilitate biomarker discovery, including epigenetic modification and single-cell RNA sequencing. This review examines new and existing technologies for biomarker discovery and the current state of research on biomarkers for identifying lung transplant rejection.
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Affiliation(s)
- Tharushi de Silva
- School of Biomedical Sciences, Centre for Genomics & Personalised Heath, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, 4032, Brisbane, Queensland, Australia
| | - Joanne Voisey
- School of Biomedical Sciences, Centre for Genomics & Personalised Heath, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Peter Hopkins
- Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, 4032, Brisbane, Queensland, Australia.,Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, The University of Queensland, 4032, Brisbane, Queensland, Australia
| | - Simon Apte
- Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, 4032, Brisbane, Queensland, Australia.,Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, The University of Queensland, 4032, Brisbane, Queensland, Australia
| | - Daniel Chambers
- School of Biomedical Sciences, Centre for Genomics & Personalised Heath, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, 4032, Brisbane, Queensland, Australia.,Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, The University of Queensland, 4032, Brisbane, Queensland, Australia
| | - Brendan O'Sullivan
- School of Biomedical Sciences, Centre for Genomics & Personalised Heath, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, 4032, Brisbane, Queensland, Australia.,Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, The University of Queensland, 4032, Brisbane, Queensland, Australia
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6
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Herrera-Luis E, Li A, Mak ACY, Perez-Garcia J, Elhawary JR, Oh SS, Hu D, Eng C, Keys KL, Huntsman S, Beckman KB, Borrell LN, Rodriguez-Santana J, Burchard EG, Pino-Yanes M. Epigenome-wide association study of lung function in Latino children and youth with asthma. Clin Epigenetics 2022; 14:9. [PMID: 35033200 PMCID: PMC8760660 DOI: 10.1186/s13148-022-01227-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Introduction
DNA methylation studies have associated methylation levels at different CpG sites or genomic regions with lung function. Moreover, genetic ancestry has been associated with lung function in Latinos. However, no epigenome-wide association study (EWAS) of lung function has been performed in this population. Here, we aimed to identify DNA methylation patterns associated with lung function in pediatric asthma among Latinos.
Results
We conducted an EWAS in whole blood from 250 Puerto Rican and 148 Mexican American children and young adults with asthma. A total of five CpGs exceeded the genome-wide significance threshold of p = 1.17 × 10−7 in the combined analyses from Puerto Ricans and Mexican Americans: cg06035600 (MAP3K6, p = 6.13 × 10−8) showed significant association with pre-bronchodilator Tiffeneau–Pinelli index, the probes cg00914963 (TBC1D16, p = 1.04 × 10−7), cg16405908 (MRGPRE, p = 2.05 × 10−8), and cg07428101 (MUC2, p = 5.02 × 10−9) were associated with post-bronchodilator forced vital capacity (FVC), and cg20515679 (KCNJ6) with post-bronchodilator Tiffeneau–Pinelli index (p = 1.13 × 10−8). However, these markers did not show significant associations in publicly available data from Europeans (p > 0.05). A methylation quantitative trait loci analysis revealed that methylation levels at these CpG sites were regulated by genetic variation in Latinos and the Biobank-based Integrative Omics Studies (BIOS) consortium. Additionally, two differentially methylated regions in REXOC and AURKC were associated with pre-bronchodilator Tiffeneau–Pinelli index (adjusted p < 0.05) in Puerto Ricans and Mexican Americans. Moreover, we replicated some of the previous differentially methylated signals associated with lung function in non-Latino populations.
Conclusions
We replicated previous associations of epigenetic markers with lung function in whole blood and identified novel population-specific associations shared among Latino subgroups.
