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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays. Epigenetics 2024; 19:2333660. [PMID: 38564759 PMCID: PMC10989698 DOI: 10.1080/15592294.2024.2333660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC v1.0 arrays. We conducted a comprehensive assessment of the EPIC v1.0 array probe reliability using 69 blood DNA samples, each measured twice, generated by the Alzheimer's Disease Neuroimaging Initiative study. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliability information for probes on the EPIC v1.0 array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Juan I Young
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael A Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - X Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Brian Kunkle
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eden R Martin
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
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2
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Farina MP, Klopack ET, Umberson D, Crimmins EM. The embodiment of parental death in early life through accelerated epigenetic aging: Implications for understanding how parental death before 18 shapes age-related health risk among older adults. SSM Popul Health 2024; 26:101648. [PMID: 38596364 PMCID: PMC11002886 DOI: 10.1016/j.ssmph.2024.101648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 04/11/2024] Open
Abstract
Parental death in early life has been linked to various adverse health outcomes in older adulthood. This study extends prior research to evaluate how parental death in early life is tied to accelerated epigenetic aging, a potentially important biological mechanism from which social and environmental exposures impact age-related health. We used data from the 2016 Venous Blood Study (VBS), a component of the Health and Retirement Study (HRS), to examine the association between parental death in early life and accelerated epigenetic aging as measured by three widely used epigenetic clocks (PCPhenoAge, PCGrimAge, and DunedinPACE). We also assessed whether some of the association is explained by differences in educational attainment, depressive symptoms, and smoking behavior. Methods included a series of linear regression models and formal mediation analysis. Findings indicated that parental death in early life is associated with accelerated epigenetic aging for PCPhenoAge and DunedinPACE. The inclusion of educational attainment, depressive symptoms, and smoking behavior attenuated this association, with formal mediation analysis providing additional support for these observations. Parental death in early life may be one of the most difficult experiences an individual may face. The elevated biological risk associated with parental death in early life may operate through immediate changes but also through more downstream risk factors. This study highlights how early life adversity can set in motion biological changes that have lifelong consequences.
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Affiliation(s)
- Mateo P. Farina
- Department of Human Development and Family Sciences, University of Texas at Austin, United States
- Population Research Center, University of Texas at Austin, United States
| | - Eric T. Klopack
- Davis School of Gerontology, University of Southern California, United States
| | - Debra Umberson
- Population Research Center, University of Texas at Austin, United States
- Department of Sociology, University of Texas at Austin, United States
| | - Eileen M. Crimmins
- Davis School of Gerontology, University of Southern California, United States
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Caspi A, Shireby G, Mill J, Moffitt TE, Sugden K, Hannon E. Accelerated Pace of Aging in Schizophrenia: Five Case-Control Studies. Biol Psychiatry 2024; 95:1038-1047. [PMID: 37924924 PMCID: PMC11063120 DOI: 10.1016/j.biopsych.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/29/2023] [Accepted: 10/21/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Schizophrenia is associated with increased risk of developing multiple aging-related diseases, including metabolic, respiratory, and cardiovascular diseases, and Alzheimer's and related dementias, leading to the hypothesis that schizophrenia is accompanied by accelerated biological aging. This has been difficult to test because there is no widely accepted measure of biological aging. Epigenetic clocks are promising algorithms that are used to calculate biological age on the basis of information from combined cytosine-phosphate-guanine sites (CpGs) across the genome, but they have yielded inconsistent and often negative results about the association between schizophrenia and accelerated aging. Here, we tested the schizophrenia-aging hypothesis using a DNA methylation measure that is uniquely designed to predict an individual's rate of aging. METHODS We brought together 5 case-control datasets to calculate DunedinPACE (Pace of Aging Calculated from the Epigenome), a new measure trained on longitudinal data to detect differences between people in their pace of aging over time. Data were available from 1812 psychosis cases (schizophrenia or first-episode psychosis) and 1753 controls. Mean chronological age was 38.9 (SD = 13.6) years. RESULTS We observed consistent associations across datasets between schizophrenia and accelerated aging as measured by DunedinPACE. These associations were not attributable to tobacco smoking or clozapine medication. CONCLUSIONS Schizophrenia is accompanied by accelerated biological aging by midlife. This may explain the wide-ranging risk among people with schizophrenia for developing multiple different age-related physical diseases, including metabolic, respiratory, and cardiovascular diseases, and dementia. Measures of biological aging could prove valuable for assessing patients' risk for physical and cognitive decline and for evaluating intervention effectiveness.
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Affiliation(s)
- Avshalom Caspi
- Department of Psychology & Neuroscience, Duke University, Durham, North Carolina; Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, Psychology, & Neuroscience, King's College London, London, United Kingdom; PROMENTA, Department of Psychology, University of Oslo, Oslo, Norway.
| | - Gemma Shireby
- Centre of Longitudinal Studies, University College London, Exeter, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Terrie E Moffitt
- Department of Psychology & Neuroscience, Duke University, Durham, North Carolina; Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, Psychology, & Neuroscience, King's College London, London, United Kingdom; PROMENTA, Department of Psychology, University of Oslo, Oslo, Norway
| | - Karen Sugden
- Department of Psychology & Neuroscience, Duke University, Durham, North Carolina
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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4
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Csordas A, Sipos B, Kurucova T, Volfova A, Zamola F, Tichy B, Hicks DG. Cell Tree Rings: the structure of somatic evolution as a human aging timer. GeroScience 2024; 46:3005-3019. [PMID: 38172489 PMCID: PMC11009167 DOI: 10.1007/s11357-023-01053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
Biological age is typically estimated using biomarkers whose states have been observed to correlate with chronological age. A persistent limitation of such aging clocks is that it is difficult to establish how the biomarker states are related to the mechanisms of aging. Somatic mutations could potentially form the basis for a more fundamental aging clock since the mutations are both markers and drivers of aging and have a natural timescale. Cell lineage trees inferred from these mutations reflect the somatic evolutionary process, and thus, it has been conjectured, the aging status of the body. Such a timer has been impractical thus far, however, because detection of somatic variants in single cells presents a significant technological challenge. Here, we show that somatic mutations detected using single-cell RNA sequencing (scRNA-seq) from thousands of cells can be used to construct a cell lineage tree whose structure correlates with chronological age. De novo single-nucleotide variants (SNVs) are detected in human peripheral blood mononuclear cells using a modified protocol. A default model based on penalized multiple regression of chronological age on 31 metrics characterizing the phylogenetic tree gives a Pearson correlation of 0.81 and a median absolute error of ~4 years between predicted and chronological ages. Testing of the model on a public scRNA-seq dataset yields a Pearson correlation of 0.85. In addition, cell tree age predictions are found to be better predictors of certain clinical biomarkers than chronological age alone, for instance glucose, albumin levels, and leukocyte count. The geometry of the cell lineage tree records the structure of somatic evolution in the individual and represents a new modality of aging timer. In addition to providing a numerical estimate of "cell tree age," it unveils a temporal history of the aging process, revealing how clonal structure evolves over life span. Cell Tree Rings complements existing aging clocks and may help reduce the current uncertainty in the assessment of geroprotective trials.
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Affiliation(s)
- Attila Csordas
- AgeCurve Limited, Cambridge, CB2 1SD, UK.
- Doctoral School of Clinical Medicine, University of Szeged, Szeged, H-6720, Hungary.
| | | | - Terezia Kurucova
- CEITEC - Central European Institute of Technology, Masaryk University, 62500, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500, Brno, Czechia
| | - Andrea Volfova
- HealthyLongevity.clinic Inc, 540 University Ave, Palo Alto, CA, 94301, USA
| | - Frantisek Zamola
- HealthyLongevity.clinic Inc, 540 University Ave, Palo Alto, CA, 94301, USA
| | - Boris Tichy
- CEITEC - Central European Institute of Technology, Masaryk University, 62500, Brno, Czechia
| | - Damien G Hicks
- AgeCurve Limited, Cambridge, CB2 1SD, UK
- Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
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5
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Harvanek ZM, Kudinova AY, Wong SA, Xu K, Brick L, Daniels TE, Marsit C, Burt A, Sinha R, Tyrka AR. Childhood adversity, accelerated GrimAge, and associated health consequences. J Behav Med 2024:10.1007/s10865-024-00496-0. [PMID: 38762606 DOI: 10.1007/s10865-024-00496-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 05/01/2024] [Indexed: 05/20/2024]
Abstract
Childhood adversity is linked to psychological, behavioral, and physical health problems, including obesity and cardiometabolic disease. Epigenetic alterations are one pathway through which the effects of early life stress and adversity might persist into adulthood. Epigenetic mechanisms have also been proposed to explain why cardiometabolic health can vary greatly between individuals with similar Body Mass Index (BMIs). We evaluated two independent cross-sectional cohorts of adults without known medical illness, one of which explicitly recruited individuals with early life stress (ELS) and control participants (n = 195), and the other a general community sample (n = 477). In these cohorts, we examine associations between childhood adversity, epigenetic aging, and metabolic health. Childhood adversity was associated with increased GrimAge Acceleration (GAA) in both cohorts, both utilizing a dichotomous yes/no classification (both p < 0.01) as well as a continuous measure using the Childhood Trauma Questionnaire (CTQ) (both p < 0.05). Further investigation demonstrated that CTQ subscales for physical and sexual abuse (both p < 0.05) were associated with increased GAA in both cohorts, whereas physical and emotional neglect were not. In both cohorts, higher CTQ was also associated with higher BMI and increased insulin resistance (both p < 0.05). Finally, we demonstrate a moderating effect of BMI on the relationship between GAA and insulin resistance where GAA correlated with insulin resistance specifically at higher BMIs. These results, which were largely replicated between two independent cohorts, suggest that interactions between epigenetics, obesity, and metabolic health may be important mechanisms through which childhood adversity contributes to long-term physical and metabolic health effects.
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Affiliation(s)
- Zachary M Harvanek
- Department of Psychiatry, Yale University, New Haven, CT, USA.
