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Martínez-Magaña JJ, Hurtado-Soriano J, Rivero-Segura NA, Montalvo-Ortiz JL, Garcia-delaTorre P, Becerril-Rojas K, Gomez-Verjan JC. Towards a Novel Frontier in the Use of Epigenetic Clocks in Epidemiology. Arch Med Res 2024; 55:103033. [PMID: 38955096 DOI: 10.1016/j.arcmed.2024.103033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/10/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
Health problems associated with aging are a major public health concern for the future. Aging is a complex process with wide intervariability among individuals. Therefore, there is a need for innovative public health strategies that target factors associated with aging and the development of tools to assess the effectiveness of these strategies accurately. Novel approaches to measure biological age, such as epigenetic clocks, have become relevant. These clocks use non-sequential variable information from the genome and employ mathematical algorithms to estimate biological age based on DNA methylation levels. Therefore, in the present study, we comprehensively review the current status of the epigenetic clocks and their associations across the human phenome. We emphasize the potential utility of these tools in an epidemiological context, particularly in evaluating the impact of public health interventions focused on promoting healthy aging. Our review describes associations between epigenetic clocks and multiple traits across the life and health span. Additionally, we highlighted the evolution of studies beyond mere associations to establish causal mechanisms between epigenetic age and disease. We explored the application of epigenetic clocks to measure the efficacy of interventions focusing on rejuvenation.
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Affiliation(s)
- José Jaime Martínez-Magaña
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; U.S. Department of Veterans Affairs National Center for Post-Traumatic Stress Disorder, Clinical Neuroscience Division, West Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | | | | | - Janitza L Montalvo-Ortiz
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; U.S. Department of Veterans Affairs National Center for Post-Traumatic Stress Disorder, Clinical Neuroscience Division, West Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | - Paola Garcia-delaTorre
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Área de Envejecimiento, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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Hernandez Cordero AI, Li X, Yang J, Yang CX, Shaipanich T, MacIsaac JL, Dever K, Kobor MS, Montaner J, Harris M, Guillemi S, Man SFP, Sin DD, Leung JM. DNA Methylation Demonstrates Bronchoalveolar Cell Senescence in People Living with HIV: An Observational Cohort Study. Biomedicines 2024; 12:1261. [PMID: 38927468 PMCID: PMC11201658 DOI: 10.3390/biomedicines12061261] [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: 05/03/2024] [Revised: 05/25/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND DNA methylation may be a link between HIV, aging, and the increased risk of lung comorbidities. We investigated whether bronchoalveolar lavage (BAL) cells of people living with HIV (PLWH) demonstrate epigenetic disruptions and advanced epigenetic aging. METHODS BAL cell DNA methylation from 25 PLWH and 16 HIV-uninfected individuals were tested for differential methylation of Alu and LINE-1 sites, markers of aging. We used a weighted gene correlation network analysis to identify HIV- and age-associated co-methylation networks. We tested the effect of HIV on DNA methylation using a robust linear model (false discovery rate < 0.10). RESULTS The BAL cells of PLWH were marked by global hypomethylation in both Alu and LINE-1 elements. Six co-methylated CpG networks were identified that were significantly associated with age; of these, the red module was significantly differentially methylated in PLWH and enriched pathways (e.g., Ras signaling and T-cell receptors). We identified 6428 CpG sites associated with HIV. CONCLUSIONS We have shown here for the first time that alterations in the DNA methylation of BAL cells in the lung with HIV show a pattern of advanced aging. This study strongly supports that HIV may contribute to an increased the risk of lung comorbidities through the epigenetics of aging.
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Affiliation(s)
- Ana I. Hernandez Cordero
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
- Edwin S. H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Xuan Li
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Julia Yang
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Tawimas Shaipanich
- Division of Respiratory Medicine, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Julie L. MacIsaac
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V6H 0B3, Canada
| | - Kristy Dever
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V6H 0B3, Canada
| | - Michael S. Kobor
- Edwin S. H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V6H 0B3, Canada
| | - Julio Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Shu Fan Paul Man
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Don D. Sin
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
- Edwin S. H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Division of Respiratory Medicine, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Janice M. Leung
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
- Edwin S. H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Division of Respiratory Medicine, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
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Hernandez Cordero AI, Li X, Yang CX, Ambalavanan A, MacIsaac JL, Kobor MS, Doiron D, Tan W, Bourbeau J, Sin DD, Duan Q, Leung JM. Cannabis smoking is associated with advanced epigenetic age. Eur Respir J 2024; 63:2400458. [PMID: 38609099 PMCID: PMC11063617 DOI: 10.1183/13993003.00458-2024] [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: 09/16/2023] [Accepted: 03/18/2024] [Indexed: 04/14/2024]
Abstract
Cannabis use has been controversial, largely having been designated a controlled substance over the past century. While certain studies have linked cannabis smoking with harmful effects such as increased respiratory symptoms and faster lung function decline in older adults [1, 2], these findings have not been fully replicated by others [3]. The link between cannabis and disease pathogenesis may best be explored through DNA methylation. This mechanism consists of the addition or removal of a methyl group at a cytosine–guanine residue (CpG), can be influenced by exposures, and can modify transcription. Methylation changes can accumulate over time in patterns that are highly associated with age, leading to the development of epigenetic clocks that can estimate biological age [4]. Current cannabis smoking is significantly associated with faster peripheral blood epigenetic age acceleration; interestingly, cannabis smoking cessation is shown to normalise this age acceleration signal. https://bit.ly/3x7s2CU
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Affiliation(s)
- Ana I Hernandez Cordero
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada