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7
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Marín-Hinojosa C, Eraso CC, Sanchez-Lopez V, Hernández LC, Otero-Candelera R, Lopez-Campos JL. Nutriepigenomics and chronic obstructive pulmonary disease: potential role of dietary and epigenetics factors in disease development and management. Am J Clin Nutr 2021; 114:1894-1906. [PMID: 34477827 DOI: 10.1093/ajcn/nqab267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Over recent decades, a number of studies have revealed the possible role of different types of diets, as well as the nutritional elements they are made up of, in the pathogenesis of chronic obstructive pulmonary disease (COPD). To date, dietary factors have been identified to play a role in the prevention of COPD, with evidence from antioxidant nutrients, vitamins, and fiber intake. Additionally, certain dietary patterns such as the Mediterranean diet, together with other Western diets, provide evidence of the influence on COPD development, promoting lung health through nutritional approaches, and giving us an opportunity for intervention. The effect of diet on COPD is conveyed by 3 mechanisms: regulation of inflammation, oxidative stress, and carbon dioxide produced/oxygen intake. Current advances have begun to highlight the possible role of diet in modifying gene expression in certain individuals that predisposes them to COPD through epigenetic modifications. The relation between dietary intake and epigenetic factors has therefore outlined nutriepigenomics as a possible missing link in the relation between environmental exposure to smoke and the appearance of a subsequent chronic bronchial obstruction. This review summarizes the evidence regarding the influence of dietary patterns and nutrients and epigenetic regulatory mechanisms on COPD development and prevention with the aim of encouraging clinical research on the impact of dietary modifications on COPD-related clinical outcomes. This review highlights the importance of proposing and carrying out future studies focused on the modulating effects of certain nutrients on epigenetic changes in patients with specific COPD phenotypes (bronchiectasis, emphysema, asthma/COPD, chronic bronchitis), and their individual responses to cigarette smoking, environmental pollution, or other noxious particles. The objectives of these future studies must be directed to the development of novel therapeutic approaches and personalized management of COPD.
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Affiliation(s)
- Carmen Marín-Hinojosa
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Candelaria Caballero Eraso
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Veronica Sanchez-Lopez
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Carrasco Hernández
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Remedios Otero-Candelera
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Luis Lopez-Campos
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
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8
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Benincasa G, DeMeo DL, Glass K, Silverman EK, Napoli C. Epigenetics and pulmonary diseases in the horizon of precision medicine: a review. Eur Respir J 2021; 57:13993003.03406-2020. [PMID: 33214212 DOI: 10.1183/13993003.03406-2020] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
Epigenetic mechanisms represent potential molecular routes which could bridge the gap between genetic background and environmental risk factors contributing to the pathogenesis of pulmonary diseases. In patients with COPD, asthma and pulmonary arterial hypertension (PAH), there is emerging evidence of aberrant epigenetic marks, mainly including DNA methylation and histone modifications which directly mediate reversible modifications to the DNA without affecting the genomic sequence. Post-translational events and microRNAs can be also regulated epigenetically and potentially participate in disease pathogenesis. Thus, novel pathogenic mechanisms and putative biomarkers may be detectable in peripheral blood, sputum, nasal and buccal swabs or lung tissue. Besides, DNA methylation plays an important role during the early phases of fetal development and may be impacted by environmental exposures, ultimately influencing an individual's susceptibility to COPD, asthma and PAH later in life. With the advances in omics platforms and the application of computational biology tools, modelling the epigenetic variability in a network framework, rather than as single molecular defects, provides insights into the possible molecular pathways underlying the pathogenesis of COPD, asthma and PAH. Epigenetic modifications may have clinical applications as noninvasive biomarkers of pulmonary diseases. Moreover, combining molecular assays with network analysis of epigenomic data may aid in clarifying the multistage transition from a "pre-disease" to "disease" state, with the goal of improving primary prevention of lung diseases and its subsequent clinical management.We describe epigenetic mechanisms known to be associated with pulmonary diseases and discuss how network analysis could improve our understanding of lung diseases.
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Affiliation(s)
- Giuditta Benincasa
- Dept of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Dawn L DeMeo
- Channing Division of Network Medicine and the Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine and the Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine and the Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Claudio Napoli
- Dept of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy .,Clinical Dept of Internal and Specialty Medicine (DAI), University Hospital (AOU), University of Campania "Luigi Vanvitelli", Naples, Italy
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9
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Madden RA, McCartney DL, Walker RM, Hillary RF, Bermingham ML, Rawlik K, Morris SW, Campbell A, Porteous DJ, Deary IJ, Evans KL, Hafferty J, McIntosh AM, Marioni RE. Birth weight associations with DNA methylation differences in an adult population. Epigenetics 2021; 16:783-796. [PMID: 33079621 PMCID: PMC8216207 DOI: 10.1080/15592294.2020.1827713] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022] Open
Abstract
The Developmental Origins of Health and Disease (DOHaD) theory predicts that prenatal and early life events shape adult health outcomes. Birth weight is a useful indicator of the foetal experience and has been associated with multiple adult health outcomes. DNA methylation (DNAm) is one plausible mechanism behind the relationship of birth weight to adult health. Through data linkage between Generation Scotland and historic Scottish birth cohorts, and birth records held through the NHS Information and Statistics Division, a sample of 1,757 individuals with available birth weight and DNAm data was derived. Epigenome-wide association studies (EWAS) were performed in two independently generated DNAm subgroups (nSet1 = 1,395, nSet2 = 362), relating adult DNAm from whole blood to birth weight. Meta-analysis yielded one genome-wide significant CpG site (p = 5.97x10-9), cg00966482. There was minimal evidence for attenuation of the effect sizes for the lead loci upon adjustment for numerous potential confounder variables (body mass index, educational attainment, and socioeconomic status). Associations between birth weight and epigenetic measures of biological age were also assessed. Associations between lower birth weight and higher Grim Age acceleration (p(FDR) = 3.6x10-3) and shorter DNAm-derived telomere length (p(FDR) = 1.7x10-3) are described, although results for three other epigenetic clocks were null. Our results provide support for an association between birth weight and DNAm both locally at one CpG site, and globally via biological ageing estimates.
