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Rahman ML, Breeze CE, Shu XO, Wong JYY, Blechter B, Cardenas A, Wang X, Ji BT, Hu W, Cai Q, Hosgood HD, Yang G, Shi J, Long J, Gao YT, Bell DA, Zheng W, Rothman N, Lan Q. Epigenome-wide association study of lung cancer among never smokers in two prospective cohorts in Shanghai, China. Thorax 2024; 79:735-744. [PMID: 38702190 PMCID: PMC11251856 DOI: 10.1136/thorax-2023-220352] [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: 04/19/2023] [Accepted: 02/17/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND The aetiology of lung cancer among individuals who never smoked remains elusive, despite 15% of lung cancer cases in men and 53% in women worldwide being unrelated to smoking. Epigenetic alterations, particularly DNA methylation (DNAm) changes, have emerged as potential drivers. Yet, few prospective epigenome-wide association studies (EWAS), primarily focusing on peripheral blood DNAm with limited representation of never smokers, have been conducted. METHODS We conducted a nested case-control study of 80 never-smoking incident lung cancer cases and 83 never-smoking controls within the Shanghai Women's Health Study and Shanghai Men's Health Study. DNAm was measured in prediagnostic oral rinse samples using Illumina MethylationEPIC array. Initially, we conducted an EWAS to identify differentially methylated positions (DMPs) associated with lung cancer in the discovery sample of 101 subjects. The top 50 DMPs were further evaluated in a replication sample of 62 subjects, and results were pooled using fixed-effect meta-analysis. RESULTS Our study identified three DMPs significantly associated with lung cancer at the epigenome-wide significance level of p<8.22×10-8. These DMPs were identified as cg09198866 (MYH9; TXN2), cg01411366 (SLC9A10) and cg12787323. Furthermore, examination of the top 1000 DMPs indicated significant enrichment in epithelial regulatory regions and their involvement in small GTPase-mediated signal transduction pathways. Additionally, GrimAge acceleration was identified as a risk factor for lung cancer (OR=1.19 per year; 95% CI 1.06 to 1.34). CONCLUSIONS While replication in a larger sample size is necessary, our findings suggest that DNAm patterns in prediagnostic oral rinse samples could provide novel insights into the underlying mechanisms of lung cancer in never smokers.
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Affiliation(s)
- Mohammad L Rahman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Xiao-Ou Shu
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jason Y Y Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Batel Blechter
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Stanford, California, USA
| | - Xuting Wang
- Immunity, Inflammation and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Qiuyin Cai
- Vanderbilt University, Nashville, Tennessee, USA
| | - H Dean Hosgood
- Albert Einstein College of Medicine, Bronx, New York, USA
| | - Gong Yang
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Jirong Long
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | | | - Douglas A Bell
- Immunity, Inflammation and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Wei Zheng
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
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2
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Herzog C, Jones A, Evans I, Raut JR, Zikan M, Cibula D, Wong A, Brenner H, Richmond RC, Widschwendter M. Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis. Cancer Res 2024; 84:1898-1914. [PMID: 38503267 PMCID: PMC11148547 DOI: 10.1158/0008-5472.can-23-2957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
Tobacco use is a major modifiable risk factor for adverse health outcomes, including cancer, and elicits profound epigenetic changes thought to be associated with long-term cancer risk. While electronic cigarettes (e-cigarettes) have been advocated as harm reduction alternatives to tobacco products, recent studies have revealed potential detrimental effects, highlighting the urgent need for further research into the molecular and health impacts of e-cigarettes. Here, we applied computational deconvolution methods to dissect the cell- and tissue-specific epigenetic effects of tobacco or e-cigarette use on DNA methylation (DNAme) in over 3,500 buccal/saliva, cervical, or blood samples, spanning epithelial and immune cells at directly and indirectly exposed sites. The 535 identified smoking-related DNAme loci [cytosine-phosphate-guanine sites (CpG)] clustered into four functional groups, including detoxification or growth signaling, based on cell type and anatomic site. Loci hypermethylated in buccal epithelial cells of smokers associated with NOTCH1/RUNX3/growth factor receptor signaling also exhibited elevated methylation in cancer tissue and progressing lung carcinoma in situ lesions, and hypermethylation of these sites predicted lung cancer development in buccal samples collected from smokers up to 22 years prior to diagnosis, suggesting a potential role in driving carcinogenesis. Alarmingly, these CpGs were also hypermethylated in e-cigarette users with a limited smoking history. This study sheds light on the cell type-specific changes to the epigenetic landscape induced by smoking-related products. SIGNIFICANCE The use of both cigarettes and e-cigarettes elicits cell- and exposure-specific epigenetic effects that are predictive of carcinogenesis, suggesting caution when broadly recommending e-cigarettes as aids for smoking cessation.
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Affiliation(s)
- Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Innsbruck, Austria
- Research Institute for Biomedical Aging, Universität Innsbruck, Innsbruck, Austria
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, United Kingdom
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, United Kingdom
| | - Janhavi R Raut
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michal Zikan
- Department of Gynecology and Obstetrics, First Faculty of Medicine and Hospital Na Bulovce, Charles University in Prague, Prague, Czech Republic
| | - David Cibula
- Gynecologic Oncology Center, Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University in Prague, General University Hospital in Prague, Prague, Czech Republic
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Innsbruck, Austria
- Research Institute for Biomedical Aging, Universität Innsbruck, Innsbruck, Austria
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, United Kingdom
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
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3
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Li JL, Jain N, Tamayo LI, Tong L, Jasmine F, Kibriya MG, Demanelis K, Oliva M, Chen LS, Pierce BL. The association of cigarette smoking with DNA methylation and gene expression in human tissue samples. Am J Hum Genet 2024; 111:636-653. [PMID: 38490207 PMCID: PMC11023923 DOI: 10.1016/j.ajhg.2024.02.012] [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: 08/14/2023] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 03/17/2024] Open
Abstract
Cigarette smoking adversely affects many aspects of human health, and epigenetic responses to smoking may reflect mechanisms that mediate or defend against these effects. Prior studies of smoking and DNA methylation (DNAm), typically measured in leukocytes, have identified numerous smoking-associated regions (e.g., AHRR). To identify smoking-associated DNAm features in typically inaccessible tissues, we generated array-based DNAm data for 916 tissue samples from the GTEx (Genotype-Tissue Expression) project representing 9 tissue types (lung, colon, ovary, prostate, blood, breast, testis, kidney, and muscle). We identified 6,350 smoking-associated CpGs in lung tissue (n = 212) and 2,735 in colon tissue (n = 210), most not reported previously. For all 7 other tissue types (sample sizes 38-153), no clear associations were observed (false discovery rate 0.05), but some tissues showed enrichment for smoking-associated CpGs reported previously. For 1,646 loci (in lung) and 22 (in colon), smoking was associated with both DNAm and local gene expression. For loci detected in both lung and colon (e.g., AHRR, CYP1B1, CYP1A1), top CpGs often differed between tissues, but similar clusters of hyper- or hypomethylated CpGs were observed, with hypomethylation at regulatory elements corresponding to increased expression. For lung tissue, 17 hallmark gene sets were enriched for smoking-associated CpGs, including xenobiotic- and cancer-related gene sets. At least four smoking-associated regions in lung were impacted by lung methylation quantitative trait loci (QTLs) that co-localize with genome-wide association study (GWAS) signals for lung function (FEV1/FVC), suggesting epigenetic alterations can mediate the effects of smoking on lung health. Our multi-tissue approach has identified smoking-associated regions in disease-relevant tissues, including effects that are shared across tissue types.
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Affiliation(s)
- James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL 60637, USA
| | - Niyati Jain
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Committee on Genetics, Genomics, Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lizeth I Tamayo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Farzana Jasmine
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Comprehensive Cancer Center, University of Chicago, Chicago, IL 60637, USA.
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4
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Zhao X, Yang M, Fan J, Wang M, Wang Y, Qin N, Zhu M, Jiang Y, Gorlova OY, Gorlov IP, Albanes D, Lam S, Tardón A, Chen C, Goodman GE, Bojesen SE, Landi MT, Johansson M, Risch A, Wichmann HE, Bickeböller H, Christiani DC, Rennert G, Arnold SM, Brennan P, Field JK, Shete S, Le Marchand L, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Zienolddiny S, Grankvist K, Johansson M, Caporaso NE, Woll PJ, Lazarus P, Schabath MB, Aldrich MC, Patel AV, Davies MPA, Ma H, Jin G, Hu Z, Amos CI, Shen H, Dai J. Identification of genetically predicted DNA methylation markers associated with non-small cell lung cancer risk among 34,964 cases and 448,579 controls. Cancer 2024; 130:913-926. [PMID: 38055287 PMCID: PMC11327897 DOI: 10.1002/cncr.35130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/05/2023] [Accepted: 05/22/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Although the associations between genetic variations and lung cancer risk have been explored, the epigenetic consequences of DNA methylation in lung cancer development are largely unknown. Here, the genetically predicted DNA methylation markers associated with non-small cell lung cancer (NSCLC) risk by a two-stage case-control design were investigated. METHODS The genetic prediction models for methylation levels based on genetic and methylation data of 1595 subjects from the Framingham Heart Study were established. The prediction models were applied to a fixed-effect meta-analysis of screening data sets with 27,120 NSCLC cases and 27,355 controls to identify the methylation markers, which were then replicated in independent data sets with 7844 lung cancer cases and 421,224 controls. Also performed was a multi-omics functional annotation for the identified CpGs by integrating genomics, epigenomics, and transcriptomics and investigation of the potential regulation pathways. RESULTS Of the 29,894 CpG sites passing the quality control, 39 CpGs associated with NSCLC risk (Bonferroni-corrected p ≤ 1.67 × 10-6 ) were originally identified. Of these, 16 CpGs remained significant in the validation stage (Bonferroni-corrected p ≤ 1.28 × 10-3 ), including four novel CpGs. Multi-omics functional annotation showed nine of 16 CpGs were potentially functional biomarkers for NSCLC risk. Thirty-five genes within a 1-Mb window of 12 CpGs that might be involved in regulatory pathways of NSCLC risk were identified. CONCLUSIONS Sixteen promising DNA methylation markers associated with NSCLC were identified. Changes of the methylation level at these CpGs might influence the development of NSCLC by regulating the expression of genes nearby. PLAIN LANGUAGE SUMMARY The epigenetic consequences of DNA methylation in lung cancer development are still largely unknown. This study used summary data of large-scale genome-wide association studies to investigate the associations between genetically predicted levels of methylation biomarkers and non-small cell lung cancer risk at the first time. This study looked at how well larotrectinib worked in adult patients with sarcomas caused by TRK fusion proteins. These findings will provide a unique insight into the epigenetic susceptibility mechanisms of lung cancer.
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Affiliation(s)
- Xiaoyu Zhao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Statistics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Meiqi Yang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jingyi Fan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
- Health Management Center, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Mei Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yifan Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Na Qin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Olga Y Gorlova
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, Texas, USA
| | - Ivan P Gorlov
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, Texas, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Adonina Tardón
- Department of Public Health IUOPA, University of Oviedo, ISPA and CIBERESP, Oviedo, Spain
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Gary E Goodman
- Public Health Sciences Division, Swedish Cancer Institute, Seattle, Washington, USA
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Mattias Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Angela Risch
- Department of Biosciences, Allergy-Cancer-BioNano Research Centre, University of Salzburg, Salzburg, Austria
- Division of Epigenomics and Cancer Risk Factors, DKFZ-German Cancer Research Center, Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
| | - H-Erich Wichmann
- Institute of Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center Goettingen, Goettingen, Germany
| | - David C Christiani
- Departments of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Gad Rennert
- Technion Faculty of Medicine, Carmel Medical Center, Haifa, Israel
| | - Susanne M Arnold
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - John K Field
- Molecular and Clinical Cancer Medicine, Roy Castle Lung Cancer Research Programme, The University of Liverpool Institute of Translational Medicine, Liverpool, UK
| | - Sanjay Shete
- Department of Epidemiology, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawai'i Cancer Center, Honolulu, Hawaii, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Rayjean J Hung
- Prosseman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Angeline S Andrew
- Department of Neurology, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Lambertus A Kiemeney
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umea, Sweden
| | | | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Penella J Woll
- Academic Unit of Clinical Oncology, University of Sheffield, Sheffield, UK
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Melinda C Aldrich
- Department of Medicine (Division of Genetic Medicine), Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alpa V Patel
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia, USA
| | - Michael P A Davies
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Christopher I Amos
- Baylor College of Medicine, Institute for Clinical and Translational Research, Houston, Texas, USA
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Gusu School, Nanjing Medical University, Nanjing, China
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Pelland-St-Pierre L, Pham MC, Nguyen AQH, Pasquet R, Taylor SA, Bosson-Rieutort D, Koushik A, Ho V. The Influence of Smoking and Occupational Risk Factors on DNA Methylation in the AHRR and F2RL3 Genes. Cancer Epidemiol Biomarkers Prev 2024; 33:224-233. [PMID: 38051301 DOI: 10.1158/1055-9965.epi-23-0828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/26/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND AHRR and F2RL3 hypomethylation has been associated with lung cancer. In this study, we investigated the cross-sectional association between smoking and occupational exposures, and AHRR and F2RL3 methylation. METHODS A case-control study was nested in CARTaGENE to examine the association between AHRR and F2RL3 methylation and lung cancer risk (200 cases; 400 controls). A secondary analysis was conducted using the data collected from this nested study; namely, baseline information on participants' smoking behavior and longest-held job was obtained. A cumulative smoking index summarized information on the number of cigarettes smoked, duration of smoking, and time since cessation. Exposure to 13 occupational agents was estimated using the Canadian Job Exposure Matrix. In baseline blood samples, methylation ratios of 40 CpG sites in the AHRR and F2RL3 genes were measured using Sequenom EpiTYPER. Separate least squares regression models were used to estimate the associations between smoking and occupational exposures, and average AHRR and F2RL3 methylation levels, while adjusting for confounders identified from directed acyclic graphs. RESULTS In both genes, smoking was associated with lower average methylation levels. Occupational exposure to aromatic amines, cadmium, and formaldehyde were associated with lower AHRR methylation while, only benzene was associated with F2RL3 hypomethylation; these associations were stronger among ever smokers. CONCLUSIONS Our findings support that smoking and occupational exposures to some agents are associated with AHRR and F2RL3 hypomethylation. IMPACT Our results inform on mechanisms underlying environmental exposures in lung cancer etiology; future studies should prioritize studying joint exposures.
