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Jeddi F, Faghfuri E, Mehranfar S, Soozangar N. The common bisulfite-conversion-based techniques to analyze DNA methylation in human cancers. Cancer Cell Int 2024; 24:240. [PMID: 38982390 PMCID: PMC11234524 DOI: 10.1186/s12935-024-03405-2] [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: 01/29/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024] Open
Abstract
DNA methylation is an important molecular modification that plays a key role in the expression of cancer genes. Evaluation of epigenetic changes, hypomethylation and hypermethylation, in specific genes are applied for cancer diagnosis. Numerous studies have concentrated on describing DNA methylation patterns as biomarkers for cancer diagnosis monitoring and predicting response to cancer therapy. Various techniques for detecting DNA methylation status in cancers are based on sodium bisulfite treatment. According to the application of these methods in research and clinical studies, they have a number of advantages and disadvantages. The current review highlights sodium bisulfite treatment-based techniques, as well as, the advantages, drawbacks, and applications of these methods in the evaluation of human cancers.
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Affiliation(s)
- Farhad Jeddi
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Elnaz Faghfuri
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sahar Mehranfar
- Department of Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Narges Soozangar
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
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Silva N, Rajado AT, Esteves F, Brito D, Apolónio J, Roberto VP, Binnie A, Araújo I, Nóbrega C, Bragança J, Castelo-Branco P. Measuring healthy ageing: current and future tools. Biogerontology 2023; 24:845-866. [PMID: 37439885 PMCID: PMC10615962 DOI: 10.1007/s10522-023-10041-2] [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: 04/05/2023] [Accepted: 05/23/2023] [Indexed: 07/14/2023]
Abstract
Human ageing is a complex, multifactorial process characterised by physiological damage, increased risk of age-related diseases and inevitable functional deterioration. As the population of the world grows older, placing significant strain on social and healthcare resources, there is a growing need to identify reliable and easy-to-employ markers of healthy ageing for early detection of ageing trajectories and disease risk. Such markers would allow for the targeted implementation of strategies or treatments that can lessen suffering, disability, and dependence in old age. In this review, we summarise the healthy ageing scores reported in the literature, with a focus on the past 5 years, and compare and contrast the variables employed. The use of approaches to determine biological age, molecular biomarkers, ageing trajectories, and multi-omics ageing scores are reviewed. We conclude that the ideal healthy ageing score is multisystemic and able to encompass all of the potential alterations associated with ageing. It should also be longitudinal and able to accurately predict ageing complications at an early stage in order to maximize the chances of successful early intervention.
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Affiliation(s)
- Nádia Silva
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Ana Teresa Rajado
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Filipa Esteves
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - David Brito
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Joana Apolónio
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Vânia Palma Roberto
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
| | - Alexandra Binnie
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Department of Critical Care, William Osler Health System, Etobicoke, ON, Canada
| | - Inês Araújo
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Clévio Nóbrega
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - José Bragança
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Pedro Castelo-Branco
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal.
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal.
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal.
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal.
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Silva N, Rajado AT, Esteves F, Brito D, Apolónio J, Roberto VP, Binnie A, Araújo I, Nóbrega C, Bragança J, Castelo-Branco P, Andrade RP, Calado S, Faleiro ML, Matos C, Marques N, Marreiros A, Nzwalo H, Pais S, Palmeirim I, Simão S, Joaquim N, Miranda R, Pêgas A, Sardo A. Measuring healthy ageing: current and future tools. Biogerontology 2023. [DOI: https:/doi.org/10.1007/s10522-023-10041-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/23/2023] [Indexed: 09/01/2023]
Abstract
AbstractHuman ageing is a complex, multifactorial process characterised by physiological damage, increased risk of age-related diseases and inevitable functional deterioration. As the population of the world grows older, placing significant strain on social and healthcare resources, there is a growing need to identify reliable and easy-to-employ markers of healthy ageing for early detection of ageing trajectories and disease risk. Such markers would allow for the targeted implementation of strategies or treatments that can lessen suffering, disability, and dependence in old age. In this review, we summarise the healthy ageing scores reported in the literature, with a focus on the past 5 years, and compare and contrast the variables employed. The use of approaches to determine biological age, molecular biomarkers, ageing trajectories, and multi-omics ageing scores are reviewed. We conclude that the ideal healthy ageing score is multisystemic and able to encompass all of the potential alterations associated with ageing. It should also be longitudinal and able to accurately predict ageing complications at an early stage in order to maximize the chances of successful early intervention.