- Yale Stress Center, Yale University, New Haven, CT, USA.
| | - Anastacia Y Kudinova
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA
- Bradley Hospital, Providence, RI, USA
| | - Samantha A Wong
- New York University Grossman School of Medicine, New York, USA
| | - Ke Xu
- Department of Psychiatry, Yale University, New Haven, CT, USA
- Department of Psychiatry, Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Leslie Brick
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA
| | - Teresa E Daniels
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA
- Bradley Hospital, Providence, RI, USA
- Initiative for Stress, Trauma, and Resilience, Alpert Medical School of Brown University, Providence, RI, USA
- Laboratory for Clinical and Translational Neuroscience, Butler Hospital, Providence, RI, USA
| | - Carmen Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Amber Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Rajita Sinha
- Department of Psychiatry, Yale University, New Haven, CT, USA
- Yale Stress Center, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale University, New Haven, CT, USA
- Child Study Center, Yale University, New Haven, CT, USA
| | - Audrey R Tyrka
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA
- Initiative for Stress, Trauma, and Resilience, Alpert Medical School of Brown University, Providence, RI, USA
- Laboratory for Clinical and Translational Neuroscience, Butler Hospital, Providence, RI, USA
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6
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Markov Y, Levine M, Higgins-Chen AT. Reliable detection of stochastic epigenetic mutations and associations with cardiovascular aging. GeroScience 2024:10.1007/s11357-024-01191-3. [PMID: 38736015 DOI: 10.1007/s11357-024-01191-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/01/2024] [Indexed: 05/14/2024] Open
Abstract
Stochastic epigenetic mutations (SEMs) have been proposed as novel aging biomarkers to capture heterogeneity in age-related DNA methylation changes. SEMs are defined as outlier methylation patterns at cytosine-guanine dinucleotide sites, categorized as hypermethylated (hyperSEM) or hypomethylated (hypoSEM) relative to a reference. Because SEMs are defined by their outlier status, it is critical to differentiate extreme values due to technical noise or data artifacts from those due to real biology. Using technical replicate data, we found SEM detection is not reliable: across 3 datasets, 24 to 39% of hypoSEM and 46 to 67% of hyperSEM are not shared between replicates. We identified factors influencing SEM reliability-including blood cell type composition, probe beta-value statistics, genomic location, and presence of SNPs. We used these factors in a training dataset to build a machine learning-based filter that removes unreliable SEMs, and found this filter enhances reliability in two independent validation datasets. We assessed associations between SEM loads and aging phenotypes in the Framingham Heart Study and discovered that associations with aging outcomes were in large part driven by hypoSEMs at baseline methylated probes and hyperSEMs at baseline unmethylated probes, which are the same subsets that demonstrate highest technical reliability. These aging associations were preserved after filtering out unreliable SEMs and were enhanced after adjusting for blood cell composition. Finally, we utilized these insights to formulate best practices for SEM detection and introduce a novel R package, SEMdetectR, which uses parallel programming for efficient SEM detection with comprehensive options for detection, filtering, and analysis.
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Affiliation(s)
- Yaroslav Markov
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Morgan Levine
- Altos Labs, San Diego Institute of Sciences, San Diego, CA, USA
| | - Albert T Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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7
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Hillary RF, Ng HK, McCartney DL, Elliott HR, Walker RM, Campbell A, Huang F, Direk K, Welsh P, Sattar N, Corley J, Hayward C, McIntosh AM, Sudlow C, Evans KL, Cox SR, Chambers JC, Loh M, Relton CL, Marioni RE, Yousefi PD, Suderman M. Blood-based epigenome-wide analyses of chronic low-grade inflammation across diverse population cohorts. Cell Genom 2024; 4:100544. [PMID: 38692281 PMCID: PMC11099341 DOI: 10.1016/j.xgen.2024.100544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/09/2024] [Accepted: 04/03/2024] [Indexed: 05/03/2024]
Abstract
Chronic inflammation is a hallmark of age-related disease states. The effectiveness of inflammatory proteins including C-reactive protein (CRP) in assessing long-term inflammation is hindered by their phasic nature. DNA methylation (DNAm) signatures of CRP may act as more reliable markers of chronic inflammation. We show that inter-individual differences in DNAm capture 50% of the variance in circulating CRP (N = 17,936, Generation Scotland). We develop a series of DNAm predictors of CRP using state-of-the-art algorithms. An elastic-net-regression-based predictor outperformed competing methods and explained 18% of phenotypic variance in the Lothian Birth Cohort of 1936 (LBC1936) cohort, doubling that of existing DNAm predictors. DNAm predictors performed comparably in four additional test cohorts (Avon Longitudinal Study of Parents and Children, Health for Life in Singapore, Southall and Brent Revisited, and LBC1921), including for individuals of diverse genetic ancestry and different age groups. The best-performing predictor surpassed assay-measured CRP and a genetic score in its associations with 26 health outcomes. Our findings forge new avenues for assessing chronic low-grade inflammation in diverse populations.
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Affiliation(s)
- Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hong Kiat Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; School of Psychology, University of Exeter, Exeter EX4 4QG, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Felicia Huang
- MRC Unit for Lifelong Health and Ageing, University College London, London WC1E 7HB, UK
| | - Kenan Direk
- Imperial Clinical Trials Unit, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Paul Welsh
- School of Cardiovascular and Metabolic Health, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Naveed Sattar
- School of Cardiovascular and Metabolic Health, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Janie Corley
- Lothian Birth Cohort Studies, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK
| | - Cathie Sudlow
- Centre for Clinical Brain Sciences, Edinburgh Imaging and UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; British Heart Foundation Data Science Centre, Health Data Research UK, London NW1 2BE, UK; Health Data Research UK, London NW1 2BE, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Simon R Cox
- Lothian Birth Cohort Studies, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - John C Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London W2 1PG, UK; National Skin Centre, Singapore 308205, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
| | - Paul D Yousefi
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK.
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK.
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8
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Gilchrist JJ, Fang H, Danielli S, Tomkova M, Nassiri I, Ng E, Tong O, Taylor C, Muldoon D, Cohen LRZ, Al-Mossawi H, Lau E, Neville M, Schuster-Boeckler B, Knight JC, Fairfax BP. Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes. Cell Genom 2024; 4:100541. [PMID: 38663408 PMCID: PMC11099345 DOI: 10.1016/j.xgen.2024.100541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/24/2023] [Accepted: 03/27/2024] [Indexed: 05/12/2024]
Abstract
To better understand inter-individual variation in sensitivity of DNA methylation (DNAm) to immune activity, we characterized effects of inflammatory stimuli on primary monocyte DNAm (n = 190). We find that monocyte DNAm is site-dependently sensitive to lipopolysaccharide (LPS), with LPS-induced demethylation occurring following hydroxymethylation. We identify 7,359 high-confidence immune-modulated CpGs (imCpGs) that differ in genomic localization and transcription factor usage according to whether they represent a gain or loss in DNAm. Demethylated imCpGs are profoundly enriched for enhancers and colocalize to genes enriched for disease associations, especially cancer. DNAm is age associated, and we find that 24-h LPS exposure triggers approximately 6 months of gain in epigenetic age, directly linking epigenetic aging with innate immune activity. By integrating LPS-induced changes in DNAm with genetic variation, we identify 234 imCpGs under local genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of disease-associated loci that modulate imCpG formation.
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Affiliation(s)
- James J Gilchrist
- Department of Paediatrics, University of Oxford, Oxford OX3 9DU, UK; MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Hai Fang
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sara Danielli
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Marketa Tomkova
- Ludwig Cancer Research Oxford, University of Oxford, Oxford OX3 7DQ, UK
| | - Isar Nassiri
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Esther Ng
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Orion Tong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Chelsea Taylor
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Dylan Muldoon
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lea R Z Cohen
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Hussein Al-Mossawi
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Evelyn Lau
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Matt Neville
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LE, UK
| | | | - Julian C Knight
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Benjamin P Fairfax
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Department of Oncology, University of Oxford, Oxford OX3 9DS, UK.
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9
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Pham H, Thompson-Felix T, Czamara D, Rasmussen JM, Lombroso A, Entringer S, Binder EB, Wadhwa PD, Buss C, O'Donnell KJ. The effects of pregnancy, its progression, and its cessation on human (maternal) biological aging. Cell Metab 2024; 36:877-878. [PMID: 38521058 DOI: 10.1016/j.cmet.2024.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/29/2024] [Accepted: 02/28/2024] [Indexed: 03/25/2024]
Affiliation(s)
- Hung Pham
- Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA; Department of Obstetrics Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Tara Thompson-Felix
- Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA; Department of Obstetrics Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Darina Czamara
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Jerod M Rasmussen
- Development, Health and Disease Research Program, University of California, Irvine, Irvine, CA, USA; Department of Pediatrics, University of California, Irvine, Irvine, CA, USA
| | - Adam Lombroso
- Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA; Department of Obstetrics Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Sonja Entringer
- Development, Health and Disease Research Program, University of California, Irvine, Irvine, CA, USA; Department of Pediatrics, University of California, Irvine, Irvine, CA, USA; Department of Medical Psychology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Elisabeth B Binder
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Pathik D Wadhwa
- Development, Health and Disease Research Program, University of California, Irvine, Irvine, CA, USA; Department of Pediatrics, University of California, Irvine, Irvine, CA, USA; Departments of Psychiatry & Human Behavior, Obstetrics & Gynecology, and Epidemiology, University of California, Irvine, Irvine, CA, USA
| | - Claudia Buss
- Development, Health and Disease Research Program, University of California, Irvine, Irvine, CA, USA; Department of Pediatrics, University of California, Irvine, Irvine, CA, USA; Department of Medical Psychology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kieran J O'Donnell
- Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA; Department of Obstetrics Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA.