- Edwin S.H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Xuan Li
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada
| | - Amirtha Ambalavanan
- Department of Biomedical and Molecular Sciences, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Julie L MacIsaac
- Edwin S.H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Kobor
- Edwin S.H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Dany Doiron
- McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Wan Tan
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada
| | - Jean Bourbeau
- McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada
- Edwin S.H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Qingling Duan
- Department of Biomedical and Molecular Sciences, School of Medicine, Queen's University, Kingston, ON, Canada
- School of Computing, Queen's University, Kingston, ON, Canada
- Q. Duan and J.M. Leung contributed equally as senior authors
| | - Janice M Leung
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, BC, Canada
- Edwin S.H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Q. Duan and J.M. Leung contributed equally as senior authors
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Song MA, Mori KM, McElroy JP, Freudenheim JL, Weng DY, Reisinger SA, Brasky TM, Wewers MD, Shields PG. Accelerated epigenetic age, inflammation, and gene expression in lung: comparisons of smokers and vapers with non-smokers. Clin Epigenetics 2023; 15:160. [PMID: 37821974 PMCID: PMC10568901 DOI: 10.1186/s13148-023-01577-8] [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: 03/11/2023] [Accepted: 10/01/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Cigarette smoking and aging are the main risk factors for pulmonary diseases, including cancer. Epigenetic aging may explain the relationship between smoking, electronic cigarette vaping, and pulmonary health. No study has examined smoking and vaping-related epigenetic aging in relation to lung biomarkers. METHODS Lung epigenetic aging measured by DNA methylation (mAge) and its acceleration (mAA) was assessed in young (age 21-30) electronic cigarette vapers (EC, n = 14, including 3 never-smoking EC), smokers (SM, n = 16), and non-EC/non-SM (NS, n = 39). We investigated relationships of mAge estimates with chronological age (Horvath-mAge), lifespan/mortality (Grim-mAge), telomere length (TL-mAge), smoking/EC history, urinary biomarkers, lung cytokines, and transcriptome. RESULTS Compared to NS, EC and SM had significantly older Grim-mAge, shorter TL-mAge, significantly accelerated Grim-mAge and decelerated TL-mAge. Among SM, Grim-mAA was associated with nicotine intake and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL). For EC, Horvath-mAA was significantly correlated with puffs per day. Overall, cytokines (IL-1β, IL-6, and IL-8) and 759 transcripts (651 unique genes) were significantly associated with Grim-mAA. Grim-mAA-associated genes were highly enriched in immune-related pathways and genes that play a role in the morphology and structures of cells/tissues. CONCLUSIONS Faster lung mAge for SM is consistent with prior studies of blood. Faster lung mAge for EC compared to NS indicates possible adverse pulmonary effects of EC on biological aging. Our findings support further research, particularly on epigenetic markers, on effects of smoking and vaping on pulmonary health. Given that most EC are former smokers, further study is needed to understand unique effects of electronic cigarettes on biological aging.
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Affiliation(s)
- Min-Ae Song
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, 404 Cunz Hall, 1841 Neil Ave., Columbus, OH, 43210, USA.
| | - Kellie M Mori
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, 404 Cunz Hall, 1841 Neil Ave., Columbus, OH, 43210, USA
| | - Joseph P McElroy
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Daniel Y Weng
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Sarah A Reisinger
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Theodore M Brasky
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Mark D Wewers
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Peter G Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
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Swart G, Meeks K, Chilunga F, Venema A, Agyemang C, van der Linden E, Henneman P. Associations between epigenome-wide DNA methylation and height-related traits among Sub-Saharan Africans: the RODAM study. J Dev Orig Health Dis 2023; 14:658-669. [PMID: 38044700 DOI: 10.1017/s204017442300034x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Human height and related traits are highly complex, and extensively research has shown that these traits are determined by both genetic and environmental factors. Such factors may partially affect these traits through epigenetic programing. Epigenetic programing is dynamic and plays an important role in controlling gene expression and cell differentiation during (early) development. DNA methylation (DNAm) is the most commonly studied epigenetic feature. In this study we conducted an epigenome-wide DNAm association analysis on height-related traits in a Sub-Saharan African population, in order to detect DNAm biomarkers across four height-related traits. DNAm profiles were acquired in whole blood samples of 704 Ghanaians, sourced from the Research on Obesity and Diabetes among African Migrants study, using the Illumina Infinium HumanMethylation450 BeadChip. Linear models were fitted to detect differentially methylated positions (DMPs) and regions (DMRs) associated with height, leg-to-height ratio (LHR), leg length, and sitting height. No epigenome-wide significant DMPs were recorded. However we did observe among our top DMPs five informative probes associated with the height-related traits: cg26905768 (leg length), cg13268132 (leg length), cg19776793 (height), cg23072383 (LHR), and cg24625894 (sitting height). All five DMPs are annotated to genes whose functions were linked to bone cell regulation and development. DMR analysis identified overlapping DMRs within the gene body of HLA-DPB1 gene, and the HOXA gene cluster. In this first epigenome-wide association studies of these traits, our findings suggest DNAm associations with height-related heights, and might influence development and maintenance of these traits. Further studies are needed to replicate our findings, and to elucidate the molecular mechanism underlying human height-related traits.
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Affiliation(s)
- Galatea Swart
- Department of Human Genetics, Department of Human Genetics, Genome Diagnostic Laboratory, Amsterdam Reproduction and Development, Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Karlijn Meeks
- Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Felix Chilunga
- Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Andrea Venema
- Department of Human Genetics, Department of Human Genetics, Genome Diagnostic Laboratory, Amsterdam Reproduction and Development, Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eva van der Linden
- Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Department of Human Genetics, Genome Diagnostic Laboratory, Amsterdam Reproduction and Development, Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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