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Affiliation(s)
- Laura Pelland-St-Pierre
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
- Centre de recherche en santé publique (CReSP), University of Montréal and CIUSSS Centre-Sud, Montréal, Québec, Canada
| | - Michael C Pham
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
| | - Alice Quynh Huong Nguyen
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
| | - Romain Pasquet
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
| | - Sherryl A Taylor
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Delphine Bosson-Rieutort
- Centre de recherche en santé publique (CReSP), University of Montréal and CIUSSS Centre-Sud, Montréal, Québec, Canada
- Department of Health Management, Evaluation and Policy, University of Montreal, Montreal, Quebec, Canada
| | - Anita Koushik
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
| | - Vikki Ho
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
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6
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Qiao R, Zhu Q, Di F, Liu C, Song Y, Zhang J, Xu T, Wang Y, Dai L, Gu W, Han B, Yang R. Hypomethylation of DYRK4 in peripheral blood is associated with increased lung cancer risk. Mol Carcinog 2023; 62:1745-1754. [PMID: 37530470 DOI: 10.1002/mc.23612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 06/01/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
Lung cancer (LC) is the leading cause of cancer-related deaths worldwide. It is urgent to identify new biomarkers for the early detection of LC. DNA methylation in peripheral blood has been reported to be associated with cancers. We conducted two independent case-control studies and a nested case-control study (168 LC cases and 167 controls in study Ⅰ, 677 LC cases and 833 controls in study Ⅱ, 147 precancers and 21 controls in the nested case-control study). The methylation levels of DYRK4 CpG sites were measured using mass spectrometry and their correlations with LC were analyzed by logistic regression and nonparametric tests. Bonferroni correction was used for the multiple comparisons. LC-related decreased DYRK4 methylation was discovered in Study I and validated in Study II (the odds ratios [ORs] for the lowest vs. highest quartile of all three DYRK4 CpG sites ranged from 1.64 to 2.09, all p < 0.001). Combining the two studies, hypomethylation of DYRK4 was observed in stage I cases (ORs per -10% methylation ranged from 1.16 to 1.38, all p < 5.9E-04), and could be enhanced by male gender (ORs ranged from 1.77 to 4.17 via interquartile analyses, all p < 0.017). Hypomethylation of DYRK4_A_CpG_2 was significantly correlated with tumor size, length, and stage (p = 0.034, 0.002, and 0.002, respectively) in LC cases. Our study disclosed the association between DYRK4 hypomethylation in peripheral blood and LC, suggesting the feasibility of blood-based DNA methylation as new biomarker for LC detection.
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Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Qiang Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yakang Song
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Jin Zhang
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Yue Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
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7
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Domingo-Relloso A, Joehanes R, Rodriguez-Hernandez Z, Lahousse L, Haack K, Fallin MD, Herreros-Martinez M, Umans JG, Best LG, Huan T, Liu C, Ma J, Yao C, Jerolon A, Bermudez JD, Cole SA, Rhoades DA, Levy D, Navas-Acien A, Tellez-Plaza M. Smoking, blood DNA methylation sites and lung cancer risk. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122153. [PMID: 37442331 PMCID: PMC10528956 DOI: 10.1016/j.envpol.2023.122153] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/07/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Altered DNA methylation (DNAm) might be a biological intermediary in the pathway from smoking to lung cancer. In this study, we investigated the contribution of differential blood DNAm to explain the association between smoking and lung cancer incidence. Blood DNAm was measured in 2321 Strong Heart Study (SHS) participants. Incident lung cancer was assessed as time to event diagnoses. We conducted mediation analysis, including validation with DNAm and paired gene expression data from the Framingham Heart Study (FHS). In the SHS, current versus never smoking and pack-years single-mediator models showed, respectively, 29 and 21 differentially methylated positions (DMPs) for lung cancer with statistically significant mediated effects (14 of 20 available, and five of 14 available, positions, replicated, respectively, in FHS). In FHS, replicated DMPs showed gene expression downregulation largely in trans, and were related to biological pathways in cancer. The multimediator model identified that DMPs annotated to the genes AHRR and IER3 jointly explained a substantial proportion of lung cancer. Thus, the association of smoking with lung cancer was partly explained by differences in baseline blood DNAm at few relevant sites. Experimental studies are needed to confirm the biological role of identified eQTMs and to evaluate potential implications for early detection and control of lung cancer.
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Affiliation(s)
- Arce Domingo-Relloso
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain; Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA; Department of Statistics and Operations Research, University of Valencia, Spain.
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung, And Blood Institute, National Institutes of Health, Bethesda, MD, USA; Framingham Heart Study, Framingham, MA, USA
| | - Zulema Rodriguez-Hernandez
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Lies Lahousse
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins University, Baltimore, USA; Department of Epidemiology, Johns Hopkins University, Baltimore, USA
| | | | - Jason G Umans
- MedStar Health Research Institute, Washington DC, USA; Georgetown-Howard Universities Center for Clinical and Translational Science, Washington DC, USA
| | - Lyle G Best
- Missouri Breaks Industries and Research Inc., Eagle Butte, SD, USA
| | - Tianxiao Huan
- Framingham Heart Study, Framingham, MA, USA; University of Massachusetts Medical School, Worcester, MA, USA
| | - Chunyu Liu
- Framingham Heart Study, Framingham, MA, USA; Boston University School of Public Health, Boston, MA, USA
| | - Jiantao Ma
- Framingham Heart Study, Framingham, MA, USA; Tufts University Friedman School of Nutrition Science and Policy, Boston, MA, USA
| | - Chen Yao
- Framingham Heart Study, Framingham, MA, USA; Bristol Myers Squibb, Cambridge, MA, USA
| | - Allan Jerolon
- Université Paris Cité, CNRS, MAP5, F-75006, Paris, France
| | - Jose D Bermudez
- Department of Statistics and Operations Research, University of Valencia, Spain
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Dorothy A Rhoades
- Stephenson Cancer Center, University of Oklahoma Health Sciences Department of Medicine, Oklahoma City, OK, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, And Blood Institute, National Institutes of Health, Bethesda, MD, USA; Framingham Heart Study, Framingham, MA, USA
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Maria Tellez-Plaza
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
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8
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Bhardwaj M, Schöttker B, Holleczek B, Brenner H. Enhanced selection of people for lung cancer screening using AHRR (cg05575921) or F2RL3 (cg03636183) methylation as biological markers of smoking exposure. Cancer Commun (Lond) 2023; 43:956-959. [PMID: 37278142 PMCID: PMC10397557 DOI: 10.1002/cac2.12450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 06/07/2023] Open
Affiliation(s)
- Megha Bhardwaj
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Division of Preventive OncologyGerman Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT)HeidelbergGermany
- German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Network Aging ResearchUniversity of HeidelbergHeidelbergGermany
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Division of Preventive OncologyGerman Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT)HeidelbergGermany
- German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
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9
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Dugué PA, Yu C, Hodge AM, Wong EM, Joo JE, Jung CH, Schmidt D, Makalic E, Buchanan DD, Severi G, English DR, Hopper JL, Milne RL, Giles GG, Southey MC. Methylation scores for smoking, alcohol consumption and body mass index and risk of seven types of cancer. Int J Cancer 2023; 153:489-498. [PMID: 36919377 DOI: 10.1002/ijc.34513] [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: 01/28/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 03/16/2023]
Abstract
Methylation marks of exposure to health risk factors may be useful markers of cancer risk as they might better capture current and past exposures than questionnaires, and reflect different individual responses to exposure. We used data from seven case-control studies nested within the Melbourne Collaborative Cohort Study of blood DNA methylation and risk of colorectal, gastric, kidney, lung, prostate and urothelial cancer, and B-cell lymphoma (N cases = 3123). Methylation scores (MS) for smoking, body mass index (BMI), and alcohol consumption were calculated based on published data as weighted averages of methylation values. Rate ratios (RR) and 95% confidence intervals for association with cancer risk were estimated using conditional logistic regression and expressed per SD increase of the MS, with and without adjustment for health-related confounders. The contribution of MS to discriminate cases from controls was evaluated using the area under the curve (AUC). After confounder adjustment, we observed: large associations (RR = 1.5-1.7) with lung cancer risk for smoking MS; moderate associations (RR = 1.2-1.3) with urothelial cancer risk for smoking MS and with mature B-cell neoplasm risk for BMI and alcohol MS; moderate to small associations (RR = 1.1-1.2) for BMI and alcohol MS with several cancer types and cancer overall. Generally small AUC increases were observed after inclusion of several MS in the same model (colorectal, gastric, kidney, urothelial cancers: +3%; lung cancer: +7%; B-cell neoplasms: +8%). Methylation scores for smoking, BMI and alcohol consumption show independent associations with cancer risk, and may provide some improvements in risk prediction.
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Affiliation(s)
- Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Chenglong Yu
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Allison M Hodge
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - JiHoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia
| | - Daniel Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Department of Data Science and AI, Faculty of IT, Monash University, Clayton, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
- Melbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Gianluca Severi
- Centre de Recherche en Epidémiologie et Santé des Populations (CESP, Inserm U1018), Facultés de Médecine Universités Paris-Saclay, UVSQ, Gustave Roussy, Villejuif, France
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Roger L Milne
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
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10
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Blechter B, Cardenas A, Shi J, Wong JYY, Hu W, Rahman ML, Breeze C, Downward GS, Portengen L, Zhang Y, Ning B, Ji BT, Cawthon R, Li J, Yang K, Bozack A, Dean Hosgood H, Silverman DT, Huang Y, Rothman N, Vermeulen R, Lan Q. Household air pollution and epigenetic aging in Xuanwei, China. ENVIRONMENT INTERNATIONAL 2023; 178:108041. [PMID: 37354880 DOI: 10.1016/j.envint.2023.108041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/19/2023] [Accepted: 06/13/2023] [Indexed: 06/26/2023]
Abstract
BACKGROUND Household air pollution (HAP) from indoor combustion of solid fuel is a global health burden linked to lung cancer. In Xuanwei, China, lung cancer rate for nonsmoking women is among the highest in the world and largely attributed to high levels of polycyclic aromatic hydrocarbons (PAHs) that are produced from combustion of smoky (bituminous) coal used for cooking and heating. Epigenetic age acceleration (EAA), a DNA methylation-based biomarker of aging, has been shown to be highly correlated with biological processes underlying the susceptibility of age-related diseases. We aim to assess the association between HAP exposure and EAA. METHODS We analyzed data from 106 never-smoking women from Xuanwei, China. Information on fuel type was collected using a questionnaire, and validated exposure models were used to predict levels of 43 HAP constituents. Exposure clusters were identified using hierarchical clustering. EAA was derived for five epigenetic clocks defined as the residuals resulting from regressing each clock on chronological age. We used generalized estimating equations to test associations between exposure clusters derived from predicted levels of HAP exposure, ambient 5-methylchrysene (5-MC), a PAH previously found to be associated with risk of lung cancer, and EAA, while accounting for repeated-measurements and confounders. RESULTS We observed an increase in GrimAge EAA for clusters with 31 and 33 PAHs reflecting current (β = 0.77 y per standard deviation (SD) increase, 95 % CI:0.36,1.19) and childhood (β = 0.92 y per SD, 95 % CI:0.40,1.45) exposure, respectively. 5-MC (ng/m3-year) was found to be associated with GrimAge EAA for current (β = 0.15 y, 95 % CI:0.05,0.25) and childhood (β = 0.30 y, 95 % CI:0.13,0.47) exposure. CONCLUSIONS Our findings suggest that exposure to PAHs from indoor smoky coal combustion, particularly 5-MC, is associated with GrimAge EAA, a biomarker of mortality.
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Affiliation(s)
- Batel Blechter
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Junming Shi
- Department of Biostatistics, UC Berkeley School of Public Health, Berkeley, CA, USA
| | - Jason Y Y Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mohammad L Rahman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Charles Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - George S Downward
- Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Utrecht, Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Lützen Portengen
- Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Utrecht, Netherlands
| | - Yongliang Zhang
- Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Utrecht, Netherlands
| | - Bofu Ning
- Xuanwei Center of Diseases Control, Xuanwei, Yunnan, China
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Richard Cawthon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jihua Li
- Quijing Center for Diseases Control and Prevention, Quijing, Yunnan, China
| | - Kaiyun Yang
- Department of Cardiothoracic Surgery, Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, Yunnan, China
| | - Anne Bozack
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - H Dean Hosgood
- Division of Epidemiology, Albert Einstein College of Medicine, New York, NY, USA
| | - Debra T Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yunchao Huang
- Department of Cardiothoracic Surgery, Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, Yunnan, China
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Roel Vermeulen
- Department of Biostatistics, UC Berkeley School of Public Health, Berkeley, CA, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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11
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Skov-Jeppesen SM, Kobylecki CJ, Jacobsen KK, Bojesen SE. Changing Smoking Behavior and Epigenetics: A Longitudinal Study of 4,432 Individuals From the General Population. Chest 2023; 163:1565-1575. [PMID: 36621758 PMCID: PMC10258440 DOI: 10.1016/j.chest.2022.12.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Hypomethylation of the aryl hydrocarbon receptor repressor (AHRR) gene indicates long-term smoking exposure and might therefore be a monitor for smoking-induced disease risk. However, studies of individual longitudinal changes in AHRR methylation are sparse. RESEARCH QUESTION How does the recovery of AHRR methylation depend on change in smoking behaviors and demographic variables? STUDY DESIGN AND METHODS This study included 4,432 individuals from the Copenhagen City Heart Study, with baseline and follow-up blood samples and smoking information collected approximately 10 years apart. AHRR methylation at the cg05575921 site was measured in bisulfite-treated leukocyte DNA. Four smoking groups were defined: participants who never smoked (Never-Never), participants who formerly smoked (Former-Former), participants who quit during the study period (Current-Former), and individuals who smoked at both baseline and follow-up (Current-Current). Methylation recovery was defined as the increase in AHRR methylation between baseline and follow-up examination. RESULTS Methylation recovery was highest among participants who quit, with a median methylation recovery of 5.58% (interquartile range, 1.79; 9.15) vs 1.64% (interquartile range, -1.88; 4.96) in the Current-Current group (P < .0001). In individuals who quit smoking, older age was associated with lower methylation recovery (P < .0001). In participants who quit aged > 65 years, methylation recovery was 5.9% at 5.6 years after quitting; methylation recovery was 8.5% after 2.8 years for participants who quit aged < 55 years. INTERPRETATION AHRR methylation recovered after individuals quit smoking, and recovery was more pronounced and occurred faster in younger compared with older interim quitters.
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Affiliation(s)
- Sune Moeller Skov-Jeppesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Camilla Jannie Kobylecki
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Katja Kemp Jacobsen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, Copenhagen, Denmark
| | - Stig Egil Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark; The Copenhagen City Heart Study, Copenhagen University Hospital, Frederiksberg and Bispebjerg Hospital, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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12
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Gulhane P, Singh S. Unraveling the Post-Translational Modifications and therapeutical approach in NSCLC pathogenesis. Transl Oncol 2023; 33:101673. [PMID: 37062237 PMCID: PMC10133877 DOI: 10.1016/j.tranon.2023.101673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 04/18/2023] Open
Abstract
Non-Small Cell Lung Cancer (NSCLC) is the most prevalent kind of lung cancer with around 85% of total lung cancer cases. Despite vast therapies being available, the survival rate is low (5 year survival rate is 15%) making it essential to comprehend the mechanism for NSCLC cell survival and progression. The plethora of evidences suggests that the Post Translational Modification (PTM) such as phosphorylation, methylation, acetylation, glycosylation, ubiquitination and SUMOylation are involved in various types of cancer progression and metastasis including NSCLC. Indeed, an in-depth understanding of PTM associated with NSCLC biology will provide novel therapeutic targets and insight into the current sophisticated therapeutic paradigm. Herein, we reviewed the key PTMs, epigenetic modulation, PTMs crosstalk along with proteogenomics to analyze PTMs in NSCLC and also, highlighted how epi‑miRNA, miRNA and PTM inhibitors are key modulators and serve as promising therapeutics.