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10
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Koncevičius K, Nair A, Šveikauskaitė A, Šeštokaitė A, Kazlauskaitė A, Dulskas A, Petronis A. Epigenetic age oscillates during the day. Aging Cell 2024:e14170. [PMID: 38638005 DOI: 10.1111/acel.14170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024] Open
Abstract
Since their introduction, epigenetic clocks have been extensively used in aging, human disease, and rejuvenation studies. In this article, we report an intriguing pattern: epigenetic age predictions display a 24-h periodicity. We tested a circadian blood sample collection using 17 epigenetic clocks addressing different aspects of aging. Thirteen clocks exhibited significant oscillations with the youngest and oldest age estimates around midnight and noon, respectively. In addition, daily oscillations were consistent with the changes of epigenetic age across different times of day observed in an independant populational dataset. While these oscillations can in part be attributed to variations in white blood cell type composition, cell count correction methods might not fully resolve the issue. Furthermore, some epigenetic clocks exhibited 24-h periodicity even in the purified fraction of neutrophils pointing at plausible contributions of intracellular epigenomic oscillations. Evidence for circadian variation in epigenetic clocks emphasizes the importance of the time-of-day for obtaining accurate estimates of epigenetic age.
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Affiliation(s)
- Karolis Koncevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Akhil Nair
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Aušrinė Šveikauskaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Agnė Šeštokaitė
- Laboratory for Genetic Diagnostics, National Cancer Institute, Vilnius, Lithuania
| | - Auksė Kazlauskaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Audrius Dulskas
- Department of Abdominal and General Surgery and Oncology, National Cancer Institute, Vilnius, Lithuania
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Artūras Petronis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
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11
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Ryan CP, Lee NR, Carba DB, MacIsaac JL, Lin DTS, Atashzay P, Belsky DW, Kobor MS, Kuzawa CW. Pregnancy is linked to faster epigenetic aging in young women. Proc Natl Acad Sci U S A 2024; 121:e2317290121. [PMID: 38588424 PMCID: PMC11032455 DOI: 10.1073/pnas.2317290121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/13/2024] [Indexed: 04/10/2024] Open
Abstract
A central prediction of evolutionary theory is that energy invested into reproduction comes at the expense of somatic maintenance and repair, accelerating biological aging. Supporting this prediction are findings that high fertility among women predicts shorter lifespan and poorer health later in life. However, biological aging is thought to begin before age-related health declines, limiting the applicability of morbidity and mortality for studying the aging process earlier in life. Here, we examine the relationship between reproductive history and biological aging in a sample of young (20 to 22yo) men and women from the Cebu Longitudinal Health and Nutrition Survey, located in the Philippines (n = 1,735). We quantify biological aging using six measures, collectively known as epigenetic clocks, reflecting various facets of cellular aging, health, and mortality risk. In a subset of women, we test whether longitudinal changes in gravidity between young and early-middle adulthood (25 to 31yo) are associated with changes in epigenetic aging during that time. Cross-sectionally, gravidity was associated with all six measures of accelerated epigenetic aging in women (n = 825). Furthermore, longitudinal increases in gravidity were linked to accelerated epigenetic aging in two epigenetic clocks (n = 331). In contrast, the number of pregnancies a man reported fathering was not associated with epigenetic aging among same-aged cohort men (n = 910). These effects were robust to socioecological, environmental, and immunological factors, consistent with the hypothesis that pregnancy accelerates biological aging and that these effects can be detected in young women in a high-fertility context.
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Affiliation(s)
- Calen P. Ryan
- Robert N. Butler Columbia Aging Center, Mailman School of Public Health, Columbia University, New York, NY10032
| | - Nanette R. Lee
- USC-Office of Population Studies Foundation, University of San Carlos, Talamban, Cebu City6000, Philippines
| | - Delia B. Carba
- USC-Office of Population Studies Foundation, University of San Carlos, Talamban, Cebu City6000, Philippines
| | - Julie L. MacIsaac
- BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BCV5Z 4H4, Canada
| | - David T. S. Lin
- BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BCV5Z 4H4, Canada
| | - Parmida Atashzay
- BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BCV5Z 4H4, Canada
| | - Daniel W. Belsky
- Robert N. Butler Columbia Aging Center, Mailman School of Public Health, Columbia University, New York, NY10032
- Department of Epidemiology, Columbia University Mailman School of Public Health, Columbia University, New York, NY10032
- Child and Brain Development Program, Canadian Institute for Advanced Research, TorontoONM5G 1M1, Canada
| | - Michael S. Kobor
- BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BCV5Z 4H4, Canada
- Child and Brain Development Program, Canadian Institute for Advanced Research, TorontoONM5G 1M1, Canada
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 2A1, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BCV5Z 4H4, Canada
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12
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Jeremian R, Lytvyn Y, Fotovati R, Li K, Malinowski A, Sachdeva M, Jack C, Gooderham M, Croitoru DO, Yeung J, Piguet V. Dysregulation of epigenetic, biological and mitotic age in the context of biologic drug treatment and phototherapy in plaque psoriasis patients. J Eur Acad Dermatol Venereol 2024. [PMID: 38619335 DOI: 10.1111/jdv.19978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/28/2024] [Indexed: 04/16/2024]
Affiliation(s)
- Richie Jeremian
- Faculty of Medicine and Health Sciences, McGill University, Montréal, Quebec, Canada
- McGill University Health Centre (MUHC) Center of Excellence for Atopic Dermatitis, Montréal, Quebec, Canada
| | - Yuliya Lytvyn
- Division of Dermatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Rayyan Fotovati
- Faculty of Medicine and Health Sciences, McGill University, Montréal, Quebec, Canada
| | - Kaiyang Li
- Faculty of Medicine and Health Sciences, McGill University, Montréal, Quebec, Canada
- McGill University Health Centre (MUHC) Center of Excellence for Atopic Dermatitis, Montréal, Quebec, Canada
| | - Alexandra Malinowski
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Muskaan Sachdeva
- Division of Dermatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Carolyn Jack
- Faculty of Medicine and Health Sciences, McGill University, Montréal, Quebec, Canada
- McGill University Health Centre (MUHC) Center of Excellence for Atopic Dermatitis, Montréal, Quebec, Canada
| | | | - David O Croitoru
- Division of Dermatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jensen Yeung
- Division of Dermatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Vincent Piguet
- Division of Dermatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Dermatology, Department of Medicine, Women's College Hospital, Toronto, Ontario, Canada
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13
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Creasey N, Leijten P, Overbeek G, Tollenaar MS. Incredible years parenting program buffers prospective association between parent-reported harsh parenting and epigenetic age deceleration in children with externalizing behavior. Psychoneuroendocrinology 2024; 165:107043. [PMID: 38593711 DOI: 10.1016/j.psyneuen.2024.107043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 04/04/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024]
Abstract
Harsh parenting has been shown to increase the risk of physical and mental health problems in later life. To improve our understanding of these risks and how they can be mitigated, we investigated associations of harsh parenting with a clinically relevant biomarker, epigenetic age deviation (EAD), using data from a randomized-control trial of the Incredible Years (IY) parenting program. This study included 281 children aged 4-8 years who were screened for heightened externalizing behavior and whose parents were randomly allocated to either IY or care-as-usual (CAU). Parents reported on their own parenting practices and their child's externalizing behavior at baseline and at a follow-up assessment approximately three years later. Epigenetic age, based on the Pediatric Buccal Epigenetic (PedBE) clock, was estimated from child DNA methylation derived from saliva collected at the follow-up assessment. PedBE clock estimates were regressed on chronological age as a measure of EAD. Moderation analyses using multiple regression revealed that harsher parenting at baseline predicted epigenetic age deceleration in children that received CAU (b = -.21, 95% CI[-0.37, -0.05]), but no association was found in children whose parents were allocated to IY (b = -.02, 95% CI [-0.13, 0.19]). These results highlight a prospective association between harsh parenting and children's EAD and indicate a potential ameliorating effect of preventive intervention. Future work is needed to replicate these findings and understand individual differences in children's responses to harsh parenting in relation to epigenetic aging.
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Affiliation(s)
- Nicole Creasey
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, the Netherlands; The Generation R Study Group, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Clinical, Educational & Health Psychology, Division of Psychology & Language Sciences, Faculty of Brain Sciences, University College London, London, UK.
| | - Patty Leijten
- Research Institute of Child Development and Education, University of Amsterdam, Amsterdam, the Netherlands
| | - Geertjan Overbeek
- Research Institute of Child Development and Education, University of Amsterdam, Amsterdam, the Netherlands
| | - Marieke S Tollenaar
- Institute of Psychology & Leiden Institute for Brain and Cognition, Leiden University, the Netherlands
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14
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Noroozi R, Rudnicka J, Pisarek A, Wysocka B, Masny A, Boroń M, Migacz-Gruszka K, Pruszkowska-Przybylska P, Kobus M, Lisman D, Zielińska G, Iljin A, Wiktorska JA, Michalczyk M, Kaczka P, Krzysztofik M, Sitek A, Ossowski A, Spólnicka M, Branicki W, Pośpiech E. Analysis of epigenetic clocks links yoga, sleep, education, reduced meat intake, coffee, and a SOCS2 gene variant to slower epigenetic aging. GeroScience 2024; 46:2583-2604. [PMID: 38103096 PMCID: PMC10828238 DOI: 10.1007/s11357-023-01029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
DNA methylation (DNAm) clocks hold promise for measuring biological age, useful for guiding clinical interventions and forensic identification. This study compared the commonly used DNAm clocks, using DNA methylation and SNP data generated from nearly 1000 human blood or buccal swab samples. We evaluated different preprocessing methods for age estimation, investigated the association of epigenetic age acceleration (EAA) with various lifestyle and sociodemographic factors, and undertook a series of novel genome-wide association analyses for different EAA measures to find associated genetic variants. Our results highlighted the Skin&Blood clock with ssNoob normalization as the most accurate predictor of chronological age. We provided novel evidence for an association between the practice of yoga and a reduction in the pace of aging (DunedinPACE). Increased sleep and physical activity were associated with lower mortality risk score (MRS) in our dataset. University degree, vegetable consumption, and coffee intake were associated with reduced levels of epigenetic aging, whereas smoking, higher BMI, meat consumption, and manual occupation correlated well with faster epigenetic aging, with FitAge, GrimAge, and DunedinPACE clocks showing the most robust associations. In addition, we found a novel association signal for SOCS2 rs73218878 (p = 2.87 × 10-8) and accelerated GrimAge. Our study emphasizes the importance of an optimized DNAm analysis workflow for accurate estimation of epigenetic age, which may influence downstream analyses. The results support the influence of genetic background on EAA. The associated SOCS2 is a member of the suppressor of cytokine signaling family known for its role in human longevity. The reported association between various risk factors and EAA has practical implications for the development of health programs to improve quality of life and reduce premature mortality associated with age-related diseases.