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Affiliation(s)
- Rebecca A. Madden
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Daniel L. McCartney
- 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
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Mairead L. Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Stewart W. Morris
- Centre for Genomic and Experimental Medicine, 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
| | - 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
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, 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
| | - Jonathan Hafferty
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Andrew M. McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- 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
| | - 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
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10
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Buttery SC, Zysman M, Vikjord SAA, Hopkinson NS, Jenkins C, Vanfleteren LEGW. Contemporary perspectives in COPD: Patient burden, the role of gender and trajectories of multimorbidity. Respirology 2021; 26:419-441. [PMID: 33751727 DOI: 10.1111/resp.14032] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 02/21/2021] [Indexed: 12/13/2022]
Abstract
An individual's experience of COPD is determined by many factors in addition to the pathological features of chronic bronchitis and emphysema and the symptoms that derive directly from them. Multimorbidity is the norm rather than the exception, so most people with COPD are living with a range of other medical problems which can decrease overall quality of life. COPD is caused by the inhalation of noxious particles or gases, in particular tobacco smoke, but also by early life disadvantage impairing lung development and by occupations where inhaled exposures are common (e.g. industrial, farming and cleaning work). Wealthy people are therefore relatively protected from developing COPD and people who do develop the condition may have reduced resources to cope. COPD is also no longer a condition that predominantly affects men. The prevalence of COPD among women has equalled that of men since 2008 in many high-income countries, due to increased exposure to tobacco, and in low-income countries due to biomass fuels. COPD is one of the leading causes of death in women in the USA, and death rates attributed to COPD in women in some countries are predicted to overtake those of men in the next decade. Many factors contribute to this phenomenon, but in addition to socioeconomic and occupational factors, there is increasing evidence of a higher susceptibility of females to smoking and pollutants. Quality of life is also more significantly impaired in women. Although most medications (bronchodilators and inhaled corticosteroids) used to treat COPD demonstrate similar trends for exacerbation prevention and lung function improvement in men and women, this is an understudied area and clinical trials frequently have a preponderance of males. A better understanding of gender-based predictors of efficacy of all therapeutic interventions is crucial for comprehensive patient care. There is an urgent need to recognize the increasing burden of COPD in women and to facilitate global improvements in disease prevention and management in this specific population. Many individuals with COPD follow a trajectory of both lung function decline and also multimorbidity. Unfavourable lung function trajectories throughout life have implications for later development of other chronic diseases. An enhanced understanding of the temporal associations underlying the development of coexisting diseases is a crucial first step in unravelling potential common disease pathways. Lessons can be learned from exploring disease trajectories of other NCD as well as multimorbidity development. Further research will be essential to explain how early life risk factors commonly influence trajectories of COPD and other diseases, how different diseases develop in relation to each other in a temporal way and how this ultimately leads to different multimorbidity patterns in COPD. This review integrates new knowledge and ideas pertaining to three broad themes (i) the overall burden of disease in COPD, (ii) an unappreciated high burden in women and (iii) the contrast of COPD trajectories and different multimorbidity patterns with trajectories of other NCD. The underlying pathology of COPD is largely irreversible, but many factors noted in the review are potentially amenable to intervention. Health and social care systems need to ensure that effective treatment is accessible to all people with the condition. Preventive strategies and treatments that alter the course of disease are crucial, particularly for patients with COPD as one of many problems.