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DNA methylation age acceleration is associated with risk of diabetes complications. COMMUNICATIONS MEDICINE 2023; 3:21. [PMID: 36765171 PMCID: PMC9918553 DOI: 10.1038/s43856-023-00250-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Patients with Type 2 diabetes mellitus (T2D) are at risk for micro- and macrovascular complications. Implementable risk scores are needed to improve targeted prevention for patients that are particularly susceptible to complications. The epigenetic clock estimates an individual's biological age using DNA methylation profiles. METHODS In this study, we examined older adults of the Berlin Aging Study II that were reexamined on average 7.4 years after baseline assessment as part of the GendAge study. DNA methylation age (DNAmA) and its deviation from chronological age DNAmA acceleration (DNAmAA) were calculated with the 7-CpG clock (available at both timepoints, n = 1,071), Horvath's clock, Hannum's clock, PhenoAge and GrimAge (available at follow-up only, n = 1,067). T2D associated complications were assessed with the Diabetes Complications Severity Index (DCSI). RESULTS We report on a statistically significant association between oral glucose tolerance test results and Hannum and PhenoAge DNAmAA. PhenoAge was also associated with fasting glucose. In contrast, we found no cross-sectional association after covariate adjustment between DNAmAA and a diagnosis of T2D. However, longitudinal analyses showed that every additional year of 7-CpG DNAmAA at baseline increased the odds for developing one or more additional complications or worsening of an already existing complication during the follow-up period by 11% in male participants with T2D. This association persisted after covariate adjustment (OR = 1.11, p = 0.045, n = 56). CONCLUSION Although our results remain to be independently validated, this study shows promising evidence of utility of the 7-CpG clock in identifying patients with diabetes who are at high risk for developing complications.
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Banszerus VL, König M, Landmesser U, Vetter VM, Demuth I. Epigenetic aging in patients diagnosed with coronary artery disease: results of the LipidCardio study. Clin Epigenetics 2023; 15:16. [PMID: 36721243 PMCID: PMC9887837 DOI: 10.1186/s13148-023-01434-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/23/2023] [Indexed: 02/01/2023] Open
Abstract
INTRODUCTION People age biologically at different rates. Epigenetic clock-derived DNA methylation age acceleration (DNAmAA) is among the most promising markers proposed to assess the interindividual differences in biological age. Further research is needed to evaluate the characteristics of the different epigenetic clock biomarkers available with respect to the health domains they reflect best. METHODS In this study, we have analyzed 779 participants of the LipidCardio study (mean chronological age 69.9 ± 11.0 years, 30.6% women) who underwent diagnostic angiography at the Charité University Hospital in Berlin, Germany. DNA methylation age (DNAm age) was measured by methylation-sensitive single nucleotide primer extension (MS-SNuPE) and calculated with the 7-CpG clock. We compared the biological age as assessed as DNAmAA of participants with an angiographically confirmed coronary artery disease (CAD, n = 554) with participants with lumen reduction of 50% or less (n = 90) and patients with a normal angiogram (n = 135). RESULTS Participants with a confirmed CAD had on average a 2.5-year higher DNAmAA than patients with a normal angiogram. This association did not persist after adjustment for sex in a logistic regression analysis. High-density lipoprotein, low-density lipoprotein, triglycerides, lipoprotein (a), estimated glomerular filtration rate, physical activity, BMI, alcohol consumption, and smoking were not associated with DNAmAA. CONCLUSION The association between higher DNAmAA and angiographically confirmed CAD seems to be mainly driven by sex.
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Affiliation(s)
- Verena Laura Banszerus
- Department of Endocrinology and Metabolic Diseases (Including Division of Lipid Metabolism), Biology of Aging Working Group, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Maximilian König
- Department of Endocrinology and Metabolic Diseases (Including Division of Lipid Metabolism), Biology of Aging Working Group, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Ulf Landmesser
- Department of Cardiology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin (CBF), Berlin, Germany
- Berlin Institute of Health (BIH), Deutsches Zentrum Für Herzkreislaufforschung (DZHK), Partner Site Berlin, Berlin, Germany
| | - Valentin Max Vetter
- Department of Endocrinology and Metabolic Diseases (Including Division of Lipid Metabolism), Biology of Aging Working Group, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Ilja Demuth
- Department of Endocrinology and Metabolic Diseases (Including Division of Lipid Metabolism), Biology of Aging Working Group, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
- BCRT - Berlin Institute of Health Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin, Germany.
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Paparazzo E, Geracitano S, Lagani V, Bartolomeo D, Aceto MA, D’Aquila P, Citrigno L, Bellizzi D, Passarino G, Montesanto A. A Blood-Based Molecular Clock for Biological Age Estimation. Cells 2022; 12:cells12010032. [PMID: 36611826 PMCID: PMC9818068 DOI: 10.3390/cells12010032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
In the last decade, extensive efforts have been made to identify biomarkers of biological age. DNA methylation levels of ELOVL fatty acid elongase 2 (ELOVL2) and the signal joint T-cell receptor rearrangement excision circles (sjTRECs) represent the most promising candidates. Although these two non-redundant biomarkers echo important biological aspects of the ageing process in humans, a well-validated molecular clock exploiting these powerful candidates has not yet been formulated. The present study aimed to develop a more accurate molecular clock in a sample of 194 Italian individuals by re-analyzing the previously obtained EVOLV2 methylation data together with the amount of sjTRECs in the same blood samples. The proposed model showed a high prediction accuracy both in younger individuals with an error of about 2.5 years and in older subjects where a relatively low error was observed if compared with those reported in previously published studies. In conclusion, an easy, cost-effective and reliable model to measure the individual rate and the quality of aging in human population has been proposed. Further studies are required to validate the model and to extend its use in an applicative context.