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Affiliation(s)
- Rezvan Noroozi
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joanna Rudnicka
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aleksandra Pisarek
- Institute of Zoology and Biomedical Research of the Jagiellonian University, Krakow, Poland
| | - Bożena Wysocka
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | | | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | | | | | - Magdalena Kobus
- Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszynski University in Warsaw, Warsaw, Poland
| | - Dagmara Lisman
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Grażyna Zielińska
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Aleksandra Iljin
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Lodz, Lodz, Poland
| | | | - Małgorzata Michalczyk
- Department of Sport Nutrition, The Jerzy Kukuczka Academy of Physical Education in Katowice, Katowice, Poland
| | - Piotr Kaczka
- Department of Sport Nutrition, The Jerzy Kukuczka Academy of Physical Education in Katowice, Katowice, Poland
| | - Michał Krzysztofik
- Department of Sport Nutrition, The Jerzy Kukuczka Academy of Physical Education in Katowice, Katowice, Poland
| | - Aneta Sitek
- Department of Anthropology, University of Lodz, Lodz, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | | | - Wojciech Branicki
- Institute of Zoology and Biomedical Research of the Jagiellonian University, Krakow, Poland
- Institute of Forensic Research, Krakow, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.
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15
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Li DL, Hodge AM, Cribb L, Southey MC, Giles GG, Milne RL, Dugué PA. Body Size, Diet Quality, and Epigenetic Aging: Cross-Sectional and Longitudinal Analyses. J Gerontol A Biol Sci Med Sci 2024; 79:glae026. [PMID: 38267386 PMCID: PMC10953795 DOI: 10.1093/gerona/glae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Indexed: 01/26/2024] Open
Abstract
Epigenetic age is an emerging marker of health that is highly predictive of disease and mortality risk. There is a lack of evidence on whether lifestyle changes are associated with changes in epigenetic aging. We used data from 1 041 participants in the Melbourne Collaborative Cohort Study with blood DNA methylation measures at baseline (1990-1994, mean age: 57.4 years) and follow-up (2003-2007, mean age: 68.8 years). The Alternative Healthy Eating Index-2010 (AHEI-2010), the Mediterranean Dietary Score, and the Dietary Inflammatory Index were used as measures of diet quality, and weight, waist circumference, and waist-to-hip ratio as measures of body size. Five age-adjusted epigenetic aging measures were considered: GrimAge, PhenoAge, PCGrimAge, PCPhenoAge, and DunedinPACE. Multivariable linear regression models including restricted cubic splines were used to assess the cross-sectional and longitudinal associations of body size and diet quality with epigenetic aging. Associations between weight and epigenetic aging cross-sectionally at both time points were positive and appeared greater for DunedinPACE (per SD: β ~0.24) than for GrimAge and PhenoAge (β ~0.10). The longitudinal associations with weight change were markedly nonlinear (U-shaped) with stable weight being associated with the lowest epigenetic aging at follow-up, except for DunedinPACE, for which only weight gain showed a positive association. We found negative, linear associations for AHEI-2010 both cross-sectionally and longitudinally. Other adiposity measures and dietary scores showed similar results. In middle-aged to older adults, declining diet quality and weight gain may increase epigenetic age, while the association for weight loss may require further investigation. Our study sheds light on the potential of weight management and dietary improvement in slowing aging processes.
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Affiliation(s)
- Danmeng Lily 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
| | - Allison M Hodge
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Lachlan Cribb
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa C Southey
- 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
| | - 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
| | - 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
| | - 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
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16
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Bozack AK, Navas-Acien A, Cardenas A. DNA Methylation-Based Biomarkers of Protein Levels and Cardiovascular Disease Risk: Opportunities and Challenges for Precision Cardiology. Circ Genom Precis Med 2024; 17:e004571. [PMID: 38348680 PMCID: PMC11021153 DOI: 10.1161/circgen.124.004571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Affiliation(s)
- Anne K Bozack
- Department of Epidemiology and Population Health (A.K.B., A.C.), Stanford University School of Medicine, CA
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY (A.N.-A.)
| | - Andres Cardenas
- Department of Epidemiology and Population Health (A.K.B., A.C.), Stanford University School of Medicine, CA
- Department of Pediatrics (A.C.), Stanford University School of Medicine, CA
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17
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de Lima Camillo LP. pyaging: a Python-based compendium of GPU-optimized aging clocks. Bioinformatics 2024; 40:btae200. [PMID: 38603598 PMCID: PMC11058068 DOI: 10.1093/bioinformatics/btae200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/28/2024] [Accepted: 04/09/2024] [Indexed: 04/13/2024] Open
Abstract
MOTIVATION Aging is intricately linked to diseases and mortality. It is reflected in molecular changes across various tissues which can be leveraged for the development of biomarkers of aging using machine learning models, known as aging clocks. Despite advancements in the field, a significant challenge remains: the lack of robust, Python-based software tools for integrating and comparing these diverse models. This gap highlights the need for comprehensive solutions that can handle the complexity and variety of data in aging research. RESULTS To address this gap, I introduce pyaging, a comprehensive open-source Python package designed to facilitate aging research. pyaging harmonizes dozens of aging clocks, covering a range of molecular data types such as DNA methylation, transcriptomics, histone mark ChIP-Seq, and ATAC-Seq. The package is not limited to traditional model types; it features a diverse array, from linear and principal component models to neural networks and automatic relevance determination models. Thanks to a PyTorch-based backend that enables GPU acceleration, pyaging is capable of rapid inference, even when dealing with large datasets and complex models. In addition, the package's support for multi-species analysis extends its utility across various organisms, including humans, various mammals, and Caenorhabditis elegans. AVAILABILITY AND IMPLEMENTATION pyaging is accessible on GitHub, at https://github.com/rsinghlab/pyaging, and the distribution is available on PyPi, at https://pypi.org/project/pyaging/. The software is also archived on Zenodo, at https://zenodo.org/doi/10.5281/zenodo.10335011.
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18
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Guida JL, Hyun G, Belsky DW, Armstrong GT, Ehrhardt MJ, Hudson MM, Green PA, Robison LL, Streck BP, Tonorezos ES, Yasui Y, Wilson CL, Wang Z, Ness KK. Associations of seven measures of biological age acceleration with frailty and all-cause mortality among adult survivors of childhood cancer in the St. Jude Lifetime Cohort. Nat Cancer 2024:10.1038/s43018-024-00745-w. [PMID: 38553617 DOI: 10.1038/s43018-024-00745-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024]
Abstract
Survivors of childhood cancer may experience accelerated biological aging, resulting in premature frailty and death. We used seven measures of biological age in the St. Jude Lifetime (SJLIFE) Cohort to compare biological age acceleration between the SJLIFE Cohort and the third United States National Health and Nutrition Examination Survey controls, explore trajectories of biological age according to cancer treatment and type, and test associations of biological age acceleration with frailty and death (mean follow-up of 26.5 years) among survivors. Survivors of cancer aged 5% faster per year and measured, on average, 0.6-6.44 years biologically older compared to controls and 5-16 years biologically older compared to age-matched individuals at the population level. Survivors treated with hematopoietic cell transplant and vinca alkaloid chemotherapy evidenced the fastest trajectories of biological aging. Biologically, older and faster-aging survivors consistently and robustly had a higher risk of frailty and died earlier than those with slower biological aging, suggesting a potential opportunity to intervene on excess aging.
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Affiliation(s)
- Jennifer L Guida
- Division of Cancer Control and Populations Sciences, National Cancer Institute, Rockville, MD, USA
| | - Geehong Hyun
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel W Belsky
- Department of Epidemiology and Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Matthew J Ehrhardt
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Melissa M Hudson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paige A Green
- Division of Cancer Control and Populations Sciences, National Cancer Institute, Rockville, MD, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brennan P Streck
- Division of Cancer Control and Populations Sciences, National Cancer Institute, Rockville, MD, USA
| | - Emily S Tonorezos
- Office of Cancer Survivorship, National Cancer Institute, Rockville, MD, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Carmen L Wilson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Harris KM, Levitt B, Gaydosh L, Martin C, Meyer JM, Mishra AA, Kelly AL, Aiello AE. The Sociodemographic and Lifestyle Correlates of Epigenetic Aging in a Nationally Representative U.S. Study of Younger Adults. bioRxiv 2024:2024.03.21.585983. [PMID: 38585956 PMCID: PMC10996523 DOI: 10.1101/2024.03.21.585983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Importance Epigenetic clocks represent molecular evidence of disease risk and aging processes and have been used to identify how social and lifestyle characteristics are associated with accelerated biological aging. However, most of this research is based on older adult samples who already have measurable chronic disease. Objective To investigate whether and how sociodemographic and lifestyle characteristics are related to biological aging in a younger adult sample across a wide array of epigenetic clock measures. Design Nationally representative prospective cohort study. Setting United States (U.S.). Participants Data come from the National Longitudinal Study of Adolescent to Adult Health, a national cohort of adolescents in grades 7-12 in U.S. in 1994 followed for 25 years over five interview waves. Our analytic sample includes participants followed-up through Wave V in 2016-18 who provided blood samples for DNA methylation (DNAm) testing (n=4237) at Wave V. Exposure Sociodemographic (sex, race/ethnicity, immigrant status, socioeconomic status, geographic location) and lifestyle (obesity status, exercise, tobacco, and alcohol use) characteristics. Main Outcome Biological aging assessed from blood DNAm using 16 epigenetic clocks when the cohort was aged 33-44 in Wave V. Results While there is considerable variation in the mean and distribution of epigenetic clock estimates and in the correlations among the clocks, we found sociodemographic and lifestyle factors are more often associated with biological aging in clocks trained to predict current or dynamic phenotypes (e.g., PhenoAge, GrimAge and DunedinPACE) as opposed to clocks trained to predict chronological age alone (e.g., Horvath). Consistent and strong associations of faster biological aging were found for those with lower levels of education and income, and those with severe obesity, no weekly exercise, and tobacco use. Conclusions and Relevance Our study found important social and lifestyle factors associated with biological aging in a nationally representative cohort of younger-aged adults. These findings indicate that molecular processes underlying disease risk can be identified in adults entering midlife before disease is manifest and represent useful targets for interventions to reduce social inequalities in heathy aging and longevity. Key Points Question: Are epigenetic clocks, measures of biological aging developed mainly on older-adult samples, meaningful for younger adults and associated with sociodemographic and lifestyle characteristics in expected patterns found in prior aging research?Findings: Sociodemographic and lifestyle factors were associated with biological aging in clocks trained to predict morbidity and mortality showing accelerated aging among those with lower levels of education and income, and those with severe obesity, no weekly exercise, and tobacco use.Meaning: Age-related molecular processes can be identified in younger-aged adults before disease manifests and represent potential interventions to reduce social inequalities in heathy aging and longevity.