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Affiliation(s)
- Pooja Gulhane
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SPPU Campus, Pune 411007, India
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SPPU Campus, Pune 411007, India.
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13
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Possible regulation of ganglioside GD3 synthase gene expression with DNA methylation in human glioma cells. Glycoconj J 2023; 40:323-332. [PMID: 36897478 DOI: 10.1007/s10719-023-10108-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/02/2023] [Accepted: 02/21/2023] [Indexed: 03/11/2023]
Abstract
Gangliosides are expressed in nervous systems and some neuroectoderm-derived tumors at high levels and play pivotal roles. However, mechanisms for the regulation of glycosyltransferase genes responsible for the ganglioside synthesis are not well understood. In this study, we analyzed DNA methylation patterns of promoter regions of GD3 synthase (ST8SIA1) as well as mRNA levels and ganglioside expression using human glioma cell lines. Among 5 cell lines examined, 4 lines showed changes in the expression levels of related genes after treatment with 5-aza-dC. LN319 showed up-regulation of St8sia1 and increased b-series gangliosides after 5-aza-dC treatment, and an astrocytoma cell line, AS showed high expression of ST8SIA1 and b-series gangliosides persistently before and after 5-Aza-2'-deoxycytidine treatment. Using these 2 cell lines, DNA methylation patterns of the promoter regions of the gene were analyzed by bisulfite-sequencing. Consequently, 2 regions that were methylated before 5-Aza-2'-deoxycytidine treatment were demethylated in LN319 after the treatment, while those regions were persistently demethylated in AS. These 2 regions corresponded with sites defined as promoter regions by Luciferase assay. Taken together, it was suggested that ST8SIA1 gene is regulated by DNA methylation at the promoter regions, leading to the regulation of tumor phenotypes.
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14
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Kuang M, Zhou Z, Lu Z, Shen W, Ge H, Tao X, Zhao Y, Zhuge L, Sun Y, Ji D, Zhang H. Prognostic prediction of lung adenocarcinoma by integrative analysis of RHOH expression and methylation. THE CLINICAL RESPIRATORY JOURNAL 2023; 17:148-156. [PMID: 36710485 PMCID: PMC9978903 DOI: 10.1111/crj.13574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/01/2022] [Accepted: 12/18/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND AND OBJECTIVE The development of epigenetics holds great promise for diagnosis and treatment of lung adenocarcinoma (LUAD). The purpose of this work was to analyze the correlation between Ras Homolog Gene Family Member H (RHOH) expression and methylation in patients with LUAD and its association with survival. METHODS Data related to gene expression, DNA methylation, and clinical features of LUAD from The Cancer Genome Atlas (TCGA) database were analyzed. A total of 50 patients were included in verification group. The methylation level of RHOH in verification group was detected by bisulfite amplicon sequencing. RESULTS The RHOH methylation level in TCGA cohort was significantly and negatively correlated with its expression level (Cor = -0.5, p = 2.687e-33). Patients with hypermethylation and low expression of RHOH had significantly worse prognosis than patients with hypomethylation and low expression of RHOH (TCGA: p = 0.004; validation cohort: p = 0.006, HR: 4.740, 95% CI: 1.567-14.340). CONCLUSION Our research revealed that RHOH may prove to be a new potential prognostic predictor for LUAD patients.
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Affiliation(s)
- Muyu Kuang
- Phase I Clinical Trial Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhenhua Zhou
- Department of Orthopaedic Oncology, Changzheng Hospital, Naval Military Medical University, Shanghai, China
| | - Zhongyuan Lu
- Department of Thoracic Surgery, 903th Hospital of PLA, Hangzhou, China
| | - Weina Shen
- Phase I Clinical Trial Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Haiyan Ge
- Department of Pulmonary Diseases, Huadong Hospital, Shanghai, China
| | - Xiaoting Tao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yue Zhao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lingdun Zhuge
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Dongmei Ji
- Department of Head & Neck tumors and Neuroendocrine tumors, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Huibiao Zhang
- Department of Thoracic Surgery, Huadong Hospital, Shanghai, China
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15
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Fernández-Carrión R, Sorlí JV, Asensio EM, Pascual EC, Portolés O, Alvarez-Sala A, Francès F, Ramírez-Sabio JB, Pérez-Fidalgo A, Villamil LV, Tinahones FJ, Estruch R, Ordovas JM, Coltell O, Corella D. DNA-Methylation Signatures of Tobacco Smoking in a High Cardiovascular Risk Population: Modulation by the Mediterranean Diet. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3635. [PMID: 36834337 PMCID: PMC9964856 DOI: 10.3390/ijerph20043635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Biomarkers based on DNA methylation are relevant in the field of environmental health for precision health. Although tobacco smoking is one of the factors with a strong and consistent impact on DNA methylation, there are very few studies analyzing its methylation signature in southern European populations and none examining its modulation by the Mediterranean diet at the epigenome-wide level. We examined blood methylation smoking signatures on the EPIC 850 K array in this population (n = 414 high cardiovascular risk subjects). Epigenome-wide methylation studies (EWASs) were performed analyzing differential methylation CpG sites by smoking status (never, former, and current smokers) and the modulation by adherence to a Mediterranean diet score was explored. Gene-set enrichment analysis was performed for biological and functional interpretation. The predictive value of the top differentially methylated CpGs was analyzed using receiver operative curves. We characterized the DNA methylation signature of smoking in this Mediterranean population by identifying 46 differentially methylated CpGs at the EWAS level in the whole population. The strongest association was observed at the cg21566642 (p = 2.2 × 10-32) in the 2q37.1 region. We also detected other CpGs that have been consistently reported in prior research and discovered some novel differentially methylated CpG sites in subgroup analyses. In addition, we found distinct methylation profiles based on the adherence to the Mediterranean diet. Particularly, we obtained a significant interaction between smoking and diet modulating the cg5575921 methylation in the AHRR gene. In conclusion, we have characterized biomarkers of the methylation signature of tobacco smoking in this population, and suggest that the Mediterranean diet can increase methylation of certain hypomethylated sites.
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Affiliation(s)
- Rebeca Fernández-Carrión
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - José V. Sorlí
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eva M. Asensio
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Olga Portolés
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Andrea Alvarez-Sala
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Francesc Francès
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Alejandro Pérez-Fidalgo
- Department of Medical Oncology, University Clinic Hospital of Valencia, 46010 Valencia, Spain
- Biomedical Research Networking Centre on Cancer (CIBERONC), Health Institute Carlos III, 28029 Madrid, Spain
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Laura V. Villamil
- Department of Physiology, School of Medicine, University Antonio Nariño, Bogotá 111511, Colombia
| | - Francisco J. Tinahones
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, 29590 Málaga, Spain
| | - Ramon Estruch
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Internal Medicine, Institut d’Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain
| | - Jose M. Ordovas
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
- Nutritional Control of the Epigenome Group, Precision Nutrition and Obesity Program, IMDEA Food, UAM + CSIC, 28049 Madrid, Spain
| | - Oscar Coltell
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain
| | - Dolores Corella
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
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16
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Michaud DS, Chung M, Zhao N, Koestler DC, Lu J, Platz EA, Kelsey KT. Epigenetic age and lung cancer risk in the CLUE II prospective cohort study. Aging (Albany NY) 2023; 15:617-629. [PMID: 36750177 PMCID: PMC9970317 DOI: 10.18632/aging.204501] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/23/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND Epigenetic age, a robust marker of biological aging, has been associated with obesity, low-grade inflammation and metabolic diseases. However, few studies have examined associations between different epigenetic age measures and risk of lung cancer, despite great interest in finding biomarkers to assist in risk stratification for lung cancer screening. METHODS A nested case-control study of lung cancer from the CLUE II cohort study was conducted using incidence density sampling with 1:1 matching of controls to lung cancer cases (n = 208 matched pairs). Prediagnostic blood samples were collected in 1989 (CLUE II study baseline) and stored at -70°C. DNA was extracted from buffy coat and DNA methylation levels were measured using Illumina MethylationEPIC BeadChip Arrays. Three epigenetic age acceleration (i.e., biological age is greater than chronological age) measurements (Horvath, Hannum and PhenoAge) were examined in relation to lung cancer risk using conditional logistic regression. RESULTS We did not observe associations between the three epigenetic age acceleration measurements and risk of lung cancer overall; however, inverse associations for the two Hannum age acceleration measures (intrinsic and extrinsic) were observed in men and among younger participants, but not in women or older participants. We did not observe effect modification by time from blood draw to diagnosis. CONCLUSION Findings from this study do not support a positive association between three different biological age acceleration measures and risk of lung cancer. Additional studies are needed to address whether epigenetic age is associated with lung cancer in never smokers.
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Affiliation(s)
- Dominique S. Michaud
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA 02111, USA
| | - Mei Chung
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA 02111, USA,Division of Nutrition Epidemiology and Data Science, Friedman School of Nutrition, Tufts University, Boston, MA 02111, USA
| | - Naisi Zhao
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA 02111, USA
| | - Devin C. Koestler
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA,University of Kansas Cancer Center, Kansas City, KS 66160, USA
| | - Jiayun Lu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Elizabeth A. Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA,The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
| | - Karl T. Kelsey
- Department of Epidemiology, Brown University, Providence, RI 02903, USA,Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
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17
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Kuśnierczyk P. Genetic differences between smokers and never-smokers with lung cancer. Front Immunol 2023; 14:1063716. [PMID: 36817482 PMCID: PMC9932279 DOI: 10.3389/fimmu.2023.1063716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023] Open
Abstract
Smoking is a major risk factor for lung cancer, therefore lung cancer epidemiological trends reflect the past trends of cigarette smoking to a great extent. The geographic patterns in mortality closely follow those in incidence. Although lung cancer is strongly associated with cigarette smoking, only about 15% of smokers get lung cancer, and also some never-smokers develop this malignancy. Although less frequent, lung cancer in never smokers is the seventh leading cause of cancer deaths in both sexes worldwide. Lung cancer in smokers and never-smokers differs in many aspects: in histological types, environmental factors representing a risk, and in genes associated with this disease. In this review, we will focus on the genetic differences between lung cancer in smokers versus never-smokers: gene expression, germ-line polymorphisms, gene mutations, as well as ethnic and gender differences. Finally, treatment options for smokers and never-smokers will be briefly reviewed.
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Affiliation(s)
- Piotr Kuśnierczyk
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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18
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Zhang G, Wang Z, Song P, Zhan X. DNA and histone modifications as potent diagnostic and therapeutic targets to advance non-small cell lung cancer management from the perspective of 3P medicine. EPMA J 2022; 13:649-669. [PMID: 36505890 PMCID: PMC9727004 DOI: 10.1007/s13167-022-00300-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/11/2022] [Indexed: 12/12/2022]
Abstract
Lung cancer has a very high mortality in females and males. Most (~ 85%) of lung cancers are non-small cell lung cancers (NSCLC). When lung cancer is diagnosed, most of them have either local or distant metastasis, with a poor prognosis. In order to achieve better outcomes, it is imperative to identify the molecular signature based on genetic and epigenetic variations for different NSCLC subgroups. We hypothesize that DNA and histone modifications play significant roles in the framework of predictive, preventive, and personalized medicine (PPPM; 3P medicine). Epigenetics has a significant impact on tumorigenicity, tumor heterogeneity, and tumor resistance to chemotherapy, targeted therapy, and immunotherapy. An increasing interest is that epigenomic regulation is recognized as a potential treatment option for NSCLC. Most attention has been paid to the epigenetic alteration patterns of DNA and histones. This article aims to review the roles DNA and histone modifications play in tumorigenesis, early detection and diagnosis, and advancements and therapies of NSCLC, and also explore the connection between DNA and histone modifications and PPPM, which may provide an important contribution to improve the prognosis of NSCLC. We found that the success of targeting DNA and histone modifications is limited in the clinic, and how to combine the therapies to improve patient outcomes is necessary in further studies, especially for predictive diagnostics, targeted prevention, and personalization of medical services in the 3P medicine approach. It is concluded that DNA and histone modifications are potent diagnostic and therapeutic targets to advance non-small cell lung cancer management from the perspective of 3P medicine.
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Affiliation(s)
- Guodong Zhang
- Thoracic Surgery Department, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Shandong 250117 Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan, Shandong 250117 People’s Republic of China
| | - Zhengdan Wang
- Thoracic Surgery Department, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Shandong 250117 Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan, Shandong 250117 People’s Republic of China
| | - Pingping Song
- Thoracic Surgery Department, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Shandong 250117 Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan, Shandong 250117 People’s Republic of China
| | - Xianquan Zhan
- Thoracic Surgery Department, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Shandong 250117 Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan, Shandong 250117 People’s Republic of China
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19
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Tsuboi Y, Yamada H, Munetsuna E, Fujii R, Yamazaki M, Ando Y, Mizuno G, Hattori Y, Ishikawa H, Ohashi K, Hashimoto S, Hamajima N, Suzuki K. Intake of vegetables and fruits rich in provitamin A is positively associated with aryl hydrocarbon receptor repressor DNA methylation in a Japanese population. Nutr Res 2022; 107:206-217. [PMID: 36334347 DOI: 10.1016/j.nutres.2022.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
DNA methylation can be affected by numerous lifestyle factors, including diet. Tobacco smoking induces aryl hydrocarbon receptor repressor (AHRR) DNA hypomethylation, which increases the risk of lung and other cancers. However, no lifestyle habits that might increase or restore percentage of AHRR DNA methylation have been identified. We hypothesized that dietary intakes of vegetables/fruits and serum carotenoid concentrations are related to AHRR DNA methylation. A total of 813 individuals participated in this cross-sectional study. A food frequency questionnaire was used to assess dietary intake of vegetables and fruits. AHRR DNA methylation in peripheral blood mononuclear cells were measured using pyrosequencing method. In men, dietary fruit intake was significantly and positively associated with AHRR DNA methylation among current smokers (P for trend = .034). A significant positive association of serum provitamin A with AHRR DNA methylation was observed among current smokers (men: standardized β = 0.141 [0.045 to 0.237], women: standardized β = 0.570 [0.153 to 0.990]). However, compared with never smokers with low provitamin A concentrations, percentages of AHRR DNA methylation were much lower among current smokers, even those with high provitamin A concentrations (men: β = -19.1% [-33.8 to -19.8], women: β = -6.0% [-10.2 to -1.7]). Dietary intake of vegetables and fruits rich in provitamin A may increase percentage of AHRR DNA methylation in current smokers. However, although we found a beneficial effect of provitamin A on AHRR DNA methylation, this beneficial effect could not completely remove the effect of smoking on AHRR DNA demethylation.