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Affiliation(s)
- Sara C Buttery
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Maéva Zysman
- Centre de Recherche cardio-thoracique de Bordeaux, Univ-Bordeaux, Pessac, France.,Service des Maladies Respiratoires, CHU Bordeaux, Pessac, France
| | - Sigrid A A Vikjord
- Department of Medicine and Rehabilitation, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway.,HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Levanger, Norway
| | | | - Christine Jenkins
- Respiratory Group, The George Institute for Global Health, Sydney, NSW, Australia
| | - Lowie E G W Vanfleteren
- COPD Center, Department of Respiratory Medicine and Allergology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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11
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Ahmad S, Manzoor S, Siddiqui S, Mariappan N, Zafar I, Ahmad A, Ahmad A. Epigenetic underpinnings of inflammation: Connecting the dots between pulmonary diseases, lung cancer and COVID-19. Semin Cancer Biol 2021; 83:384-398. [PMID: 33484868 PMCID: PMC8046427 DOI: 10.1016/j.semcancer.2021.01.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/08/2020] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
Inflammation is an essential component of several respiratory diseases, such as chronic obstructive pulmonary disease (COPD), asthma and acute respiratory distress syndrome (ARDS). It is central to lung cancer, the leading cancer in terms of associated mortality that has affected millions of individuals worldwide. Inflammation and pulmonary manifestations are also the major causes of COVID-19 related deaths. Acute hyperinflammation plays an important role in the COVID-19 disease progression and severity, and development of protective immunity against the virus is greatly sought. Further, the severity of COVID-19 is greatly enhanced in lung cancer patients, probably due to the genes such as ACE2, TMPRSS2, PAI-1 and furin that are commonly involved in cancer progression as well as SAR-CoV-2 infection. The importance of inflammation in pulmonary manifestations, cancer and COVID-19 calls for a closer look at the underlying processes, particularly the associated increase in IL-6 and other cytokines, the dysregulation of immune cells and the coagulation pathway. Towards this end, several reports have identified epigenetic regulation of inflammation at different levels. Expression of several key inflammation-related cytokines, chemokines and other genes is affected by methylation and acetylation while non-coding RNAs, including microRNAs as well as long non-coding RNAs, also affect the overall inflammatory responses. Select miRNAs can regulate inflammation in COVID-19 infection, lung cancer as well as other inflammatory lung diseases, and can serve as epigenetic links that can be therapeutically targeted. Furthermore, epigenetic changes also mediate the environmental factors-induced inflammation. Therefore, a better understanding of epigenetic regulation of inflammation can potentially help develop novel strategies to prevent, diagnose and treat chronic pulmonary diseases, lung cancer and COVID-19.
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Affiliation(s)
- Shama Ahmad
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shajer Manzoor
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Simmone Siddiqui
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nithya Mariappan
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Iram Zafar
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Aamir Ahmad
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Aftab Ahmad
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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12
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Walker RM, Vaher K, Bermingham ML, Morris SW, Bretherick AD, Zeng Y, Rawlik K, Amador C, Campbell A, Haley CS, Hayward C, Porteous DJ, McIntosh AM, Marioni RE, Evans KL. Identification of epigenome-wide DNA methylation differences between carriers of APOE ε4 and APOE ε2 alleles. Genome Med 2021; 13:1. [PMID: 33397400 PMCID: PMC7784364 DOI: 10.1186/s13073-020-00808-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 11/12/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The apolipoprotein E (APOE) ε4 allele is the strongest genetic risk factor for late onset Alzheimer's disease, whilst the ε2 allele confers protection. Previous studies report differential DNA methylation of APOE between ε4 and ε2 carriers, but associations with epigenome-wide methylation have not previously been characterised. METHODS Using the EPIC array, we investigated epigenome-wide differences in whole blood DNA methylation patterns between Alzheimer's disease-free APOE ε4 (n = 2469) and ε2 (n = 1118) carriers from the two largest single-cohort DNA methylation samples profiled to date. Using a discovery, replication and meta-analysis study design, methylation differences were identified using epigenome-wide association analysis and differentially methylated region (DMR) approaches. Results were explored using pathway and methylation quantitative trait loci (meQTL) analyses. RESULTS We obtained replicated evidence for DNA methylation differences in a ~ 169 kb region, which encompasses part of APOE and several upstream genes. Meta-analytic approaches identified DNA methylation differences outside of APOE: differentially methylated positions were identified in DHCR24, LDLR and ABCG1 (2.59 × 10-100 ≤ P ≤ 2.44 × 10-8) and DMRs were identified in SREBF2 and LDLR (1.63 × 10-4 ≤ P ≤ 3.01 × 10-2). Pathway and meQTL analyses implicated lipid-related processes and high-density lipoprotein cholesterol was identified as a partial mediator of the methylation differences in ABCG1 and DHCR24. CONCLUSIONS APOE ε4 vs. ε2 carrier status is associated with epigenome-wide methylation differences in the blood. The loci identified are located in trans as well as cis to APOE and implicate genes involved in lipid homeostasis.