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Aikins M, Willems Y, Mitchell C, Goosby B, Raffington L. Linked emergence of racial disparities in mental health and epigenetic biological aging across childhood and adolescence. bioRxiv 2024:2024.03.26.586786. [PMID: 38586008 PMCID: PMC10996608 DOI: 10.1101/2024.03.26.586786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Marginalization due to structural racism may confer an increased risk for aging-related diseases - in part - via effects on people's mental health. Here we leverage a prospective birth cohort study to examine whether the emergence of racial disparities in mental health and DNA-methylation measures of biological aging (i.e., DunedinPACE, GrimAge Acceleration, PhenoAge Acceleration) are linked across childhood and adolescence. We further consider to what extent racial disparities are statistically accounted for by perinatal and postnatal factors in preregistered analyses of N=4,898 participants from the Future of Families & Child Wellbeing Study, of which N=2,039 had repeated saliva DNA methylation at ages 9 and 15 years. We find that racially marginalized children had higher levels of externalizing and internalizing behaviors and diverging longitudinal internalizing slopes. Black compared to White identifying children, children living in more racially segregated neighborhoods, and racially marginalized children more affected by colorism tended to have higher age-9 levels of biological aging and more biological age acceleration over adolescence. Notably, longitudinal increases in internalizing and externalizing behavior were correlated with longitudinal increases in biological aging. While racial and ethnic disparities in mental health were largely statistically accounted for by socioeconomic variables, racial differences in biological aging were often still visible beyond covariate controls. Our findings indicate that racial disparities in mental health and biological aging are linked and emerge early in life. Programs promoting racial health equity must address the psychological and physical impacts of structural racism in children. Comprehensive measures of racism are lacking in current population cohorts.
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Affiliation(s)
- Muna Aikins
- Max Planck Research Group Biosocial – Biology, Social Disparities, and Development; Max Planck Institute for Human Development; Berlin, Germany
| | - Yayouk Willems
- Max Planck Research Group Biosocial – Biology, Social Disparities, and Development; Max Planck Institute for Human Development; Berlin, Germany
| | - Colter Mitchell
- Survey Research Center of the Institute for Social Research; University of Michigan, Ann Arbor, MI, USA
- Population Studies Center of the Institute for Social Research; University of Michigan, Ann Arbor, MI, USA
| | - Bridget Goosby
- Population Research Center; University of Texas at Austin, Austin, TX, USA
| | - Laurel Raffington
- Max Planck Research Group Biosocial – Biology, Social Disparities, and Development; Max Planck Institute for Human Development; Berlin, Germany
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21
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Eisenberg DTA, Ryan CP, Lee NR, Carba DB, MacIsaac JL, Dever K, Atashzay P, Kobor MS, Kuzawa C. DNA methylation-based estimators of telomere length show low correspondence with paternal age at conception and other measures of external validity of telomere length. GeroScience 2024:10.1007/s11357-024-01114-2. [PMID: 38466455 DOI: 10.1007/s11357-024-01114-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
In humans, DNA methylation (DNAm) based estimators of telomere length (TL) have been shown to better predict TL-associated variables (e.g., age, sex, and mortality) than TL itself. The biological significance of DNAm-based estimators of TL (DNAmTL) is unclear. In vitro DNAmTL shortens with cell replications, even when telomerase is maintaining TL. Telomerase is typically suppressed in humans, except in testes. Accordingly, sperm TL increases with age, and offspring with greater paternal age at conception (PAC) have longer TL. Thus, we expect that PAC associations with DNAmTL can shed light on whether in vivo cell replications in the presence of high telomerase activity (production of sperm) shorten DNAmTL or if PAC-lengthened TL causes lengthened DNAmTL. In a pre-registered analysis, using data from 1733 blood samples from the Philippines, we examined the association between paternal age at conception (PAC) and offspring DNAmTL. We did not find an association between PAC and DNAmTL but found a positive association of paternal grandfather's age at father's conception predicting grandchild's DNAmTL. In post hoc analyses, we examined how DNAmTL versus qPCR-measured TL (qPCR-TL) correlated with measures typically associated with TL. Contrary to previous findings, on almost all measures of external validity (correlations with parental TLs, southern blot TL, and age), qPCR-TL outperformed DNAmTL. The "kilobase" units of DNAm-based estimators of TL showed considerable deviations from southern blot-derived kilobase measures. Our findings suggest that DNAmTL is not a reliable index of inherited aspects of TL and underscores uncertainty about the biological meaning of DNAmTL.
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Affiliation(s)
- Dan T A Eisenberg
- Department of Anthropology, University of Washington, Seattle, WA, USA.
- Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, USA.
| | - Calen P Ryan
- Columbia Aging Center GeroScience Computational Core, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Nanette R Lee
- USC-Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | - Delia B Carba
- USC-Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | - Julie L MacIsaac
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Kristy Dever
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Parmida Atashzay
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Michael S Kobor
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Christopher Kuzawa
- Department of Anthropology, Northwestern University; Institute for Policy Research, Northwestern University, Evanston, IL, USA
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22
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Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A, Abdel-Mohsen M. Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging. Microbiome 2024; 12:31. [PMID: 38383483 PMCID: PMC10882811 DOI: 10.1186/s40168-024-01758-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND People living with HIV (PLWH), even when viral replication is controlled through antiretroviral therapy (ART), experience persistent inflammation. This inflammation is partly attributed to intestinal microbial dysbiosis and translocation, which may lead to non-AIDS-related aging-associated comorbidities. The extent to which living with HIV - influenced by the infection itself, ART usage, sexual orientation, or other associated factors - affects the biological age of the intestines is unclear. Furthermore, the role of microbial dysbiosis and translocation in the biological aging of PLWH remains to be elucidated. To investigate these uncertainties, we used a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PLWH on ART and people living without HIV (PLWoH) as controls. RESULTS PLWH exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to PLWoH. Investigating the relationship between microbial translocation and biological aging, PLWH had decreased levels of tight junction proteins in the intestines, along with increased microbial translocation. This intestinal permeability correlated with faster biological aging and increased inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PLWH had higher abundance of specific pro-inflammatory bacteria, such as Catenibacterium and Prevotella. These bacteria correlated with accelerated biological aging. Conversely, the intestines of PLWH had lower abundance of bacteria known for producing the anti-inflammatory short-chain fatty acids, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbe-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid. CONCLUSIONS We identified specific microbial compositions and microbiota-related metabolic pathways that are intertwined with intestinal and systemic biological aging. This microbial signature of biological aging is likely reflecting various factors including the HIV infection itself, ART usage, sexual orientation, and other aspects associated with living with HIV. A deeper understanding of the mechanisms underlying these connections could offer potential strategies to mitigate accelerated aging and its associated health complications. Video Abstract.
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Affiliation(s)
- Shalini Singh
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Leila B Giron
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Maliha W Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Shivanjali Shankaran
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | - Phillip A Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Zlata R Bogin
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Simona A Bambi
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Aaron R Goldman
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Joao L L C Azevedo
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | | | | | | | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aswin Verhoeven
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Elena Sánchez-López
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Toshitha Kannan
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Ceylan E Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alan L Landay
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | | | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | - Mohamed Abdel-Mohsen
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA.
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23
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Willems YE, deSteiguer A, Tanksley PT, Vinnik L, Fraemke D, Okbay A, Richter D, Wagner GG, Hertwig R, Koellinger P, Tucker-Drob EM, Harden KP, Raffington L. Self-control is associated with health-relevant disparities in buccal DNA-methylation measures of biological aging in older adults. Clin Epigenetics 2024; 16:22. [PMID: 38331797 PMCID: PMC10854186 DOI: 10.1186/s13148-024-01637-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
Self-control is a personality dimension that is associated with better physical health and a longer lifespan. Here, we examined (1) whether self-control is associated with buccal and saliva DNA-methylation (DNAm) measures of biological aging quantified in children, adolescents, and adults, and (2) whether biological aging measured in buccal DNAm is associated with self-reported health. Following preregistered analyses, we computed two DNAm measures of advanced biological age (principal-component PhenoAge and GrimAge Acceleration) and a DNAm measure of pace of aging (DunedinPACE) in buccal samples from the German Socioeconomic Panel Study (SOEP-G[ene], n = 1058, age range 0-72, Mage = 42.65) and saliva samples from the Texas Twin Project (TTP, n = 1327, age range 8-20, Mage = 13.50). We found that lower self-control was associated with advanced biological age in older adults (PhenoAge Acceleration β = - .34, [- .51, - .17], p < .001; GrimAge Acceleration β = - .34, [- .49, - .19], p < .001), but not young adults, adolescents or children. These associations remained statistically robust even after correcting for possible confounders such as socioeconomic contexts, BMI, or genetic correlates of low self-control. Moreover, a faster pace of aging and advanced biological age measured in buccal DNAm were associated with self-reported disease (PhenoAge Acceleration: β = .13 [.06, .19], p < .001; GrimAge Acceleration: β = .19 [.12, .26], p < .001; DunedinPACE: β = .09 [.02, .17], p = .01). However, effect sizes were weaker than observations in blood, suggesting that customization of DNAm aging measures to buccal and saliva tissues may be necessary. Our findings are consistent with the hypothesis that self-control is associated with health via pathways that accelerate biological aging in older adults.