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Affiliation(s)
- Yoshiki Tsuboi
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan, 470-1192.
| | - Hiroya Yamada
- Department of Hygiene, Fujita Health University School of Medicine, Toyoake, Aichi, Japan, 470-1192.
| | - Eiji Munetsuna
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan, 470-1192.
| | - Ryosuke Fujii
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan, 470-1192.
| | - Mirai Yamazaki
- Department of Medical Technology, Kagawa Prefectural University of Health Sciences, Takamatsu, Kagawa, Japan, 761-0123.
| | - Yoshitaka Ando
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan, 470-1192.
| | - Genki Mizuno
- Department of Medical Technology, Tokyo University of Technology School of Health Sciences, Ota, Tokyo, Japan, 144-8535.
| | - Yuji Hattori
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan, 470-1192.
| | - Hiroaki Ishikawa
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan, 470-1192.
| | - Koji Ohashi
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan, 470-1192.
| | - Shuji Hashimoto
- Department of Hygiene, Fujita Health University School of Medicine, Toyoake, Aichi, Japan, 470-1192.
| | - Nobuyuki Hamajima
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan, 466-8550.
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan, 470-1192.
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20
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Faltus C, Lahnsteiner A, Barrdahl M, Assenov Y, Hüsing A, Bogatyrova O, Laplana M, Johnson T, Muley T, Meister M, Warth A, Thomas M, Plass C, Kaaks R, Risch A. Identification of NHLRC1 as a Novel AKT Activator from a Lung Cancer Epigenome-Wide Association Study (EWAS). Int J Mol Sci 2022; 23:ijms231810699. [PMID: 36142605 PMCID: PMC9505874 DOI: 10.3390/ijms231810699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Changes in DNA methylation identified by epigenome-wide association studies (EWAS) have been recently linked to increased lung cancer risk. However, the cellular effects of these differentially methylated positions (DMPs) are often unclear. Therefore, we investigated top differentially methylated positions identified from an EWAS study. This included a putative regulatory region of NHLRC1. Hypomethylation of this gene was recently linked with decreased survival rates in lung cancer patients. HumanMethylation450 BeadChip array (450K) analysis was performed on 66 lung cancer case-control pairs from the European Prospective Investigation into Cancer and Nutrition Heidelberg lung cancer EWAS (EPIC HD) cohort. DMPs identified in these pre-diagnostic blood samples were then investigated for differential DNA methylation in lung tumor versus adjacent normal lung tissue from The Cancer Genome Atlas (TCGA) and replicated in two independent lung tumor versus adjacent normal tissue replication sets with MassARRAY. The EPIC HD top hypermethylated DMP cg06646708 was found to be a hypomethylated region in multiple data sets of lung tumor versus adjacent normal tissue. Hypomethylation within this region caused increased mRNA transcription of the closest gene NHLRC1 in lung tumors. In functional assays, we demonstrate attenuated proliferation, viability, migration, and invasion upon NHLRC1 knock-down in lung cancer cells. Furthermore, diminished AKT phosphorylation at serine 473 causing expression of pro-apoptotic AKT-repressed genes was detected in these knock-down experiments. In conclusion, this study demonstrates the powerful potential for discovery of novel functional mechanisms in oncogenesis based on EWAS DNA methylation data. NHLRC1 holds promise as a new prognostic biomarker for lung cancer survival and prognosis, as well as a target for novel treatment strategies in lung cancer patients.
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Affiliation(s)
- Christian Faltus
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Angelika Lahnsteiner
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Myrto Barrdahl
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
| | - Yassen Assenov
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
| | - Anika Hüsing
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Olga Bogatyrova
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
| | - Marina Laplana
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, 25198 Lleida, Spain
| | - Theron Johnson
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, University of Heidelberg, 69126 Heidelberg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, University of Heidelberg, 69126 Heidelberg, Germany
| | - Arne Warth
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Michael Thomas
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, University of Heidelberg, 69126 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Angela Risch
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +43-662-8044-7220
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21
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Meng H, Wei W, Li G, Fu M, Wang C, Hong S, Guan X, Bai Y, Feng Y, Zhou Y, Cao Q, Yuan F, He M, Zhang X, Wei S, Li Y, Guo H. Epigenome-wide DNA methylation signature of plasma zinc and their mediation roles in the association of zinc with lung cancer risk. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119563. [PMID: 35654255 DOI: 10.1016/j.envpol.2022.119563] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/17/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Essential trace element zinc is associated with decreased lung cancer risk, but underlying mechanisms remain unclear. This study aimed to investigate role of DNA methylation in zinc-lung cancer association. We conducted a case-cohort study within prospective Dongfeng-Tongji cohort, including 359 incident lung cancer cases and a randomly selected sub-cohort of 1399 participants. Epigenome-wide association study (EWAS) was used to examine association of plasma zinc with DNA methylation in peripheral blood. For the zinc-related CpGs, their mediation effects on zinc-lung cancer association were assessed; their diagnostic performance for lung cancer was testified in the case-cohort study and further validated in another 126 pairs of lung cancer case-control study. We identified 28 CpGs associated with plasma zinc at P < 1.0 × 10-5 and seven of them (cg07077080, cg01077808, cg17749033, cg15554270, cg26125625, cg10669424, and cg15409013 annotated to GSR, CALR3, SLC16A3, PHLPP2, SLC12A8, VGLL4, and ADAMTS16, respectively) were associated with incident risk of lung cancer. Moreover, the above seven CpGs were differently methylated between 126 pairs of lung cancer and adjacent normal lung tissues and had the same directions with EWAS of zinc. They could mediate a separate 7.05%∼22.65% and a joint 29.42% of zinc-lung cancer association. Compared to using traditional factors, addition of methylation risk score exerted improved discriminations for lung cancer both in case-cohort study [area under the curve (AUC) = 0.818 vs. 0.738] and in case-control study (AUC = 0.816 vs. 0.646). Our results provide new insights for the biological role of DNA methylation in the inverse association of zinc with incident lung cancer.
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Affiliation(s)
- Hua Meng
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Wei
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Guyanan Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ming Fu
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chenming Wang
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shiru Hong
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xin Guan
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yansen Bai
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yue Feng
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yuhan Zhou
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qiang Cao
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fangfang Yuan
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meian He
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Sheng Wei
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yangkai Li
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huan Guo
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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22
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Petrovic D, Bodinier B, Dagnino S, Whitaker M, Karimi M, Campanella G, Haugdahl Nøst T, Polidoro S, Palli D, Krogh V, Tumino R, Sacerdote C, Panico S, Lund E, Dugué PA, Giles GG, Severi G, Southey M, Vineis P, Stringhini S, Bochud M, Sandanger TM, Vermeulen RCH, Guida F, Chadeau-Hyam M. Epigenetic mechanisms of lung carcinogenesis involve differentially methylated CpG sites beyond those associated with smoking. Eur J Epidemiol 2022; 37:629-640. [PMID: 35595947 PMCID: PMC9288379 DOI: 10.1007/s10654-022-00877-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/25/2022] [Indexed: 12/24/2022]
Abstract
Smoking-related epigenetic changes have been linked to lung cancer, but the contribution of epigenetic alterations unrelated to smoking remains unclear. We sought for a sparse set of CpG sites predicting lung cancer and explored the role of smoking in these associations. We analysed CpGs in relation to lung cancer in participants from two nested case-control studies, using (LASSO)-penalised regression. We accounted for the effects of smoking using known smoking-related CpGs, and through conditional-independence network. We identified 29 CpGs (8 smoking-related, 21 smoking-unrelated) associated with lung cancer. Models additionally adjusted for Comprehensive Smoking Index-(CSI) selected 1 smoking-related and 49 smoking-unrelated CpGs. Selected CpGs yielded excellent discriminatory performances, outperforming information provided by CSI only. Of the 8 selected smoking-related CpGs, two captured lung cancer-relevant effects of smoking that were missed by CSI. Further, the 50 CpGs identified in the CSI-adjusted model complementarily explained lung cancer risk. These markers may provide further insight into lung cancer carcinogenesis and help improving early identification of high-risk patients.
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Affiliation(s)
- Dusan Petrovic
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
- Department and Division of Primary Care Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Barbara Bodinier
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Sonia Dagnino
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Matthew Whitaker
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Maryam Karimi
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Bureau de Biostatistique et d'Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Oncostat U1018, Inserm, Équipe Labellisée Ligue Contre Le Cancer, Université Paris-Saclay, Villejuif, France
| | - Gianluca Campanella
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Therese Haugdahl Nøst
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute-ISPO, Florence, Italy
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rosario Tumino
- Hyblean Association for Epidemiological Research, AIRE- ONLUS, Ragusa, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology Città Della Salute e della Scienza University-Hospital, Via Santena 7, 10126, Turin, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Eiliv Lund
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- The Norwegian Cancer Registry, Oslo, Norway
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Gianluca Severi
- Centre for Research in Epidemiology and Population Health, Inserm (Institut National de La Sante Et de a Recherche Medicale), Villejuif, France
| | - Melissa Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Australia
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Silvia Stringhini
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
- Department and Division of Primary Care Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Murielle Bochud
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
| | - Torkjel M Sandanger
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Roel C H Vermeulen
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
- Julius Centre for Health Sciences and Primary Care, University Medical Centre, Utrecht, Utrecht, The Netherlands
| | - Florence Guida
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Group of Genetic Epidemiology, International Agency for Research on Cancer (IARC) - World Health Organization (WHO), Lyon, France
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK.
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands.
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Yousefi PD, Suderman M, Langdon R, Whitehurst O, Davey Smith G, Relton CL. DNA methylation-based predictors of health: applications and statistical considerations. Nat Rev Genet 2022; 23:369-383. [PMID: 35304597 DOI: 10.1038/s41576-022-00465-w] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/12/2022]
Abstract
DNA methylation data have become a valuable source of information for biomarker development, because, unlike static genetic risk estimates, DNA methylation varies dynamically in relation to diverse exogenous and endogenous factors, including environmental risk factors and complex disease pathology. Reliable methods for genome-wide measurement at scale have led to the proliferation of epigenome-wide association studies and subsequently to the development of DNA methylation-based predictors across a wide range of health-related applications, from the identification of risk factors or exposures, such as age and smoking, to early detection of disease or progression in cancer, cardiovascular and neurological disease. This Review evaluates the progress of existing DNA methylation-based predictors, including the contribution of machine learning techniques, and assesses the uptake of key statistical best practices needed to ensure their reliable performance, such as data-driven feature selection, elimination of data leakage in performance estimates and use of generalizable, adequately powered training samples.
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Affiliation(s)
- Paul D Yousefi
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Oliver Whitehurst
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK.
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24
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Hoang PH, Landi MT. DNA Methylation in Lung Cancer: Mechanisms and Associations with Histological Subtypes, Molecular Alterations, and Major Epidemiological Factors. Cancers (Basel) 2022; 14:cancers14040961. [PMID: 35205708 PMCID: PMC8870477 DOI: 10.3390/cancers14040961] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the major leading cause of cancer-related mortality worldwide. Multiple epigenetic factors-in particular, DNA methylation-have been associated with the development of lung cancer. In this review, we summarize the current knowledge on DNA methylation alterations in lung tumorigenesis, as well as their associations with different histological subtypes, common cancer driver gene mutations (e.g., KRAS, EGFR, and TP53), and major epidemiological risk factors (e.g., sex, smoking status, race/ethnicity). Understanding the mechanisms of DNA methylation regulation and their associations with various risk factors can provide further insights into carcinogenesis, and create future avenues for prevention and personalized treatments. In addition, we also highlight outstanding questions regarding DNA methylation in lung cancer to be elucidated in future studies.
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25
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Corbin LJ, White SJ, Taylor AE, Williams CM, Taylor K, van den Bosch MT, Teasdale JE, Jones M, Bond M, Harper MT, Falk L, Groom A, Hazell GG, Paternoster L, Munafò MR, Nordestgaard BG, Tybjærg-Hansen A, Bojesen SE, Relton C, Min JL, Davey Smith G, Mumford AD, Poole AW, Timpson NJ. Epigenetic Regulation of F2RL3 Associates With Myocardial Infarction and Platelet Function. Circ Res 2022; 130:384-400. [PMID: 35012325 PMCID: PMC8812435 DOI: 10.1161/circresaha.121.318836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND DNA hypomethylation at the F2RL3 (F2R like thrombin or trypsin receptor 3) locus has been associated with both smoking and atherosclerotic cardiovascular disease; whether these smoking-related associations form a pathway to disease is unknown. F2RL3 encodes protease-activated receptor 4, a potent thrombin receptor expressed on platelets. Given the role of thrombin in platelet activation and the role of thrombus formation in myocardial infarction, alterations to this biological pathway could be important for ischemic cardiovascular disease. METHODS We conducted multiple independent experiments to assess whether DNA hypomethylation at F2RL3 in response to smoking is associated with risk of myocardial infarction via changes to platelet reactivity. Using cohort data (N=3205), we explored the relationship between smoking, DNA hypomethylation at F2RL3, and myocardial infarction. We compared platelet reactivity in individuals with low versus high DNA methylation at F2RL3 (N=41). We used an in vitro model to explore the biological response of F2RL3 to cigarette smoke extract. Finally, a series of reporter constructs were used to investigate how differential methylation could impact F2RL3 gene expression. RESULTS Observationally, DNA methylation at F2RL3 mediated an estimated 34% of the smoking effect on increased risk of myocardial infarction. An association between methylation group (low/high) and platelet reactivity was observed in response to PAR4 (protease-activated receptor 4) stimulation. In cells, cigarette smoke extract exposure was associated with a 4.9% to 9.3% reduction in DNA methylation at F2RL3 and a corresponding 1.7-(95% CI, 1.2-2.4, P=0.04) fold increase in F2RL3 mRNA. Results from reporter assays suggest the exon 2 region of F2RL3 may help control gene expression. CONCLUSIONS Smoking-induced epigenetic DNA hypomethylation at F2RL3 appears to increase PAR4 expression with potential downstream consequences for platelet reactivity. Combined evidence here not only identifies F2RL3 DNA methylation as a possible contributory pathway from smoking to cardiovascular disease risk but from any feature potentially influencing F2RL3 regulation in a similar manner.
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Affiliation(s)
- Laura J. Corbin
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Stephen J. White
- Department of Life Sciences, Manchester Metropolitan University, United Kingdom (S.J.W.)
| | - Amy E. Taylor
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, United Kingdom (A.E.T.)
| | - Christopher M. Williams
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
- School of Physiology, Pharmacology and Neuroscience (C.M.W., M.T.v.d.B., A.W.P.), University of Bristol, United Kingdom
| | - Kurt Taylor
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
- School of Physiology, Pharmacology and Neuroscience (C.M.W., M.T.v.d.B., A.W.P.), University of Bristol, United Kingdom
- Translational Health Sciences, Bristol Medical School (J.E.T., M.J., M.B.), University of Bristol, United Kingdom
- UK Centre for Tobacco and Alcohol Studies and School of Experimental Psychology (M.R.M.), University of Bristol, United Kingdom
- School of Cellular and Molecular Medicine (A.D.M.), University of Bristol, United Kingdom
- Department of Life Sciences, Manchester Metropolitan University, United Kingdom (S.J.W.)