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Affiliation(s)
- Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
| | - Silvana Geracitano
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
| | - Vincenzo Lagani
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23952, Saudi Arabia
- Institute of Chemical Biology, Ilia State University, 0162 Tbilisi, Georgia
- SDAIA-KAUST Center of Excellence in Data Science and Artificial Intelligence, Thuwal 23952, Saudi Arabia
| | - Denise Bartolomeo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
| | - Mirella Aurora Aceto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
| | - Patrizia D’Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
| | - Luigi Citrigno
- National Research Council (CNR)—Institute for Biomedical Research and Innovation—(IRIB), 87050 Mangone, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
- Correspondence: (G.P.); (A.M.)
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
- Correspondence: (G.P.); (A.M.)
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Epigenetic aging and perceived psychological stress in old age. Transl Psychiatry 2022; 12:410. [PMID: 36163242 PMCID: PMC9513097 DOI: 10.1038/s41398-022-02181-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 12/20/2022] Open
Abstract
Adverse effects of psychological stress on physical and mental health, especially in older age, are well documented. How perceived stress relates to the epigenetic clock measure, DNA methylation age acceleration (DNAmAA), is less well understood and existing studies reported inconsistent results. DNAmAA was estimated from five epigenetic clocks (7-CpG, Horvath's, Hannum's, PhenoAge and GrimAge DNAmAA). Cohen's Perceived Stress Scale (PSS) was used as marker of psychological stress. We analyzed data from 1,100 Berlin Aging Study II (BASE-II) participants assessed as part of the GendAge study (mean age = 75.6 years, SD = 3.8 years, 52.1% women). In a first step, we replicated well-established associations of perceived stress with morbidity, frailty, and symptoms of depression in the BASE-II cohort studied here. In a second step, we did not find any statistically significant association of perceived stress with any of the five epigenetic clocks in multiple linear regression analyses that adjusted for covariates. Although the body of literature suggests an association between higher DNAmAA and stress or trauma during early childhood, the current study found no evidence for an association of perception of stress with DNAmAA in older people. We discuss possible reasons for the lack of associations and highlight directions for future research.
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Vetter VM, Sommerer Y, Kalies CH, Spira D, Bertram L, Demuth I. Vitamin D supplementation is associated with slower epigenetic aging. GeroScience 2022; 44:1847-1859. [PMID: 35562603 PMCID: PMC9213628 DOI: 10.1007/s11357-022-00581-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/26/2022] [Indexed: 11/21/2022] Open
Abstract
Adverse effects of low vitamin D level on mortality and morbidity are controversially discussed. Especially older people are at risk for vitamin D deficiency and therefore exposed to its potentially harmful consequences. A way of measuring differences in the biological age is through DNA methylation age (DNAm age) and its deviation from chronological age, DNAm age acceleration (DNAmAA). We previously reported on an association between vitamin D deficiency and higher 7-CpG DNAmAA in participants of the Berlin Aging Study II (BASE-II). In this study, we employ a quasi-interventional study design to assess the relationship between DNAmAA of five epigenetic clocks and vitamin D supplementation. Longitudinal data were available for 1,036 participants of BASE-II that were reexamined on average 7.4 years later in the GendAge study (mean age at follow-up: 75.6 years, SD = 3.8 years, age range: 64.9-94.1 years, 51.9% female). DNAmAA was estimated with the 7-CpG clock, Horvath's clock, Hannum's clock, PhenoAge, and GrimAge. Methylation data were obtained through methylation-sensitive single nucleotide primer extension (MS-SNuPE) or Illumina's Infinium "MethylationEPIC" array. Vitamin D-deficient participants who chose to start vitamin D supplementation after baseline examination showed a 2.6-year lower 7-CpG DNAmAA (p = 0.011) and 1.3-year lower Horvath DNAmAA (p = 0.042) compared to untreated and vitamin D-deficient participants. DNAmAA did not statistically differ between participants with successfully treated vitamin D deficiency and healthy controls (p > 0.16). Therefore, we conclude that intake of vitamin D supplement is associated with lower DNAmAA in participants with vitamin D deficiency.
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Affiliation(s)
- Valentin Max Vetter
- Biology of Aging Working Group, Department of Endocrinology and Metabolic Diseases (Including Division of Lipid Metabolism), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Department of Psychology, Humboldt University Berlin, Berlin, Germany
| | - Yasmine Sommerer
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Christian Humberto Kalies
- Biology of Aging Working Group, Department of Endocrinology and Metabolic Diseases (Including Division of Lipid Metabolism), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Dominik Spira
- Biology of Aging Working Group, Department of Endocrinology and Metabolic Diseases (Including Division of Lipid Metabolism), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, Oslo, Norway
| | - Ilja Demuth
- Biology of Aging Working Group, Department of Endocrinology and Metabolic Diseases (Including Division of Lipid Metabolism), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
- BCRT - Berlin Institute of Health Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Biology of Aging Group, Lipid Clinic at the Interdisciplinary Metabolism Center, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
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