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Affiliation(s)
- Y E Willems
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany
| | - A deSteiguer
- Population Research Center, The University of Texas, Austin, USA
| | - P T Tanksley
- Population Research Center, The University of Texas, Austin, USA
| | - L Vinnik
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany
| | - D Fraemke
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany
| | - A Okbay
- School of Business and Economics, Economics Fellow, Tinbergen Institute, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - D Richter
- SHARE Berlin Institute GmbH, Berlin, Germany
- Department of Education and Psychology, Freie Universität Berlin, Berlin, Germany
| | - G G Wagner
- Max Planck Institute for Human Development, Berlin, Germany
- German Socio Economic Panel Study (SOEP), Berlin, Germany
| | - R Hertwig
- Max Planck Institute for Human Development, Berlin, Germany
| | - P Koellinger
- School of Business and Economics, Economics Fellow, Tinbergen Institute, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - E M Tucker-Drob
- Population Research Center, The University of Texas, Austin, USA
| | - K P Harden
- Population Research Center, The University of Texas, Austin, USA
| | - Laurel Raffington
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany.
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24
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Moqri M, Herzog C, Poganik JR, Ying K, Justice JN, Belsky DW, Higgins-Chen AT, Chen BH, Cohen AA, Fuellen G, Hägg S, Marioni RE, Widschwendter M, Fortney K, Fedichev PO, Zhavoronkov A, Barzilai N, Lasky-Su J, Kiel DP, Kennedy BK, Cummings S, Slagboom PE, Verdin E, Maier AB, Sebastiano V, Snyder MP, Gladyshev VN, Horvath S, Ferrucci L. Validation of biomarkers of aging. Nat Med 2024; 30:360-372. [PMID: 38355974 PMCID: PMC11090477 DOI: 10.1038/s41591-023-02784-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/19/2023] [Indexed: 02/16/2024]
Abstract
The search for biomarkers that quantify biological aging (particularly 'omic'-based biomarkers) has intensified in recent years. Such biomarkers could predict aging-related outcomes and could serve as surrogate endpoints for the evaluation of interventions promoting healthy aging and longevity. However, no consensus exists on how biomarkers of aging should be validated before their translation to the clinic. Here, we review current efforts to evaluate the predictive validity of omic biomarkers of aging in population studies, discuss challenges in comparability and generalizability and provide recommendations to facilitate future validation of biomarkers of aging. Finally, we discuss how systematic validation can accelerate clinical translation of biomarkers of aging and their use in gerotherapeutic clinical trials.
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Affiliation(s)
- Mahdi Moqri
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Obstetrics and Gynecology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening Institute, Universität Innsbruck, Innsbruck, Austria
| | - Jesse R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kejun Ying
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jamie N Justice
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Daniel W Belsky
- Department of Epidemiology, Butler Columbia Aging Center, Mailman School of Public Health, Columbia University, New York, NY, USA
| | | | - Brian H Chen
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, San Diego, CA, USA
| | - Alan A Cohen
- Department of Environmental Health Sciences, Butler Columbia Aging Center, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening Institute, Universität Innsbruck, Innsbruck, Austria
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, UK
- Department of Women's and Children's Health, Division of Obstetrics and Gynaecology, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Nir Barzilai
- Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jessica Lasky-Su
- Department of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Douglas P Kiel
- Musculoskeletal Research Center, Hinda and Arthur Marcus Institute for Aging Research and Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Brian K Kennedy
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore, Singapore
| | - Steven Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Andrea B Maier
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore, Singapore
- Department of Human Movement Sciences, @AgeAmsterdam, Amsterdam Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Vittorio Sebastiano
- Department of Obstetrics and Gynecology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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25
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Mitteldorf J. Biological Clocks: Why We Need Them, Why We Cannot Trust Them, How They Might Be Improved. Biochemistry (Mosc) 2024; 89:356-366. [PMID: 38622101 DOI: 10.1134/s0006297924020135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 04/17/2024]
Abstract
Late in life, the body is at war with itself. There is a program of self-destruction (phenoptosis) implemented via epigenetic and other changes. I refer to these as type (1) epigenetic changes. But the body retains a deep instinct for survival, and other epigenetic changes unfold in response to a perception of accumulated damage (type (2)). In the past decade, epigenetic clocks have promised to accelerate the search for anti-aging interventions by permitting prompt, reliable, and convenient measurement of their effects on lifespan without having to wait for trial results on mortality and morbidity. However, extant clocks do not distinguish between type (1) and type (2). Reversing type (1) changes extends lifespan, but reversing type (2) shortens lifespan. This is why all extant epigenetic clocks may be misleading. Separation of type (1) and type (2) epigenetic changes will lead to more reliable clock algorithms, but this cannot be done with statistics alone. New experiments are proposed. Epigenetic changes are the means by which the body implements phenoptosis, but they do not embody a clock mechanism, so they cannot be the body's primary timekeeper. The timekeeping mechanism is not yet understood, though there are hints that it may be (partially) located in the hypothalamus. For the future, we expect that the most fundamental measurement of biological age will observe this clock directly, and the most profound anti-aging interventions will manipulate it.
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26
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Föhr T, Hendrix A, Kankaanpää A, Laakkonen EK, Kujala U, Pietiläinen KH, Lehtimäki T, Kähönen M, Raitakari O, Wang X, Kaprio J, Ollikainen M, Sillanpää E. Metabolic syndrome and epigenetic aging: a twin study. Int J Obes (Lond) 2024:10.1038/s41366-024-01466-x. [PMID: 38273034 DOI: 10.1038/s41366-024-01466-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/13/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND Metabolic syndrome (MetS) is associated with premature aging, but whether this association is driven by genetic or lifestyle factors remains unclear. METHODS Two independent discovery cohorts, consisting of twins and unrelated individuals, were examined (N = 268, aged 23-69 years). The findings were replicated in two cohorts from the same base population. One consisted of unrelated individuals (N = 1 564), and the other of twins (N = 293). Participants' epigenetic age, estimated using blood DNA methylation data, was determined using the epigenetic clocks GrimAge and DunedinPACE. The individual-level linear regression models for investigating the associations of MetS and its components with epigenetic aging were followed by within-twin-pair analyses using fixed-effects regression models to account for genetic factors. RESULTS In individual-level analyses, GrimAge age acceleration was higher among participants with MetS (N = 56) compared to participants without MetS (N = 212) (mean 2.078 [95% CI = 0.996,3.160] years vs. -0.549 [-1.053,-0.045] years, between-group p = 3.5E-5). Likewise, the DunedinPACE estimate was higher among the participants with MetS compared to the participants without MetS (1.032 [1.002,1.063] years/calendar year vs. 0.911 [0.896,0.927] years/calendar year, p = 4.8E-11). An adverse profile in terms of specific MetS components was associated with accelerated aging. However, adjustments for lifestyle attenuated these associations; nevertheless, for DunedinPACE, they remained statistically significant. The within-twin-pair analyses suggested that genetics explains these associations fully for GrimAge and partly for DunedinPACE. The replication analyses provided additional evidence that the association between MetS components and accelerated aging is independent of the lifestyle factors considered in this study, however, suggesting that genetics is a significant confounder in this association. CONCLUSIONS The results of this study suggests that MetS is associated with accelerated epigenetic aging, independent of physical activity, smoking or alcohol consumption, and that the association may be explained by genetics.
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Affiliation(s)
- Tiina Föhr
- Faculty of Sport and Health Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland.
| | - Arne Hendrix
- Physical Activity, Sport & Health Research Group, Department of Movement Sciences, KU Leuven - University of Leuven, Leuven, Belgium
| | - Anna Kankaanpää
- Faculty of Sport and Health Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
| | - Eija K Laakkonen
- Faculty of Sport and Health Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
| | - Urho Kujala
- Faculty of Sport and Health Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Healthy Weight Hub, Endocrinology, Abdominal Center, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Xiaoling Wang
- Georgia Prevention Institute (GPI), Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Elina Sillanpää
- Faculty of Sport and Health Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
- The Wellbeing Services County of Central Finland, Jyväskylä, Finland
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Neytchev O, Erlandsson H, Witasp A, Nordfors L, Qureshi AR, Iseri K, Morohoshi H, Selman C, Ebert T, Kublickiene K, Stenvinkel P, Shiels PG. Epigenetic clocks indicate that kidney transplantation and not dialysis mitigate the effects of renal ageing. J Intern Med 2024; 295:79-90. [PMID: 37827529 DOI: 10.1111/joim.13724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
BACKGROUND Chronic kidney disease (CKD) is an age-related disease that displays multiple features of accelerated ageing. It is currently unclear whether the two treatment options for end-stage kidney disease (dialysis and kidney transplantation [KT]) ameliorate the accelerated uremic ageing process. METHODS Data on clinical variables and blood DNA methylation (DNAm) from CKD stage G3-G5 patients were used to estimate biological age based on blood biomarkers (phenotypic age [PA], n = 333), skin autofluorescence (SAF age, n = 199) and DNAm (Horvath, Hannum and PhenoAge clocks, n = 47). In the DNAm cohort, we also measured the change in biological age 1 year after the KT or initiation of dialysis. Healthy subjects recruited from the general population were included as controls. RESULTS All three DNAm clocks indicated an increased biological age in CKD G5. However, PA and SAF age tended to produce implausibly large estimates of biological age in CKD G5. By contrast, DNAm age was 4.9 years (p = 0.005) higher in the transplantation group and 5.9 years (p = 0.001) higher in the dialysis group compared to controls. This age acceleration was significantly reduced 1 year after KT, but not after 1 year of dialysis. CONCLUSIONS Kidney failure patients displayed an increased biological age as estimated by DNAm clocks compared to population-based controls. Our results suggest that KT, but not dialysis, partially reduces the age acceleration.