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, United Kingdom (A.E.T.)
- Department of Pharmacology, University of Cambridge, Tennis Court Road (M.T.H., G.G.J.H.)
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital (B.G.N., S.E.B.), Copenhagen University Hospital, Denmark
- The Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H., S.E.B.), Copenhagen University Hospital, Denmark
- Department of Clinical Biochemistry, Rigshospitalet (A.T.-H.), Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H., S.E.B.)
| | - Marion T. van den Bosch
- School of Physiology, Pharmacology and Neuroscience (C.M.W., M.T.v.d.B., A.W.P.), University of Bristol, United Kingdom
| | - Jack E. Teasdale
- Translational Health Sciences, Bristol Medical School (J.E.T., M.J., M.B.), University of Bristol, United Kingdom
| | - Matthew Jones
- Translational Health Sciences, Bristol Medical School (J.E.T., M.J., M.B.), University of Bristol, United Kingdom
| | - Mark Bond
- Translational Health Sciences, Bristol Medical School (J.E.T., M.J., M.B.), University of Bristol, United Kingdom
| | - Matthew T. Harper
- Department of Pharmacology, University of Cambridge, Tennis Court Road (M.T.H., G.G.J.H.)
| | - Louise Falk
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Alix Groom
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Georgina G.J. Hazell
- Department of Pharmacology, University of Cambridge, Tennis Court Road (M.T.H., G.G.J.H.)
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Marcus R. Munafò
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- UK Centre for Tobacco and Alcohol Studies and School of Experimental Psychology (M.R.M.), University of Bristol, United Kingdom
| | - Børge G. Nordestgaard
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital (B.G.N., S.E.B.), Copenhagen University Hospital, Denmark
- The Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H., S.E.B.), Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H., S.E.B.)
| | - Anne Tybjærg-Hansen
- The Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H., S.E.B.), Copenhagen University Hospital, Denmark
- Department of Clinical Biochemistry, Rigshospitalet (A.T.-H.), Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H., S.E.B.)
| | - Stig E. Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital (B.G.N., S.E.B.), Copenhagen University Hospital, Denmark
- The Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H., S.E.B.), Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H., S.E.B.)
| | - Caroline Relton
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Josine L. Min
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Andrew D. Mumford
- School of Cellular and Molecular Medicine (A.D.M.), University of Bristol, United Kingdom
| | - Alastair W. Poole
- School of Physiology, Pharmacology and Neuroscience (C.M.W., M.T.v.d.B., A.W.P.), University of Bristol, United Kingdom
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
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26
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Hao Z, Lin M, Du F, Xin Z, Wu D, Yu Q, Wu Y, Zhu Z, Li W, Chen Y, Chen X, Chai Y, Jin S, Wu P. Systemic Immune Dysregulation Correlates With Clinical Features of Early Non-Small Cell Lung Cancer. Front Immunol 2022; 12:754138. [PMID: 35116020 PMCID: PMC8804248 DOI: 10.3389/fimmu.2021.754138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/20/2021] [Indexed: 12/25/2022] Open
Abstract
Background Systemic immune dysregulation correlates with cancer progression. However, the clinical implications of systemic immune dysregulation in early non-small cell lung cancer (NSCLC) remain unclear. Methods Using a panel of 9 markers to identify 12 parameters in the peripheral blood of 326 patients (34 in the discovery group and 292 in the validation group), we investigated systemic immune dysregulation in early NSCLC. Then, we analyzed the impact of surgery on the systemic immune state of these patients. Finally, we analyzed correlations between systemic immune dysregulation and the clinical features of early NSCLC. Results We found striking systemic immune dysregulation in the peripheral blood of early NSCLC patients. This dysregulation was characterized by a significant decrease in total lymphocytes, T cells, quiescent T cells, CD4+ T cells, and NKT cells. We also observed increased proportions of activated lymphocytes and activated T cells. Systemic immune dysregulation was increased after surgery. Furthermore, systemic immune dysregulation was correlated with multiple clinical features, such as sex, age, smoking history, pathological type, tumor stage, surgical approach, tumor differentiation, and epidermal growth factor receptor (EGFR) mutation. Finally, we observed that systemic immune dysregulation was correlated with complications and systemic inflammatory response syndrome (SIRS) in early NSCLC patients. Conclusions Our results reveal systemic immune dysregulation occurring in early NSCLC and demonstrate the correlation between these dysregulations and clinical features. Our findings suggest that systemic immune dysregulation is involved in cancer development and may be a promising candidate for high-risk screening and treatment strategies for early NSCLC.
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Affiliation(s)
- Zhixing Hao
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Mingjie Lin
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Feng Du
- Department of Thoracic Surgery, Yuhang Branch of The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhongwei Xin
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Dang Wu
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- Department of Oncology Radiotherapy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Qun Yu
- Fourth Ward of Neurosurgery, Division of Nursing, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Yimin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhouyu Zhu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Wenshan Li
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongyuan Chen
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoke Chen
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Ying Chai
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Shenghang Jin
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Pin Wu, ; Shenghang Jin,
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Pin Wu, ; Shenghang Jin,
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Michaud DS, Kelsey KT. DNA Methylation in Peripheral Blood: Providing Novel Biomarkers of Exposure and Immunity to Examine Cancer Risk. Cancer Epidemiol Biomarkers Prev 2021; 30:2176-2178. [PMID: 34862269 DOI: 10.1158/1055-9965.epi-21-0866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/11/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
DNA methylation is an epigenetic phenomenon that can alter and control gene expression. Because methylation plays a key role in cell differentiation, methylation markers have been identified that are unique to a given cell type; these markers are stable and can be measured in tissue or whole blood. The article by Katzke and colleagues, published in this issue, uses methylation markers to estimate proportions of immune cell subtypes in peripheral blood samples that were collected prior to diagnosis, thus allowing them to directly examine associations with pancreatic cancer risk. Given that immune-cell counts cannot be measured from archived blood, and that retrospective case-control studies rely on blood that is collected after cancer diagnosis, few studies have been able to examine the role of the systemic immune response in cancer risk. Measurement of DNA methylation in peripheral blood, primarily through development of whole-genome approaches, has also opened new doors to examining cancer etiology.See related article by Katzke et al., p. 2179.
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Affiliation(s)
- Dominique S Michaud
- Department of Public Health & Community Medicine, Tufts University School of Medicine, Tufts University, Boston, Massachusetts.
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, Rhode Island.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
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Qiao R, Zhong R, Liu C, Di F, Zhang Z, Wang L, Xu T, Wang Y, Dai L, Gu W, Han B, Yang R. Novel blood-based hypomethylation of SH3BP5 is associated with very early-stage lung adenocarcinoma. Genes Genomics 2021; 44:445-453. [PMID: 34783986 DOI: 10.1007/s13258-021-01190-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/08/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Early detection is essential to improve the survival of lung cancer (LC). The quantitative measurement of specific DNA methylation changes in the peripheral blood could provide an efficient strategy for the detection of early cancer. OBJECTIVE We applied a candidate approach and assess the association between blood-based SH3BP5 methylation and the risk of lung adenocarcinoma (LUAD) in a case-control cohort. METHODS The methylation level of four CpG sites in the promoter of SH3BP5 gene was quantitatively determined by mass spectrometry in 171 very early-stage LUAD patients (93.6% LUAD at stage I) and 190 age and gender-matched controls. The logistic regression and non-parametric tests were used for the statistical analyses. RESULTS We observed a significant association between decreased methylation of SH3BP5_CpG_4 in the peripheral blood and increased risk of LUAD (odds ratio (OR) per-10% methylation = 1.51, P = 0.006, FDR = 0.024), and even for the LUAD at stage I (OR per-10% methylation = 1.53, P = 0.006, FDR = 0.024). Moreover, the lower quartile of SH3BP5_CpG_4 methylation was correlated with increased risk for LUAD with a P trend of 0.011. Further investigation disclosed that the hypomethylation of SH3BP5_CpG_4 was mostly associated with LUAD in younger subjects (OR per-10% methylation = 2.02, P = 0.010, age < 55 years old) and probably could be enhanced by advance stage. CONCLUSION Our study revealed an association between blood-based SH3BP5 hypomethylation and very early-stage LUAD, which provides a novel support for the blood-based methylation signatures as a potential marker for the evaluation of cancer risk.
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Affiliation(s)
- Rong Qiao
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Runbo Zhong
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Chunlan Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 210000, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Zheng Zhang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Ling Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Yue Wang
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Baohui Han
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China.
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 210000, China. .,Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China.
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29
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Sun YQ, Richmond RC, Suderman M, Min JL, Battram T, Flatberg A, Beisvag V, Nøst TH, Guida F, Jiang L, Wahl SGF, Langhammer A, Skorpen F, Walker RM, Bretherick AD, Zeng Y, Chen Y, Johansson M, Sandanger TM, Relton CL, Mai XM. Assessing the role of genome-wide DNA methylation between smoking and risk of lung cancer using repeated measurements: the HUNT study. Int J Epidemiol 2021; 50:1482-1497. [PMID: 33729499 PMCID: PMC8580278 DOI: 10.1093/ije/dyab044] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/18/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND It is unclear if smoking-related DNA methylation represents a causal pathway between smoking and risk of lung cancer. We sought to identify novel smoking-related DNA methylation sites in blood, with repeated measurements, and to appraise the putative role of DNA methylation in the pathway between smoking and lung cancer development. METHODS We derived a nested case-control study from the Trøndelag Health Study (HUNT), including 140 incident patients who developed lung cancer during 2009-13 and 140 controls. We profiled 850 K DNA methylation sites (Illumina Infinium EPIC array) in DNA extracted from blood that was collected in HUNT2 (1995-97) and HUNT3 (2006-08) for the same individuals. Epigenome-wide association studies (EWAS) were performed for a detailed smoking phenotype and for lung cancer. Two-step Mendelian randomization (MR) analyses were performed to assess the potential causal effect of smoking on DNA methylation as well as of DNA methylation (13 sites as putative mediators) on risk of lung cancer. RESULTS The EWAS for smoking in HUNT2 identified associations at 76 DNA methylation sites (P < 5 × 10-8), including 16 novel sites. Smoking was associated with DNA hypomethylation in a dose-response relationship among 83% of the 76 sites, which was confirmed by analyses using repeated measurements from blood that was collected at 11 years apart for the same individuals. Two-step MR analyses showed evidence for a causal effect of smoking on DNA methylation but no evidence for a causal link between DNA methylation and the risk of lung cancer. CONCLUSIONS DNA methylation modifications in blood did not seem to represent a causal pathway linking smoking and the lung cancer risk.
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Affiliation(s)
- Yi-Qian Sun
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Pathology, Clinic of Laboratory Medicine, St Olav’s University Hospital, Trondheim, Norway
- Center for Oral Health Services and Research Mid-Norway (TkMidt), Trondheim, Norway
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Thomas Battram
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Arnar Flatberg
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Central Administration, St Olav’s University Hospital, Trondheim, Norway
| | - Vidar Beisvag
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Central Administration, St Olav’s University Hospital, Trondheim, Norway
| | - Therese Haugdahl Nøst
- Department of Community Medicine, Faculty of Health Sciences, Arctic University of Norway, Tromsø, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Florence Guida
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Lin Jiang
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sissel Gyrid Freim Wahl
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Pathology, Clinic of Laboratory Medicine, St Olav’s University Hospital, Trondheim, Norway
| | - Arnulf Langhammer
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Frank Skorpen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Yanni Zeng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Yue Chen
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Mattias Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Torkjel M Sandanger
- Department of Community Medicine, Faculty of Health Sciences, Arctic University of Norway, Tromsø, Norway
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Xiao-Mei Mai
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
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Abstract
Substance use disorders (SUDs) are conditions in which the use of legal or illegal substances, such as nicotine, alcohol or opioids, results in clinical and functional impairment. SUDs and, more generally, substance use are genetically complex traits that are enormously costly on an individual and societal basis. The past few years have seen remarkable progress in our understanding of the genetics, and therefore the biology, of substance use and abuse. Various studies - including of well-defined phenotypes in deeply phenotyped samples, as well as broadly defined phenotypes in meta-analysis and biobank samples - have revealed multiple risk loci for these common traits. A key emerging insight from this work establishes a biological and genetic distinction between quantity and/or frequency measures of substance use (which may involve low levels of use without dependence), versus symptoms related to physical dependence.
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31
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Qiao R, Li M, Zhong R, Wei Y, Wang J, Zhang Z, Wang L, Xu T, Wang Y, Dai L, Gu W, Han B, Yang R. The Association Between PNPLA2 Methylation in Peripheral Blood and Early-Stage Lung Cancer in a Case-Control Study. Cancer Manag Res 2021; 13:7919-7927. [PMID: 34703313 PMCID: PMC8526517 DOI: 10.2147/cmar.s329629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/20/2021] [Indexed: 01/06/2023] Open
Abstract
Purpose Lung cancer (LC) brings great burden to the society worldwide. Exploring novel biomarkers in vitro for the early detection of LC would be of great importance. Patients and Methods We measured DNA methylation levels of 21 CpG sites within Patatin-like phospholipase domain containing 2 (PNPLA2) gene in the peripheral blood of 168 early-stage LC cases (94.0% LC at stage I) and 187 age- and gender-matched cancer-free controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using logistic regression adjusted for covariates. Non-parametric tests were applied for the comparisons of stratified groups. Results Hypomethylation of PNPLA2_CpG_8,10 and hypermethylation of PNPLA2_CpG_9 were correlated to the early-stage LC with the ORs of 1.44 (95% CI: 1.06–1.96, P = 0.018) and 0.82 (95% CI: 0.69–0.98, P = 0.029), respectively. The associations were still significant for the very early-stage LC patients (stage I). Further gender- and age-stratified analyses indicated that the association between hypomethylation of PNPLA2_CpG_8,10 and LC existed only in females and in subjects younger than 55 years. In addition, the association between LC and hypermethylation of PNPLA2_CpG_6 and PNPLA2_CpG_9 was also observed in the younger population. Conclusion Taken together, our study has proved the hypothesis that the altered methylation in the peripheral blood may be correlated with the burden of cancer at an early stage. Here, we find a novel association between blood-based aberrant PNPLA2 methylation and LC at a very early stage and particularly for women at a younger age.