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Affiliation(s)
- Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Present Address: Centre for Clinical Brain Sciences, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Kadi Vaher
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Present Address: MRC Centre for Reproductive Health, The Queen’s Medical Research Institute, Edinburgh BioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ UK
| | - Mairead L. Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Stewart W. Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Andrew D. Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Yanni Zeng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Present address: Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080 China
| | - Konrad Rawlik
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, UK
| | - Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Archie Campbell
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Chris S. Haley
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Andrew M. McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF UK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
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13
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Kachroo P, Morrow JD, Kho AT, Vyhlidal CA, Silverman EK, Weiss ST, Tantisira KG, DeMeo DL. Co-methylation analysis in lung tissue identifies pathways for fetal origins of COPD. Eur Respir J 2020; 56:13993003.02347-2019. [PMID: 32482784 DOI: 10.1183/13993003.02347-2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/21/2020] [Indexed: 12/21/2022]
Abstract
COPD likely has developmental origins; however, the underlying molecular mechanisms are not fully identified. Investigation of lung tissue-specific epigenetic modifications such as DNA methylation using network approaches might facilitate insights linking in utero smoke (IUS) exposure and risk for COPD in adulthood.We performed genome-wide methylation profiling for adult lung DNA from 160 surgical samples and 78 fetal lung DNA samples isolated from discarded tissue at 8-18 weeks of gestation. Co-methylation networks were constructed to identify preserved modules that shared methylation patterns in fetal and adult lung tissues and associations with fetal IUS exposure, gestational age and COPD.Weighted correlation networks highlighted preserved and co-methylated modules for both fetal and adult lung data associated with fetal IUS exposure, COPD and lower adult lung function. These modules were significantly enriched for genes involved in embryonic organ development and specific inflammation-related pathways, including Hippo, phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT), Wnt, mitogen-activated protein kinase and transforming growth factor-β signalling. Gestational age-associated modules were remarkably preserved for COPD and lung function, and were also annotated to genes enriched for the Wnt and PI3K/AKT pathways.Epigenetic network perturbations in fetal lung tissue exposed to IUS and of early lung development recapitulated in adult lung tissue from ex-smokers with COPD. Overlapping fetal and adult lung tissue network modules highlighted putative disease pathways supportive of exposure-related and age-associated developmental origins of COPD.
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Affiliation(s)
- Priyadarshini Kachroo
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jarrett D Morrow
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alvin T Kho
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Edwin K Silverman
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA .,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
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14
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Walker RM, Bermingham ML, Vaher K, Morris SW, Clarke T, Bretherick AD, Zeng Y, Amador C, Rawlik K, Pandya K, Hayward C, Campbell A, Porteous DJ, McIntosh AM, Marioni RE, Evans KL. Epigenome-wide analyses identify DNA methylation signatures of dementia risk. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2020; 12:e12078. [PMID: 32789163 PMCID: PMC7416667 DOI: 10.1002/dad2.12078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Dementia pathogenesis begins years before clinical symptom onset, necessitating the understanding of premorbid risk mechanisms. Here we investigated potential pathogenic mechanisms by assessing DNA methylation associations with dementia risk factors in Alzheimer's disease (AD)-free participants. METHODS Associations between dementia risk measures (family history, AD genetic risk score [GRS], and dementia risk scores [combining lifestyle, demographic, and genetic factors]) and whole-blood DNA methylation were assessed in discovery and replication samples (n = ~400 to ~5000) from Generation Scotland. RESULTS AD genetic risk and two dementia risk scores were associated with differential methylation. The GRS associated predominantly with methylation differences in cis but also identified a genomic region implicated in Parkinson disease. Loci associated with dementia risk scores were enriched for those previously associated with body mass index and alcohol consumption. DISCUSSION Dementia risk measures show widespread association with blood-based methylation, generating several hypotheses for assessment by future studies.