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Affiliation(s)
- Ognian Neytchev
- College of Medical, Veterinary & Life Sciences, School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Helen Erlandsson
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Witasp
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Louise Nordfors
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Abdul Rashid Qureshi
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ken Iseri
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Hokuto Morohoshi
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Colin Selman
- College of Medical, Veterinary & Life Sciences, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Thomas Ebert
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Karolina Kublickiene
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Peter Stenvinkel
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paul G Shiels
- College of Medical, Veterinary & Life Sciences, School of Molecular Biosciences, University of Glasgow, Glasgow, UK
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28
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Voisin S, Seale K, Jacques M, Landen S, Harvey NR, Haupt LM, Griffiths LR, Ashton KJ, Coffey VG, Thompson JM, Doering TM, Lindholm ME, Walsh C, Davison G, Irwin R, McBride C, Hansson O, Asplund O, Heikkinen AE, Piirilä P, Pietiläinen KH, Ollikainen M, Blocquiaux S, Thomis M, Coletta DK, Sharples AP, Eynon N. Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle. Aging Cell 2024; 23:e13859. [PMID: 37128843 PMCID: PMC10776126 DOI: 10.1111/acel.13859] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
Exercise training prevents age-related decline in muscle function. Targeting epigenetic aging is a promising actionable mechanism and late-life exercise mitigates epigenetic aging in rodent muscle. Whether exercise training can decelerate, or reverse epigenetic aging in humans is unknown. Here, we performed a powerful meta-analysis of the methylome and transcriptome of an unprecedented number of human skeletal muscle samples (n = 3176). We show that: (1) individuals with higher baseline aerobic fitness have younger epigenetic and transcriptomic profiles, (2) exercise training leads to significant shifts of epigenetic and transcriptomic patterns toward a younger profile, and (3) muscle disuse "ages" the transcriptome. Higher fitness levels were associated with attenuated differential methylation and transcription during aging. Furthermore, both epigenetic and transcriptomic profiles shifted toward a younger state after exercise training interventions, while the transcriptome shifted toward an older state after forced muscle disuse. We demonstrate that exercise training targets many of the age-related transcripts and DNA methylation loci to maintain younger methylome and transcriptome profiles, specifically in genes related to muscle structure, metabolism, and mitochondrial function. Our comprehensive analysis will inform future studies aiming to identify the best combination of therapeutics and exercise regimes to optimize longevity.
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Affiliation(s)
- Sarah Voisin
- Institute for Health and Sport (iHeS)Victoria UniversityFootscrayVictoriaAustralia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Kirsten Seale
- Institute for Health and Sport (iHeS)Victoria UniversityFootscrayVictoriaAustralia
| | - Macsue Jacques
- Institute for Health and Sport (iHeS)Victoria UniversityFootscrayVictoriaAustralia
| | - Shanie Landen
- Institute for Health and Sport (iHeS)Victoria UniversityFootscrayVictoriaAustralia
| | - Nicholas R. Harvey
- Faculty of Health Sciences and MedicineBond UniversityGold CoastQueenslandAustralia
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Larisa M. Haupt
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
- ARC Training Centre for Cell and Tissue Engineering TechnologiesQueensland University of Technology (QUT)BrisbaneQueenslandAustralia
- Max Planck Queensland Centre for the Materials Sciences of Extracellular MatricesBrisbaneQueenslandAustralia
| | - Lyn R. Griffiths
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Kevin J. Ashton
- Faculty of Health Sciences and MedicineBond UniversityGold CoastQueenslandAustralia
| | - Vernon G. Coffey
- Faculty of Health Sciences and MedicineBond UniversityGold CoastQueenslandAustralia
| | | | - Thomas M. Doering
- School of Health, Medical and Applied SciencesCentral Queensland UniversityRockhamptonQueenslandAustralia
| | - Malene E. Lindholm
- Department of Medicine, School of MedicineStanford UniversityStanfordCaliforniaUSA
| | - Colum Walsh
- Genomic Medicine Research Group, School of Biomedical SciencesUlster UniversityColeraineUK
| | - Gareth Davison
- Sport and Exercise Sciences Research InstituteUlster UniversityBelfastUK
| | - Rachelle Irwin
- Genomic Medicine Research Group, School of Biomedical SciencesUlster UniversityColeraineUK
| | - Catherine McBride
- Sport and Exercise Sciences Research InstituteUlster UniversityBelfastUK
| | - Ola Hansson
- Department of Clinical Sciences, Genomics, Diabetes and Endocrinology Unit, Lund University Diabetes CenterLund UniversityLundSweden
- Institute for Molecular Medicine Finland (FIMM)Helsinki UniversityHelsinkiFinland
| | - Olof Asplund
- Department of Clinical Sciences, Genomics, Diabetes and Endocrinology Unit, Lund University Diabetes CenterLund UniversityLundSweden
| | - Aino E. Heikkinen
- Institute for Molecular Medicine Finland (FIMM)Helsinki UniversityHelsinkiFinland
| | - Päivi Piirilä
- Unit of Clinical PhysiologyHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Kirsi H. Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- HealthyWeightHub, Endocrinology, Abdominal CenterHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM)Helsinki UniversityHelsinkiFinland
- Minerva Foundation Institute for Medical ResearchHelsinkiFinland
| | - Sara Blocquiaux
- Department of Movement Sciences, Physical Activity, Sports and Health Research GroupKU LeuvenLeuvenBelgium
| | - Martine Thomis
- Department of Movement Sciences, Physical Activity, Sports and Health Research GroupKU LeuvenLeuvenBelgium
| | - Dawn K. Coletta
- Department of Medicine, Division of EndocrinologyUniversity of ArizonaTucsonArizonaUSA
- UA Center for Disparities in Diabetes Obesity and MetabolismUniversity of ArizonaTucsonArizonaUSA
- Department of PhysiologyUniversity of ArizonaTucsonArizonaUSA
| | - Adam P. Sharples
- Institute of Physical PerformanceNorwegian School of Sport SciencesOsloNorway
| | - Nir Eynon
- Institute for Health and Sport (iHeS)Victoria UniversityFootscrayVictoriaAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoriaAustralia
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Corley MJ, Pang APS, Shikuma CM, Ndhlovu LC. Cell-type specific impact of metformin on monocyte epigenetic age reversal in virally suppressed older people living with HIV. Aging Cell 2024; 23:e13926. [PMID: 37675817 PMCID: PMC10776116 DOI: 10.1111/acel.13926] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 09/08/2023] Open
Abstract
The anti-diabetic drug metformin may promote healthy aging. However, few clinical trials of metformin assessing biomarkers of aging have been completed. In this communication, we retrospectively examined the effect of metformin on epigenetic age using principal component (PC)-based epigenetic clocks, mitotic clocks, and pace of aging in peripheral monocytes and CD8+ T cells from participants in two clinical trials of virologically-suppressed people living with HIV (PLWH) with normal glucose receiving metformin. In a small 24-week clinical trial that randomized participants to receive either adjunctive metformin or observation, we observed significantly decreased PCPhenoAge and PCGrimAge estimates of monocytes from only participants in the metformin arm by a mean decrease of 3.53 and 1.84 years from baseline to Week 24. In contrast, we observed no significant differences in all PC clocks for participants in the observation arm over 24 weeks. Notably, our analysis of epigenetic mitotic clocks revealed significant increases for monocytes in the metformin arm when comparing baseline to Week 24, suggesting an impact of metformin on myeloid cell kinetics. Analysis of a single-arm clinical trial of adjunctive metformin in eight PLWH revealed no significant differences across all epigenetic clocks assessed in CD8+ T cells at 4- and 8-week time points. Our results suggest cell-type-specific myeloid effects of metformin captured by PC-based epigenetic clock biomarkers. Larger clinical studies of metformin are needed to validate these observations and this report highlights the need for further inclusion of PLWH in geroscience trials evaluating the effect of metformin on increasing healthspan and lifespan.
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Affiliation(s)
- Michael J. Corley
- Department of Medicine, Division of Infectious DiseasesWeill Cornell MedicineNew York CityNew YorkUSA
| | - Alina P. S. Pang
- Department of Medicine, Division of Infectious DiseasesWeill Cornell MedicineNew York CityNew YorkUSA
| | - Cecilia M. Shikuma
- Hawaii Center for AIDS, John A. Burns School of MedicineUniversity of HawaiiHonoluluHawaiiUSA
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious DiseasesWeill Cornell MedicineNew York CityNew YorkUSA
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Drouard G, Wang Z, Heikkinen A, Foraster M, Julvez J, Kanninen KM, van Kamp I, Pirinen M, Ollikainen M, Kaprio J. Lifestyle differences between co-twins are associated with decreased similarity in their internal and external exposome profiles. medRxiv 2023:2023.12.12.23299868. [PMID: 38168348 PMCID: PMC10760270 DOI: 10.1101/2023.12.12.23299868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Whether differences in lifestyle between co-twins are reflected in differences in their internal or external exposome profiles remains largely underexplored. We therefore investigated whether within-pair differences in lifestyle were associated with within-pair differences in exposome profiles across four domains: the external exposome, proteome, metabolome and epigenetic age acceleration (EAA). For each domain, we assessed the similarity of co-twin profiles using Gaussian similarities in up to 257 young adult same-sex twin pairs (54% monozygotic). We additionally tested whether similarity in one domain translated into greater similarity in another. Results suggest that a lower degree of similarity in co-twins' exposome profiles was associated with greater differences in their behavior and substance use. The strongest association was identified between excessive drinking behavior and the external exposome. Overall, our study demonstrates how social behavior and especially substance use are connected to the internal and external exposomes, while controlling for familial confounders.