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Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, People's Republic of China
| | - Mengxia Li
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Runbo Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, People's Republic of China
| | - Yujie Wei
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, People's Republic of China
| | - Jun Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, People's Republic of China
| | - Zheng Zhang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, People's Republic of China
| | - Ling Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, People's Republic of China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, People's Republic of China
| | - Yue Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, People's Republic of China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, People's Republic of China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, People's Republic of China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China.,Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, People's Republic of China
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32
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Yu C, Dugué PA, Dowty JG, Hammet F, Joo JE, Wong EM, Hosseinpour M, Giles GG, Hopper JL, Nguyen-Dumont T, MacInnis RJ, Southey MC. Repeatability of methylation measures using a QIAseq targeted methyl panel and comparison with the Illumina HumanMethylation450 assay. BMC Res Notes 2021; 14:394. [PMID: 34689793 PMCID: PMC8543877 DOI: 10.1186/s13104-021-05809-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE In previous studies using Illumina Infinium methylation arrays, we have identified DNA methylation marks associated with cancer predisposition and progression. In the present study, we have sought to find appropriate technology to both technically validate our data and expand our understanding of DNA methylation in these genomic regions. Here, we aimed to assess the repeatability of methylation measures made using QIAseq targeted methyl panel and to compare them with those obtained from the Illumina HumanMethylation450 (HM450K) assay. We included in the analysis high molecular weight DNA extracted from whole blood (WB) and DNA extracted from formalin-fixed paraffin-embedded tissues (FFPE). RESULTS The repeatability of QIAseq-methylation measures was assessed at 40 CpGs, using the Intraclass Correlation Coefficient (ICC). The mean ICCs and 95% confidence intervals (CI) were 0.72 (0.62-0.81), 0.59 (0.47-0.71) and 0.80 (0.73-0.88) for WB, FFPE and both sample types combined, respectively. For technical replicates measured using QIAseq and HM450K, the mean ICCs (95% CI) were 0.53 (0.39-0.68), 0.43 (0.31-0.56) and 0.70 (0.59-0.80), respectively. Bland-Altman plots indicated good agreement between QIAseq and HM450K measurements. These results demonstrate that the QIAseq targeted methyl panel produces reliable and reproducible methylation measurements across the 40 CpGs that were examined.
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Affiliation(s)
- Chenglong Yu
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Fleur Hammet
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - JiHoon E Joo
- Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Mahnaz Hosseinpour
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
- Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
| | - Robert J MacInnis
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia.
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia.
- Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia.
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Liang R, Li X, Li W, Zhu X, Li C. DNA methylation in lung cancer patients: Opening a "window of life" under precision medicine. Biomed Pharmacother 2021; 144:112202. [PMID: 34654591 DOI: 10.1016/j.biopha.2021.112202] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is a work of adding a methyl group to the 5th carbon atom of cytosine in DNA sequence under the catalysis of DNA methyltransferase (DNMT) to produce 5-methyl cytosine. Some current studies have elucidated the mechanism of lung cancer occurrence and causes of lung cancer progression and metastasis from the perspective of DNA methylation. Moreover, many studies have shown that smoking can change the methylation status of some gene loci, leading to the occurrence of lung cancer, especially central lung cancer. This review mainly introduces the role of DNA methylation in the pathogenesis, early diagnosis and screening, progression and metastasis, treatment, and prognosis of lung cancer, as well as the latest progress. We point out that methylation markers, sample tests, and methylation detection limit the clinical application of DNA methylation. If the liquid biopsy is to become the main force in lung cancer diagnosis, it must make efficient use of limited samples and improve the sensitivity and specificity of the tests. In addition, we also put forward our views on the future development direction of DNA methylation.
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Affiliation(s)
- Runzhang Liang
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou 310053, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang 524023, China
| | - Xiaosong Li
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Weiquan Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang 524023, China
| | - Xiao Zhu
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou 310053, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang 524023, China.
| | - Chen Li
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, Berlin 14195, Germany.
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34
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Yu C, Jordahl KM, Bassett JK, Joo JE, Wong EM, Brinkman MT, Schmidt DF, Bolton DM, Makalic E, Brasky TM, Shadyab AH, Tinker LF, Longano A, Hopper JL, English DR, Milne RL, Bhatti P, Southey MC, Giles GG, Dugué PA. Smoking Methylation Marks for Prediction of Urothelial Cancer Risk. Cancer Epidemiol Biomarkers Prev 2021; 30:2197-2206. [PMID: 34526299 DOI: 10.1158/1055-9965.epi-21-0313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/22/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Self-reported information may not accurately capture smoking exposure. We aimed to evaluate whether smoking-associated DNA methylation markers improve urothelial cell carcinoma (UCC) risk prediction. METHODS Conditional logistic regression was used to assess associations between blood-based methylation and UCC risk using two matched case-control samples: 404 pairs from the Melbourne Collaborative Cohort Study (MCCS) and 440 pairs from the Women's Health Initiative (WHI) cohort. Results were pooled using fixed-effects meta-analysis. We developed methylation-based predictors of UCC and evaluated their prediction accuracy on two replication data sets using the area under the curve (AUC). RESULTS The meta-analysis identified associations (P < 4.7 × 10-5) for 29 of 1,061 smoking-associated methylation sites, but these were substantially attenuated after adjustment for self-reported smoking. Nominally significant associations (P < 0.05) were found for 387 (36%) and 86 (8%) of smoking-associated markers without/with adjustment for self-reported smoking, respectively, with same direction of association as with smoking for 387 (100%) and 79 (92%) markers. A Lasso-based predictor was associated with UCC risk in one replication data set in MCCS [N = 134; odds ratio per SD (OR) = 1.37; 95% CI, 1.00-1.90] after confounder adjustment; AUC = 0.66, compared with AUC = 0.64 without methylation information. Limited evidence of replication was found in the second testing data set in WHI (N = 440; OR = 1.09; 95% CI, 0.91-1.30). CONCLUSIONS Combination of smoking-associated methylation marks may provide some improvement to UCC risk prediction. Our findings need further evaluation using larger data sets. IMPACT DNA methylation may be associated with UCC risk beyond traditional smoking assessment and could contribute to some improvements in stratification of UCC risk in the general population.
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Affiliation(s)
- Chenglong Yu
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Kristina M Jordahl
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - Julie K Bassett
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Jihoon Eric Joo
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Maree T Brinkman
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia.,Department of Data Science & AI, Faculty of IT, Monash University, Clayton, Victoria, Australia
| | - Damien M Bolton
- Department of Surgery, University of Melbourne and Olivia Newton-John Cancer Centre, Austin Hospital, Melbourne, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Theodore M Brasky
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, California
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Anthony Longano
- Department of Anatomical Pathology, Eastern Health, Box Hill Hospital, Box Hill, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Roger L Milne
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia. .,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
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35
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Schamschula E, Lahnsteiner A, Assenov Y, Hagmann W, Zaborsky N, Wiederstein M, Strobl A, Stanke F, Muley T, Plass C, Tümmler B, Risch A. Disease-related blood-based differential methylation in cystic fibrosis and its representation in lung cancer revealed a regulatory locus in PKP3 in lung epithelial cells. Epigenetics 2021; 17:837-860. [PMID: 34415821 PMCID: PMC9423854 DOI: 10.1080/15592294.2021.1959976] [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] [Indexed: 12/24/2022] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease, characterized by massive chronic lung inflammation. The observed variability in clinical phenotypes in monozygotic CF twins is likely associated with the extent of inflammation. This study sought to investigate inflammation-related aberrant DNA methylation in CF twins and to determine to what extent acquired methylation changes may be associated with lung cancer. Blood-based genome-wide DNA methylation analysis was performed to compare the DNA methylomes of monozygotic twins, from the European CF Twin and Sibling Study with various degrees of disease severity. Putatively inflammation-related and differentially methylated positions were selected from a large lung cancer case-control study and investigated in blood by targeted bisulphite next-generation-sequencing. An inflammation-related locus located in the Plakophilin-3 (PKP3) gene was functionally analysed regarding promoter and enhancer activity in presence and absence of methylation using luciferase reporter assays. We confirmed in a unique cohort that monozygotic twins, even if clinically discordant, have only minor differences in global DNA methylation patterns and blood cell composition. Further, we determined the most differentially methylated positions, a high proportion of which are blood cell-type-specific, whereas others may be acquired and thus have potential relevance in the context of inflammation as lung cancer risk factors. We identified a sequence in the gene body of PKP3 which is hypermethylated in blood from CF twins with severe phenotype and highly variably methylated in lung cancer patients and controls, independent of known clinical parameters, and showed that this region exhibits methylation-dependent promoter activity in lung epithelial cells.
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Affiliation(s)
| | | | - Yassen Assenov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Hagmann
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria.,Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Anna Strobl
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Frauke Stanke
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology and NeonatologyClinic for Pediatric Pneumology, Allergology and Neonatology, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik Heidelberg, University of Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Burkhard Tümmler
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology and NeonatologyClinic for Pediatric Pneumology, Allergology and Neonatology, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Angela Risch
- Department of Biosciences, University of Salzburg, Salzburg, Austria.,Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Cancer Cluster Salzburg, Salzburg, Austria.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
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36
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Meng H, Li G, Wei W, Bai Y, Feng Y, Fu M, Guan X, Li M, Li H, Wang C, Jie J, Wu X, He M, Zhang X, Wei S, Li Y, Guo H. Epigenome-wide DNA methylation signature of benzo[a]pyrene exposure and their mediation roles in benzo[a]pyrene-associated lung cancer development. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125839. [PMID: 33887567 DOI: 10.1016/j.jhazmat.2021.125839] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Benzo[a]pyrene (B[a]P) is a typical carcinogen associated with increased lung cancer risk, but the underlying mechanisms remain unclear. This study aimed to investigate epigenome-wide DNA methylation associated with B[a]P exposure and their mediation effects on B[a]P-lung cancer association in two lung cancer case-control studies of 462 subjects. Their plasma levels of benzo[a]pyrene diol epoxide-albumin (BPDE-Alb) adducts and genome-wide DNA methylations were separately detected in peripheral blood by using enzyme-linked immunosorbent assay (ELISA) and genome-wide methylation arrays. The epigenome-wide meta-analysis was performed to analyze the associations between BPDE-Alb adducts and DNA methylations. Mediation analysis was applied to assess effect of DNA methylation on the B[a]P-lung cancer association. We identified 15 CpGs associated with BPDE-Alb adducts (P-meta < 1.0 × 10-5), among which the methylation levels at five loci (cg06245338, cg24256211, cg15107887, cg02211741, and cg04354393 annotated to UBE2O, SAMD4A, ACBD6, DGKZ, and SLFN13, respectively) mediated a separate 38.5%, 29.2%, 41.5%, 47.7%, 56.5%, and a joint 58.2% of the association between BPDE-Alb adducts and lung cancer risk. Compared to the traditional factors [area under the curve (AUC) = 0.788], addition of these CpGs exerted improved discriminations for lung cancer, with AUC ranging 0.828-0.861. Our results highlight DNA methylation alterations as potential mediators in lung tumorigenesis induced by B[a]P exposure.
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Affiliation(s)
- Hua Meng
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guyanan Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Wei
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yansen Bai
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yue Feng
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ming Fu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xin Guan
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mengying Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hang Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chenming Wang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiali Jie
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiulong Wu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meian He
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Sheng Wei
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yangkai Li
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huan Guo
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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37
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Ponzi E, Thoresen M, Haugdahl Nøst T, Møllersen K. Integrative, multi-omics, analysis of blood samples improves model predictions: applications to cancer. BMC Bioinformatics 2021; 22:395. [PMID: 34353282 PMCID: PMC8340537 DOI: 10.1186/s12859-021-04296-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 07/08/2021] [Indexed: 12/04/2022] Open
Abstract
Background Cancer genomic studies often include data collected from several omics platforms. Each omics data source contributes to the understanding of the underlying biological process via source specific (“individual”) patterns of variability. At the same time, statistical associations and potential interactions among the different data sources can reveal signals from common biological processes that might not be identified by single source analyses. These common patterns of variability are referred to as “shared” or “joint”. In this work, we show how the use of joint and individual components can lead to better predictive models, and to a deeper understanding of the biological process at hand. We identify joint and individual contributions of DNA methylation, miRNA and mRNA expression collected from blood samples in a lung cancer case–control study nested within the Norwegian Women and Cancer (NOWAC) cohort study, and we use such components to build prediction models for case–control and metastatic status. To assess the quality of predictions, we compare models based on simultaneous, integrative analysis of multi-source omics data to a standard non-integrative analysis of each single omics dataset, and to penalized regression models. Additionally, we apply the proposed approach to a breast cancer dataset from The Cancer Genome Atlas. Results Our results show how an integrative analysis that preserves both components of variation is more appropriate than standard multi-omics analyses that are not based on such a distinction. Both joint and individual components are shown to contribute to a better quality of model predictions, and facilitate the interpretation of the underlying biological processes in lung cancer development. Conclusions In the presence of multiple omics data sources, we recommend the use of data integration techniques that preserve the joint and individual components across the omics sources. We show how the inclusion of such components increases the quality of model predictions of clinical outcomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04296-0.
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Affiliation(s)
- Erica Ponzi
- Oslo Center for Biostatistics and Epidemiology, UiO, University of Oslo, Oslo, Norway.
| | - Magne Thoresen
- Oslo Center for Biostatistics and Epidemiology, UiO, University of Oslo, Oslo, Norway
| | - Therese Haugdahl Nøst
- Department of Community Medicine, UiT, The Arctic University of Norway, Tromsö, Norway
| | - Kajsa Møllersen
- Department of Community Medicine, UiT, The Arctic University of Norway, Tromsö, Norway
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38
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Salas LA, Lundgren SN, Browne EP, Punska EC, Anderton DL, Karagas MR, Arcaro KF, Christensen BC. Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer. Hum Mol Genet 2021; 29:662-673. [PMID: 31943067 PMCID: PMC7068171 DOI: 10.1093/hmg/ddz301] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/30/2019] [Accepted: 12/06/2019] [Indexed: 12/16/2022] Open
Abstract
Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis, we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts. DNA methylation was assessed using Illumina HumanMethylation450k in 87 breast milk samples. Through an epigenome-wide association study we explored CpG sites associated with a breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer using linear mixed effects models adjusted for history of breast biopsy, age, RefFreeCellMix cell estimates, time of delivery, array chip and subject as random effect. We identified 58 differentially methylated CpG sites associated with a subsequent breast cancer diagnosis (q-value <0.05). Nearly all CpG sites associated with a breast cancer diagnosis were hypomethylated in cases compared with controls and were enriched for CpG islands. In addition, inferred repeat element methylation was lower in breast milk DNA from cases compared to controls, and cases exhibited increased estimated epigenetic mitotic tick rate as well as DNA methylation age compared with controls. Breast milk has utility as a biospecimen for prospective assessment of disease risk, for understanding the underlying molecular basis of breast cancer risk factors and improving primary and secondary prevention of breast cancer.