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Affiliation(s)
- Rosie M. Walker
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Mairead L. Bermingham
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Kadi Vaher
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Stewart W. Morris
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Toni‐Kim Clarke
- Division of PsychiatryUniversity of EdinburghRoyal Edinburgh HospitalEdinburghUK
| | - Andrew D. Bretherick
- MRC Human Genetics UnitInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Yanni Zeng
- Faculty of Forensic MedicineZhongshan School of MedicineSun Yat‐Sen University74 Zhongshan 2nd RoadGuangzhou510080China
| | - Carmen Amador
- MRC Human Genetics UnitInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Konrad Rawlik
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh, Easter Bush, RoslinEdinburghUK
| | - Kalyani Pandya
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Caroline Hayward
- MRC Human Genetics UnitInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Archie Campbell
- Generation ScotlandCentre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - David J. Porteous
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
- Generation ScotlandCentre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Andrew M. McIntosh
- MRC Centre for Reproductive HealthThe Queen's Medical Research InstituteEdinburgh Bioquarter47 Little France CrescentEdinburghEH16 4TJUK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
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16
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Du X, Yuan L, Wu M, Men M, He R, Wang L, Wu S, Xiang Y, Qu X, Liu H, Qin X, Hu C, Qin L, Liu C. Variable DNA methylation of aging-related genes is associated with male COPD. Respir Res 2019; 20:243. [PMID: 31684967 PMCID: PMC6829949 DOI: 10.1186/s12931-019-1215-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a chronic lung inflammatory disease which has a close relationship with aging. Genome-wide analysis reveals that DNA methylation markers vary obviously with age. DNA methylation variations in peripheral blood have the potential to be biomarkers for COPD. However, the specific DNA methylation of aging-related genes in the peripheral blood of COPD patients remains largely unknown. Methods Firstly, 9 aging-related differentially expressed genes (DEGs) in COPD patients were screened out from the 25 aging-related genes profile through a comprehensive screening strategy. Secondly, qPCR and multiple targeted bisulfite enrichment sequencing (MethTarget) were used to detect the mRNA level and DNA methylation level of the 9 differentially expressed genes in the peripheral blood of 60 control subjects and 45 COPD patients. The candidate functional CpG sites were selected on the basis of the regulation ability of the target gene expression. Thirdly, the correlation was evaluated between the DNA methylation level of the key CpG sites and the clinical parameters of COPD patients, including forced expiratory volume in one second (FEV1), forced expiratory volume in one second as percentage of predicted volume (FEV1%), forced expiratory volume/ forced vital capacity (FEV/FVC), modified British medical research council (mMRC) score, acute exacerbation frequency and the situation of frequent of acute aggravation (CAT) score. Lastly, differentially methylated CpG sites unrelated to smoking were also determined in COPD patients. Results Of the 9 differentially expressed aging-related genes, the mRNA expression of 8 genes were detected to be significantly down-regulated in COPD group, compared with control group. Meanwhile, the methylated level of all aging-related genes was changed in COPD group containing 219 COPD-related CpG sites in total. Notably, 27 CpG sites of FOXO3 gene showed a lower False Discovery Rate (FDR) and higher methylation difference values. Also, some variable DNA methylation is associated with the severity of COPD. Additionally, of the 219 COPD-related CpG sites, 147 CpG sites were not related to smoking. Conclusion These results identified that the mRNA expression and DNA methylation level of aging-related genes were changed in male COPD patients, which provides a molecular link between aging and COPD. The identified CpG markers are associated with the severity of COPD and provide new insights into the prediction and identification of COPD.
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Affiliation(s)
- Xizi Du
- Department of Physiology; China-Africa Infection Diseases Research Center, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China.,Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lin Yuan
- Department of Physiology; China-Africa Infection Diseases Research Center, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Mengping Wu
- Department of Physiology; China-Africa Infection Diseases Research Center, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Meichao Men
- Health Management Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruoxi He
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Leyuan Wang
- Department of Physiology; China-Africa Infection Diseases Research Center, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Shuangyan Wu
- Department of Physiology; China-Africa Infection Diseases Research Center, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Yang Xiang
- Department of Physiology; China-Africa Infection Diseases Research Center, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Xiangping Qu
- Department of Physiology; China-Africa Infection Diseases Research Center, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Huijun Liu
- Department of Physiology; China-Africa Infection Diseases Research Center, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Xiaoqun Qin
- Department of Physiology; China-Africa Infection Diseases Research Center, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Chengping Hu
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ling Qin
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Chi Liu
- Department of Physiology; China-Africa Infection Diseases Research Center, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China.
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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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