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Affiliation(s)
- Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA.,The Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Hanover, NH 03766, USA
| | - Sara N Lundgren
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA.,The Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Hanover, NH 03766, USA
| | - Eva P Browne
- Department of Veterinary & Animal Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Elizabeth C Punska
- Department of Veterinary & Animal Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Douglas L Anderton
- Department of Sociology, University of South Carolina, Columbus, SC 29208, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA.,The Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Hanover, NH 03766, USA
| | - Kathleen F Arcaro
- Department of Veterinary & Animal Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA
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39
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Dugué PA, Hodge AM, Wong EM, Joo JE, Jung CH, Hopper JL, English DR, Giles GG, Milne RL, Southey MC. Methylation marks of prenatal exposure to maternal smoking and risk of cancer in adulthood. Int J Epidemiol 2021; 50:105-115. [PMID: 33169152 DOI: 10.1093/ije/dyaa210] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Prenatal exposure to maternal smoking is detrimental to child health but its association with risk of cancer has seldom been investigated. Maternal smoking induces widespread and long-lasting DNA methylation changes, which we study here for association with risk of cancer in adulthood. METHODS Eight prospective case-control studies nested within the Melbourne Collaborative Cohort Study were used to assess associations between maternal-smoking-associated methylation marks in blood and risk of several cancers: breast (n = 406 cases), colorectal (n = 814), gastric (n = 166), kidney (n = 139), lung (n = 327), prostate (n = 847) and urothelial (n = 404) cancer and B-cell lymphoma (n = 426). We used conditional logistic regression models to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for associations between cancer and five methylation scores calculated as weighted averages for 568, 19, 15, 28 and 17 CpG sites. Models were adjusted for confounders, including personal smoking history (smoking status, pack-years, age at starting and quitting) and methylation scores for personal smoking. RESULTS All methylation scores for maternal smoking were strongly positively associated with risk of urothelial cancer. Risk estimates were only slightly attenuated after adjustment for smoking history, other potential confounders and methylation scores for personal smoking. Potential negative associations were observed with risk of lung cancer and B-cell lymphoma. No associations were observed for other cancers. CONCLUSIONS We found that methylation marks of prenatal exposure to maternal smoking are associated with increased risk of urothelial cancer. Our study demonstrates the potential for using DNA methylation to investigate the impact of early-life, unmeasured exposures on later-life cancer risk.
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Affiliation(s)
- Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Allison M Hodge
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - JiHoon E Joo
- Department of Clinical Pathology, Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, The University of Melbourne, Parkville, VIC, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, The University of Melbourne, Parkville VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Roger L Milne
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
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40
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Zhao N, Ruan M, Koestler DC, Lu J, Marsit CJ, Kelsey KT, Platz EA, Michaud DS. Epigenome-wide scan identifies differentially methylated regions for lung cancer using pre-diagnostic peripheral blood. Epigenetics 2021; 17:460-472. [PMID: 34008478 DOI: 10.1080/15592294.2021.1923615] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
BACKGROUND DNA methylation markers have been associated with lung cancer risk and may identify aetiologically relevant genomic regions, or alternatively, be markers of disease risk factors or biological processes associated with disease development. METHODS In a nested case-control study, we measured blood leukocyte DNA methylation levels in pre-diagnostic samples collected from 430 participants (208 cases; 222 controls) in the 1989 CLUE II cohort. We compared DNA methylation levels with case/control status to identify novel genomic regions, both single CpG sites and differentially methylated regions (DMRs), while controlling for known DNA methylation changes associated with smoking using a previously described pack-years-based smoking methylation score. Stratification analyses were conducted over time from blood draw to diagnosis, histology, and smoking status. RESULTS We identified 16 single CpG sites and 40 DMRs significantly associated with lung cancer risk (q < 0.05). The identified genomic regions were associated with genes including H19, HOXA3/HOXA4, RUNX3, BRICD5, PLXNB2, and RP13. For the single CpG sites, the strongest association was noted for cg09736286 in the DIABLO gene (OR [for 1 SD] = 2.99, 95% CI: 1.95-4.59, P-value = 4.81 × 10-7). We found that CpG sites in the HOXA3/HOXA4 region were hypermethylated in cases compared to controls. CONCLUSION The single CpG sites and DMRs that we identified represented significant measurable differences in lung cancer risk, providing potential biomarkers for lung cancer risk stratification. Future studies will need to examine whether these regions are causally related to lung cancer.
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Affiliation(s)
- Naisi Zhao
- Department of Public Health & Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA, USA
| | - Mengyuan Ruan
- Department of Public Health & Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA, USA
| | - Devin C Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jiayun Lu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Carmen J Marsit
- Department of Environmental Health and Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA.,Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Dominique S Michaud
- Department of Public Health & Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA, USA.,Department of Epidemiology, Brown University, Providence, RI, USA
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41
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Jiang W, Wu H, Yu X, Wang Y, Gu W, Wei W, Li B, Jiang X, Wang Y, Hou W, Dong Q, Yan X, Li Y, Sun C, Han T. Third-hand smoke exposure is associated with abnormal serum melatonin level via hypomethylation of CYP1A2 promoter: Evidence from human and animal studies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116669. [PMID: 33652180 DOI: 10.1016/j.envpol.2021.116669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 01/08/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to examine whether and how third-hand smoke (THS) exposure would influence serum melatonin level. 1083 participants with or without exposure to THS were enrolled. Serum ROS, SOD, GSH-Px, and melatonin were measured by ELISA. Methylation microarrays detection and WGCNA were performed to identify hub methylated-sites. The methylation levels of hub-sites were validated in addtional samples. Moreover, mice were exposed to THS for 6 months mimicking exposure of human and the serum, liver, and pineal were collected. Oxidative stress-related indicators in serum, pineal, and liver were measured by ELISA. The expressions of mRNA and protein and methylation levels of hub-gene discovered in human data were further explored by RT-PCR, western-blot, and TBS. The results showed the participants exposed to THS had lower melatonin-level. 820 differentially methylated sites associated with THS were identified. And the hub-site located on the CYP1A2 promoter was identified, which mediated the association between THS and decreased melatonin-level. Decreased peak of serum melatonin, increased ROS and reduced SOD and GSH-Px in pineal and liver, and elevated CYP1A2 expression in liver was also found in the THS-exposed mice. Hypo-methylation of 7 CPG sites on the CYP1A2 promoter was identified, which accelerated the catabolism of melatonin. Overall, THS exposure is associated with abnormal melatonin catabolism through hypo-methylation of CYP1A2-promoter.
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Affiliation(s)
- Wenbo Jiang
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Huanyu Wu
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Xinyang Yu
- Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Wenbo Gu
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Wei Wei
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Bai Li
- University of Ottawa, Ottawa K1N 6N5, Canada
| | - XiTao Jiang
- IT and Environment, College of Engineering, Charles Darwin University, Darwin, Northern Territory 0810, Australia
| | - Yue Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Wanying Hou
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Qiuying Dong
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Xuemin Yan
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Ying Li
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Changhao Sun
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Tianshu Han
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China.
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42
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Nøst TH, Holden M, Dønnem T, Bøvelstad H, Rylander C, Lund E, Sandanger TM. Transcriptomic signals in blood prior to lung cancer focusing on time to diagnosis and metastasis. Sci Rep 2021; 11:7406. [PMID: 33795786 PMCID: PMC8017014 DOI: 10.1038/s41598-021-86879-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/02/2021] [Indexed: 12/21/2022] Open
Abstract
Recent studies have indicated that there are functional genomic signals that can be detected in blood years before cancer diagnosis. This study aimed to assess gene expression in prospective blood samples from the Norwegian Women and Cancer cohort focusing on time to lung cancer diagnosis and metastatic cancer using a nested case–control design. We employed several approaches to statistically analyze the data and the methods indicated that the case–control differences were subtle but most distinguishable in metastatic case–control pairs in the period 0–3 years prior to diagnosis. The genes of interest along with estimated blood cell populations could indicate disruption of immunological processes in blood. The genes identified from approaches focusing on alterations with time to diagnosis were distinct from those focusing on the case–control differences. Our results support that explorative analyses of prospective blood samples could indicate circulating signals of disease-related processes.
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Affiliation(s)
- Therese H Nøst
- Department of Community Medicine, UiT - The Arctic University of Norway, Langnes, P.O. Box 6050, 9037, Tromsø, Norway.
| | | | - Tom Dønnem
- Department of Oncology, University Hospital of Northern Norway, Tromsø, Norway.,Department of Clinical Medicine, UiT - The Artic University of Norway, Tromsø, Norway
| | - Hege Bøvelstad
- Department of Child Health and Development, Norwegian Institute of Public Health, Oslo, Norway
| | - Charlotta Rylander
- Department of Community Medicine, UiT - The Arctic University of Norway, Langnes, P.O. Box 6050, 9037, Tromsø, Norway
| | - Eiliv Lund
- Department of Community Medicine, UiT - The Arctic University of Norway, Langnes, P.O. Box 6050, 9037, Tromsø, Norway.,Department of Research, Institute of Population-Based Cancer Research, Cancer Registry of Norway, Oslo, Norway
| | - Torkjel M Sandanger
- Department of Community Medicine, UiT - The Arctic University of Norway, Langnes, P.O. Box 6050, 9037, Tromsø, Norway
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Dugué PA, Bassett JK, Wong EM, Joo JE, Li S, Yu C, Schmidt DF, Makalic E, Doo NW, Buchanan DD, Hodge AM, English DR, Hopper JL, Giles GG, Southey MC, Milne RL. Biological Aging Measures Based on Blood DNA Methylation and Risk of Cancer: A Prospective Study. JNCI Cancer Spectr 2021; 5:pkaa109. [PMID: 33442664 PMCID: PMC7791618 DOI: 10.1093/jncics/pkaa109] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 09/16/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
Background We previously investigated the association between 5 "first-generation" measures of epigenetic aging and cancer risk in the Melbourne Collaborative Cohort Study. This study assessed cancer risk associations for 3 recently developed methylation-based biomarkers of aging: PhenoAge, GrimAge, and predicted telomere length. Methods We estimated rate ratios (RRs) for the association between these 3 age-adjusted measures and risk of colorectal (N = 813), gastric (N = 165), kidney (N = 139), lung (N = 327), mature B-cell (N = 423), prostate (N = 846), and urothelial (N = 404) cancer using conditional logistic regression models. We also assessed associations by time since blood draw and by cancer subtype, and we investigated potential nonlinearity. Results We observed relatively strong associations of age-adjusted PhenoAge with risk of colorectal, kidney, lung, mature B-cell, and urothelial cancers (RR per SD was approximately 1.2-1.3). Similar findings were obtained for age-adjusted GrimAge, but the association with lung cancer risk was much larger (RR per SD = 1.82, 95% confidence interval [CI] = 1.44 to 2.30), after adjustment for smoking status, pack-years, starting age, time since quitting, and other cancer risk factors. Most associations appeared linear, larger than for the first-generation measures, and were virtually unchanged after adjustment for a large set of sociodemographic, lifestyle, and anthropometric variables. For cancer overall, the comprehensively adjusted rate ratio per SD was 1.13 (95% CI = 1.07 to 1.19) for PhenoAge and 1.12 (95% CI = 1.05 to 1.20) for GrimAge and appeared larger within 5 years of blood draw (RR = 1.29, 95% CI = 1.15 to 1.44 and 1.19, 95% CI = 1.06 to 1.33, respectively). Conclusions The methylation-based measures PhenoAge and GrimAge may provide insights into the relationship between biological aging and cancer and be useful to predict cancer risk, particularly for lung cancer.
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Affiliation(s)
- Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council, Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Julie K Bassett
- Cancer Epidemiology Division, Cancer Council, Victoria, Melbourne, Victoria, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - JiHoon E Joo
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Shuai Li
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Chenglong Yu
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Daniel F Schmidt
- Faculty of Information Technology, Monash University, Clayton, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicole Wong Doo
- Cancer Epidemiology Division, Cancer Council, Victoria, Melbourne, Victoria, Australia
- Concord Clinical School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia
| | - Daniel D Buchanan
- Department of Clinical Pathology, Colorectal Oncogenomics Group, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Allison M Hodge
- Cancer Epidemiology Division, Cancer Council, Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council, Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council, Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council, Victoria, Melbourne, Victoria, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Roger L Milne
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council, Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
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Dugué PA, Wilson R, Lehne B, Jayasekara H, Wang X, Jung CH, Joo JE, Makalic E, Schmidt DF, Baglietto L, Severi G, Gieger C, Ladwig KH, Peters A, Kooner JS, Southey MC, English DR, Waldenberger M, Chambers JC, Giles GG, Milne RL. Alcohol consumption is associated with widespread changes in blood DNA methylation: Analysis of cross-sectional and longitudinal data. Addict Biol 2021; 26:e12855. [PMID: 31789449 DOI: 10.1111/adb.12855] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 09/29/2019] [Accepted: 11/04/2019] [Indexed: 12/26/2022]
Abstract
DNA methylation may be one of the mechanisms by which alcohol consumption is associated with the risk of disease. We conducted a large-scale, cross-sectional, genome-wide DNA methylation association study of alcohol consumption and a longitudinal analysis of repeated measurements taken several years apart. Using the Illumina HumanMethylation450 BeadChip, DNA methylation was measured in blood samples from 5606 Melbourne Collaborative Cohort Study (MCCS) participants. For 1088 of them, these measures were repeated using blood samples collected a median of 11 years later. Associations between alcohol intake and blood DNA methylation were assessed using linear mixed-effects regression models. Independent data from the London Life Sciences Prospective Population (LOLIPOP) (N = 4042) and Cooperative Health Research in the Augsburg Region (KORA) (N = 1662) cohorts were used to replicate associations discovered in the MCCS. Cross-sectional analyses identified 1414 CpGs associated with alcohol intake at P < 10-7 , 1243 of which had not been reported previously. Of these novel associations, 1078 were replicated (P < .05) using LOLIPOP and KORA data. Using the MCCS data, we also replicated 403 of 518 previously reported associations. Interaction analyses suggested that associations were stronger for women, non-smokers, and participants genetically predisposed to consume less alcohol. Of the 1414 CpGs, 530 were differentially methylated (P < .05) in former compared with current drinkers. Longitudinal associations between the change in alcohol intake and the change in methylation were observed for 513 of the 1414 cross-sectional associations. Our study indicates that alcohol intake is associated with widespread changes in DNA methylation across the genome. Longitudinal analyses showed that the methylation status of alcohol-associated CpGs may change with alcohol consumption changes in adulthood.
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Affiliation(s)
- Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Harindra Jayasekara
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Xiaochuan Wang
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, Australia
| | - JiHoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Gianluca Severi
- CESP, INSERM U1018, Univ. Paris-Sud, UVSQ, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Karl-Heinz Ladwig
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Klinik und Poliklinik für Psychosomatische Medizin und Psychotherapie des Klinikums Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, Middlesex, UK
- Imperial College Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, Middlesex, UK
- Imperial College Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
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Pei Y, Lou X, Li K, Xu X, Guo Y, Xu D, Yang Z, Xu D, Cui W, Zhang D. Peripheral Blood Leukocyte N6-methyladenosine is a Noninvasive Biomarker for Non-small-cell Lung Carcinoma. Onco Targets Ther 2020; 13:11913-11921. [PMID: 33239892 PMCID: PMC7682600 DOI: 10.2147/ott.s267344] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Background N6-methyladenosine (m6A) triggers a new layer of epi-transcription. However, the potential noninvasive screening and diagnostic value of peripheral blood m6A for cancer are still unknown. Here, we intend to investigate whether leukocyte m6A can be a novel biomarker for non-small-cell lung cancer (NSCLC). Materials and Methods Peripheral blood was collected from 119 NSCLC patients and 74 age-matched healthy controls. Total RNA was isolated from leukocytes for m6A measurement, and clinical information of participants was reviewed. The sensitivity, specificity, and area under the curve (AUC) of m6A for cancer diagnosis were evaluated by the receiver-operating characteristic (ROC) curve analysis. Flow cytometry and the Human Protein Atlas (HPA) database were used to characterize m6A in leukocyte differentials. Pearson's correlation was applied to indicate the relationship between m6A level and hematology variables. qPCR and bioinformatic analysis were used to identity the expression of m6A regulators in leukocyte. Results Leukocyte m6A was significantly elevated in 119 NSCLC patients compared with 74 healthy controls (P<0.001). We did not find significant association between m6A and age or gender. Elevated m6A level in NSCLC was associated with tumor stage (P<0.05) and tumor differentiation (P<0.05), and was significantly reduced after surgery (P<0.01). ROC curve analysis revealed that leukocyte m6A could significantly discriminate patients with lung adenocarcinoma (LUAD) (AUC=0.736, P<0.001) and lung squamous cell carcinoma (LUSC) (AUC=0.963, P<0.001) from healthy individuals. m6A displayed superior sensitivity (100%) and specificity (85.7%) for LUSC than squamous cell carcinoma (SCC) antigen and cytokeratin fragment 211 (Cyfra211). Flow cytometry analysis showed m6A modification was mainly localized on T cells and monocytes among leukocyte differentials. Leukocyte m6A was positively correlated with the number of lymphocytes and negatively correlated with monocytes in NSCLC but not in healthy controls. qPCR and bioinformatic analysis showed that elevated leukocyte m6A in NSCLC was caused by upregulated methyltransferase complex and downregulated FTO and ALKBH5. Conclusion Leukocyte m6A represents a potential noninvasive biomarker for NSCLC screening, monitoring and diagnosis.
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Affiliation(s)
- Yuqing Pei
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Xiaoying Lou
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Kexin Li
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Xiaotian Xu
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Ye Guo
- Department of Laboratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Danfei Xu
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Zhenxi Yang
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Dongsheng Xu
- Hematopathology Program, CBL Path, Inc, Rye Brook, NY 10753, USA
| | - Wei Cui
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Donghong Zhang
- Center for Molecular and Translational Medicine, Georgia State University, Research Science Center, Atlanta, GA 30303, USA
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Grieshober L, Graw S, Barnett MJ, Thornquist MD, Goodman GE, Chen C, Koestler DC, Marsit CJ, Doherty JA. AHRR methylation in heavy smokers: associations with smoking, lung cancer risk, and lung cancer mortality. BMC Cancer 2020; 20:905. [PMID: 32962699 PMCID: PMC7510160 DOI: 10.1186/s12885-020-07407-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A low level of methylation at cg05575921 in the aryl-hydrocarbon receptor repressor (AHRR) gene is robustly associated with smoking, and some studies have observed associations between cg05575921 methylation and increased lung cancer risk and mortality. To prospectively examine whether decreased methylation at cg05575921 may identify high risk subpopulations for lung cancer screening among heavy smokers, and mortality in cases, we evaluated associations between cg05575921 methylation and lung cancer risk and mortality, by histotype, in heavy smokers. METHODS The β-Carotene and Retinol Efficacy Trial (CARET) included enrollees ages 45-69 with ≥ 20 pack-year smoking histories and/or occupational asbestos exposure. A subset of CARET participants had cg05575921 methylation available from HumanMethylationEPIC assays of blood collected on average 4.3 years prior to lung cancer diagnosis in cases. Cg05575921 methylation β-values were treated continuously for a 10% methylation decrease and as quintiles, where quintile 1 (Q1, referent) represents high methylation and Q5, low methylation. We used conditional logistic regression models to examine lung cancer risk overall and by histotype in a nested case-control study including 316 lung cancer cases (diagnosed through 2005) and 316 lung cancer-free controls matched on age (±5 years), sex, race/ethnicity, enrollment year, current/former smoking, asbestos exposure, and follow-up time. Mortality analyses included 372 lung cancer cases diagnosed between 1985 and 2013 with available methylation data. We used Cox proportional hazards models to examine mortality overall and by histotype. RESULTS Decreased cg05575921 methylation was strongly associated with smoking, even in our population of heavy smokers. We did not observe associations between decreased pre-diagnosis cg05575921 methylation and increased lung cancer risk, overall or by histotype. We observed linear increasing trends for lung cancer-specific mortality across decreasing cg05575921 methylation quintiles for adenocarcinoma and small cell carcinoma (P-trends = 0.01 and 0.04, respectively). CONCLUSIONS In our study of heavy smokers, decreased cg05575921 methylation was strongly associated with smoking but not increased lung cancer risk. The observed association between cg05575921 methylation and increased mortality in adenocarcinoma and small cell histotypes requires further examination. Our results do not support using decreased cg05575921 methylation as a biomarker for lung cancer screening risk stratification.
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Affiliation(s)
- Laurie Grieshober
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Room 4746, Salt Lake City, UT, 84112, USA.
| | - Stefan Graw
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Matt J Barnett
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark D Thornquist
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gary E Goodman
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA.,Department of Otolaryngology: Head and Neck Surgery, School of Medicine, University of Washington, Seattle, WA, USA
| | - Devin C Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jennifer A Doherty
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Room 4746, Salt Lake City, UT, 84112, USA.,Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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47
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You C, Wu S, Zheng SC, Zhu T, Jing H, Flagg K, Wang G, Jin L, Wang S, Teschendorff AE. A cell-type deconvolution meta-analysis of whole blood EWAS reveals lineage-specific smoking-associated DNA methylation changes. Nat Commun 2020; 11:4779. [PMID: 32963246 PMCID: PMC7508850 DOI: 10.1038/s41467-020-18618-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Highly reproducible smoking-associated DNA methylation changes in whole blood have been reported by many Epigenome-Wide-Association Studies (EWAS). These epigenetic alterations could have important implications for understanding and predicting the risk of smoking-related diseases. To this end, it is important to establish if these DNA methylation changes happen in all blood cell subtypes or if they are cell-type specific. Here, we apply a cell-type deconvolution algorithm to identify cell-type specific DNA methylation signals in seven large EWAS. We find that most of the highly reproducible smoking-associated hypomethylation signatures are more prominent in the myeloid lineage. A meta-analysis further identifies a myeloid-specific smoking-associated hypermethylation signature enriched for DNase Hypersensitive Sites in acute myeloid leukemia. These results may guide the design of future smoking EWAS and have important implications for our understanding of how smoking affects immune-cell subtypes and how this may influence the risk of smoking related diseases. Smoking-associated DNA methylation changes in whole blood have been reported by many EWAS. Here, the authors use a cell-type deconvolution algorithm to identify cell-type specific DNA methylation signals in seven EWAS, identifying lineage-specific smoking-associated DNA methylation changes.
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Affiliation(s)
- Chenglong You
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Sijie Wu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.,Human Phenome Institute, Fudan University, 825 Zhangheng Road, Shanghai, China.,State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Shijie C Zheng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tianyu Zhu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Han Jing
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Ken Flagg
- Guangzhou Regenerative Medicine Guangdong Laboratory, Guangzhou, China
| | - Guangyu Wang
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Li Jin
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.,Human Phenome Institute, Fudan University, 825 Zhangheng Road, Shanghai, China.,State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China. .,UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
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48
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Chen Z, Wen W, Cai Q, Long J, Wang Y, Lin W, Shu XO, Zheng W, Guo X. From tobacco smoking to cancer mutational signature: a mediation analysis strategy to explore the role of epigenetic changes. BMC Cancer 2020; 20:880. [PMID: 32928150 PMCID: PMC7488848 DOI: 10.1186/s12885-020-07368-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/31/2020] [Indexed: 01/01/2023] Open
Abstract
Background Tobacco smoking is associated with a unique mutational signature in the human cancer genome. It is unclear whether tobacco smoking-altered DNA methylations and gene expressions affect smoking-related mutational signature. Methods We systematically analyzed the smoking-related DNA methylation sites reported from five previous casecontrol studies in peripheral blood cells to identify possible target genes. Using the mediation analysis approach, we evaluated whether the association of tobacco smoking with mutational signature is mediated through altered DNA methylation and expression of these target genes in lung adenocarcinoma tumor tissues. Results Based on data obtained from 21,108 blood samples, we identified 374 smoking-related DNA methylation sites, annotated to 248 target genes. Using data from DNA methylations, gene expressions and smoking-related mutational signature generated from ~ 7700 tumor tissue samples across 26 cancer types from The Cancer Genome Atlas (TCGA), we found 11 of the 248 target genes whose expressions were associated with smoking-related mutational signature at a Bonferroni-correction P < 0.001. This included four for head and neck cancer, and seven for lung adenocarcinoma. In lung adenocarcinoma, our results showed that smoking increased the expression of three genes, AHRR, GPR15, and HDGF, and decreased the expression of two genes, CAPN8, and RPS6KA1, which were consequently associated with increased smoking-related mutational signature. Additional evidence showed that the elevated expression of AHRR and GPR15 were associated with smoking-altered hypomethylations at cg14817490 and cg19859270, respectively, in lung adenocarcinoma tumor tissues. Lastly, we showed that decreased expression of RPS6KA1, were associated with poor survival of lung cancer patients. Conclusions Our findings provide novel insight into the contributions of tobacco smoking to carcinogenesis through the underlying mechanisms of the elevated mutational signature by altered DNA methylations and gene expressions.
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Affiliation(s)
- Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Ying Wang
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Weiqiang Lin
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37203, USA. .,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
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Brägelmann J, Lorenzo Bermejo J. A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets. Brief Bioinform 2020; 20:2055-2065. [PMID: 30099476 PMCID: PMC6954449 DOI: 10.1093/bib/bby068] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/11/2018] [Accepted: 07/06/2018] [Indexed: 12/26/2022] Open
Abstract
Technological advances and reduced costs of high-density methylation arrays have led to an increasing number of association studies on the possible relationship between human disease and epigenetic variability. DNA samples from peripheral blood or other tissue types are analyzed in epigenome-wide association studies (EWAS) to detect methylation differences related to a particular phenotype. Since information on the cell-type composition of the sample is generally not available and methylation profiles are cell-type specific, statistical methods have been developed for adjustment of cell-type heterogeneity in EWAS. In this study we systematically compared five popular adjustment methods: the factored spectrally transformed linear mixed model (FaST-LMM-EWASher), the sparse principal component analysis algorithm ReFACTor, surrogate variable analysis (SVA), independent SVA (ISVA) and an optimized version of SVA (SmartSVA). We used real data and applied a multilayered simulation framework to assess the type I error rate, the statistical power and the quality of estimated methylation differences according to major study characteristics. While all five adjustment methods improved false-positive rates compared with unadjusted analyses, FaST-LMM-EWASher resulted in the lowest type I error rate at the expense of low statistical power. SVA efficiently corrected for cell-type heterogeneity in EWAS up to 200 cases and 200 controls, but did not control type I error rates in larger studies. Results based on real data sets confirmed simulation findings with the strongest control of type I error rates by FaST-LMM-EWASher and SmartSVA. Overall, ReFACTor, ISVA and SmartSVA showed the best comparable statistical power, quality of estimated methylation differences and runtime.
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Affiliation(s)
- Johannes Brägelmann
- University Hospital of Cologne, Germany.,Departement of medical biometry and biostatistics, University of Heidelberg, Germany
| | - Justo Lorenzo Bermejo
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany
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50
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Gagliardi A, Dugué PA, Nøst TH, Southey MC, Buchanan DD, Schmidt DF, Makalic E, Hodge AM, English DR, Doo NW, Hopper JL, Severi G, Baglietto L, Naccarati A, Tarallo S, Pace L, Krogh V, Palli D, Panico S, Sacerdote C, Tumino R, Lund E, Giles GG, Pardini B, Sandanger TM, Milne RL, Vineis P, Polidoro S, Fiorito G. Stochastic Epigenetic Mutations Are Associated with Risk of Breast Cancer, Lung Cancer, and Mature B-cell Neoplasms. Cancer Epidemiol Biomarkers Prev 2020; 29:2026-2037. [PMID: 32788174 DOI: 10.1158/1055-9965.epi-20-0451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/18/2020] [Accepted: 07/29/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Age-related epigenetic dysregulations are associated with several diseases, including cancer. The number of stochastic epigenetic mutations (SEM) has been suggested as a biomarker of life-course accumulation of exposure-related DNA damage; however, the predictive role of SEMs in cancer has seldom been investigated. METHODS A SEM, at a given CpG site, was defined as an extreme outlier of DNA methylation value distribution across individuals. We investigated the association of the total number of SEMs with the risk of eight cancers in 4,497 case-control pairs nested in three prospective cohorts. Furthermore, we investigated whether SEMs were randomly distributed across the genome or enriched in functional genomic regions. RESULTS In the three-study meta-analysis, the estimated ORs per one-unit increase in log(SEM) from logistic regression models adjusted for age and cancer risk factors were 1.25; 95% confidence interval (CI), 1.11-1.41 for breast cancer, and 1.23; 95% CI, 1.07-1.42 for lung cancer. In the Melbourne Collaborative Cohort Study, the OR for mature B-cell neoplasm was 1.46; 95% CI, 1.25-1.71. Enrichment analyses indicated that SEMs frequently occur in silenced genomic regions and in transcription factor binding sites regulated by EZH2 and SUZ12 (P < 0.0001 and P = 0.0005, respectively): two components of the polycomb repressive complex 2 (PCR2). Finally, we showed that PCR2-specific SEMs are generally more stable over time compared with SEMs occurring in the whole genome. CONCLUSIONS The number of SEMs is associated with a higher risk of different cancers in prediagnostic blood samples. IMPACT We identified a candidate biomarker for cancer early detection, and we described a carcinogenesis mechanism involving PCR2 complex proteins worthy of further investigations.
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Affiliation(s)
- Amedeo Gagliardi
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy.
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Therese H Nøst
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Department of Clinical Pathology | Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research Level 10, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Allison M Hodge
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicole W Doo
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Concord Repatriation General Hospital, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Concord Clinical School, University of Sydney, Concord, New South Wales, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Gianluca Severi
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, USQ, Gustave Roussy, Villejuif, France
| | - Laura Baglietto
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, USQ, Gustave Roussy, Villejuif, France
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Luigia Pace
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Vittorio Krogh
- Fondazione IRCCS - Istituto Nazionale dei Tumori, Milan, Italy
| | - Domenico Palli
- Institute for Cancer Research, Prevention and Clinical Network - ISPRO, Villa delle Rose, Via Cosimo il Vecchio, Florence, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Corso Umberto I, Naples, Italy
| | - Carlotta Sacerdote
- Piedmont Reference Centre for Epidemiology and Cancer Prevention (CPO Piemonte), Turin, Italy
| | - Rosario Tumino
- Department of Cancer Registry and Histopathology, Provincial Health Authority (ASP 7) Ragusa, Piazza Igea, Ragusa, Italy
| | - Eiliv Lund
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- The Cancer Registry of Norway, Oslo, Norway
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Torkjel M Sandanger
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Paolo Vineis
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Silvia Polidoro
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Giovanni Fiorito
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Department of Biomedical Sciences, Laboratory of Biostatistics, University of Sassari, Sassari, Italy
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