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Affiliation(s)
- Gabin Drouard
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Zhiyang Wang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Maria Foraster
- PHAGEX Research Group, Blanquerna School of Health Science, Universitat Ramon Llull (URL), Barcelona, Spain
| | - Jordi Julvez
- Clinical and epidemiological Neuroscience (NeuroÈpia), Institut d’Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
- ISGlobal, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Katja M. Kanninen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Irene van Kamp
- National Institute for Public Health and the Environment, centre for Sustainability, Environment and Health, Netherlands
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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31
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Markov Y, Levine M, Higgins-Chen AT. Stochastic Epigenetic Mutations: Reliable Detection and Associations with Cardiovascular Aging. bioRxiv 2023:2023.12.12.571149. [PMID: 38168247 PMCID: PMC10760000 DOI: 10.1101/2023.12.12.571149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Stochastic Epigenetic Mutations (SEMs) have been proposed as novel aging biomarkers that have the potential to capture heterogeneity in age-related DNA methylation (DNAme) changes. SEMs are defined as outlier methylation patterns at cytosine-guanine dinucleotide (CpG) sites, categorized as hypermethylated (hyperSEM) or hypomethylated (hypoSEM) relative to a reference. While individual SEMs are rarely consistent across subjects, the SEM load - the total number of SEMs - increases with age. However, given poor technical reliability of measurement for many DNA methylation sites, we posited that many outliers might represent technical noise. Our study of whole blood samples from 36 individuals, each measured twice, found that 23.3% of hypoSEM and 45.6% hyperSEM are not shared between replicates. This diminishes the reliability of SEM loads, where intraclass correlation coefficients are 0.96 for hypoSEM and 0.90 for hyperSEM. We linked SEM reliability to multiple factors, including blood cell type composition, probe beta-value statistics, and presence of SNPs. A machine learning approach, leveraging these factors, filtered unreliable SEMs, enhancing reliability in a separate dataset of technical replicates from 128 individuals. Analysis of the Framingham Heart Study confirmed previously reported SEM association with mortality and revealed novel connections to cardiovascular disease. We discover that associations with aging outcomes are primarily driven by hypoSEMs at baseline methylated probes and hyperSEMs at baseline unmethylated probes, which are the same subsets that demonstrate highest technical reliability. These aging associations are preserved after filtering out unreliable SEMs and are enhanced after adjusting for blood cell composition. Finally, we utilize these insights to formulate best practices for SEM detection and introduce a novel R package, SEMdetectR, which utilizes parallel programming for efficient SEM detection with comprehensive options for detection, filtering, and analysis.
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Affiliation(s)
- Yaroslav Markov
- Program in Computational Biology & Bioinformatics, Yale Graduate School of Arts and Sciences, New Haven, CT, USA
| | - Morgan Levine
- Altos Labs, San Diego Institute of Sciences, San Diego, CA, USA
| | - Albert T Higgins-Chen
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
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32
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Ndhlovu LC, Bendall ML, Dwaraka V, Pang APS, Dopkins N, Carreras N, Smith R, Nixon DF, Corley MJ. Retroelement-Age Clocks: Epigenetic Age Captured by Human Endogenous Retrovirus and LINE-1 DNA methylation states. bioRxiv 2023:2023.12.06.570422. [PMID: 38106164 PMCID: PMC10723416 DOI: 10.1101/2023.12.06.570422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human endogenous retroviruses (HERVs), the remnants of ancient viral infections embedded within the human genome, and long interspersed nuclear elements 1 (LINE-1), a class of autonomous retrotransposons, are silenced by host epigenetic mechanisms including DNA methylation. The resurrection of particular retroelements has been linked to biological aging. Whether the DNA methylation states of locus specific HERVs and LINEs can be used as a biomarker of chronological age in humans remains unclear. We show that highly predictive epigenetic clocks of chronological age can be constructed from retroelement DNA methylation states in the immune system, across human tissues, and pan-mammalian species. We found retroelement epigenetic clocks were reversed during transient epigenetic reprogramming, accelerated in people living with HIV-1, responsive to antiretroviral therapy, and accurate in estimating long-term culture ages of human brain organoids. Our findings support the hypothesis of epigenetic dysregulation of retroelements as a potential contributor to the biological hallmarks of aging.
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Affiliation(s)
- Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Matthew L. Bendall
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | - Alina PS Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Nicholas Dopkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | | | - Douglas F. Nixon
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
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33
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Kalyakulina A, Yusipov I, Kondakova E, Bacalini MG, Giuliani C, Sivtseva T, Semenov S, Ksenofontov A, Nikolaeva M, Khusnutdinova E, Zakharova R, Vedunova M, Franceschi C, Ivanchenko M. Epigenetics of the far northern Yakutian population. Clin Epigenetics 2023; 15:189. [PMID: 38053163 PMCID: PMC10699032 DOI: 10.1186/s13148-023-01600-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Yakuts are one of the indigenous populations of the subarctic and arctic territories of Siberia characterized by a continental subarctic climate with severe winters, with the regular January average temperature in the regional capital city of Yakutsk dipping below - 40 °C. The epigenetic mechanisms of adaptation to such ecologies and environments and, in particular, epigenetic age acceleration in the local population have not been studied before. RESULTS This work reports the first epigenetic study of the Yakutian population using whole-blood DNA methylation data, supplemented with the comparison to the residents of Central Russia. Gene set enrichment analysis revealed, among others, geographic region-specific differentially methylated regions associated with adaptation to climatic conditions (water consumption, digestive system regulation), aging processes (actin filament activity, cell fate), and both of them (channel activity, regulation of steroid and corticosteroid hormone secretion). Further, it is demonstrated that the epigenetic age acceleration of the Yakutian representatives is significantly higher than that of Central Russia counterparts. For both geographic regions, we showed that epigenetically males age faster than females, whereas no significant sex differences were found between the regions. CONCLUSIONS We performed the first study of the epigenetic data of the Yakutia cohort, paying special attention to region-specific features, aging processes, age acceleration, and sex specificity.
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Affiliation(s)
- Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Elena Kondakova
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | | | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126, Bologna, Italy
| | - Tatiana Sivtseva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Sergey Semenov
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Artem Ksenofontov
- State Budgetary Institution of the Republic of Sakha (Yakutia) Republican Center for Public Health and Medical Prevention, Yakutsk, 677001, Russia
| | - Maria Nikolaeva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
| | - Raisa Zakharova
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Maria Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
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Andrasfay T, Crimmins E. Occupational characteristics and epigenetic aging among older adults in the United States. Epigenetics 2023; 18:2218763. [PMID: 37300823 PMCID: PMC10259313 DOI: 10.1080/15592294.2023.2218763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/30/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Occupational characteristics have been studied as risk factors for several age-related diseases and are thought to impact the ageing process, although there has been limited empirical work demonstrating an association between adverse occupational characteristics and accelerated ageing and this prior work has yielded mixed results. We used the 2010 and 2016 waves of the Health and Retirement Study (n = 1,251) to examine the association between occupation categories and self-reported working conditions of American adults at midlife and their subsequent epigenetic ageing as measured through five epigenetic clocks: PCHorvath, PCHannum, PCPhenoAge, PCGrimAge, and DunedinPACE. We found that individuals working in sales/clerical, service, and manual work show evidence of epigenetic age acceleration compared to those working in managerial/professional jobs and that the associations were stronger with second- and third-generation clocks. Individuals reporting high stress and high physical effort at work showed evidence of epigenetic age acceleration only on PCGrimAge and DunedinPACE. Most of these associations were attenuated after adjustment for race/ethnicity, educational attainment, and lifestyle-related risk factors. Sales/clerical work remained significantly associated with PCHorvath and PCHannum, while service work remained significantly associated with PCGrimAge. The results suggest that manual work and occupational physical activity may appear to be risk factors for epigenetic age acceleration through their associations with socioeconomic status, while stress at work may be a risk factor for epigenetic age acceleration through its associations with health behaviours outside of work. Additional work is needed to understand when in the life course and the specific mechanisms through which these associations occur.
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Affiliation(s)
- Theresa Andrasfay
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Eileen Crimmins
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
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Apsley AT, Ye Q, Etzel L, Wolf S, Hastings WJ, Mattern BC, Siegel SR, Shalev I. Biological stability of DNA methylation measurements over varying intervals of time and in the presence of acute stress. Epigenetics 2023; 18:2230686. [PMID: 37393564 PMCID: PMC10316737 DOI: 10.1080/15592294.2023.2230686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
Identifying factors that influence the stability of DNA methylation measurements across biological replicates is of critical importance in basic and clinical research. Using a within-person between-group experimental design (n = 31, number of observations = 192), we report the stability of biological replicates over a variety of unique temporal scenarios, both in the absence and presence of acute psychosocial stress, and between individuals who have experienced early life adversity (ELA) and non-exposed individuals. We found that varying time intervals, acute stress, and ELA exposure influenced the stability of repeated DNA methylation measurements. In the absence of acute stress, probes were less stable as time passed; however, stress exerted a stabilizing influence on probes over longer time intervals. Compared to non-exposed individuals, ELA-exposed individuals had significantly lower probe stability immediately following acute stress. Additionally, we found that across all scenarios, probes used in most epigenetic-based algorithms for estimating epigenetic age or immune cell proportions had average or below-average stability, except for the Principal Component and DunedinPACE epigenetic ageing clocks, which were enriched for more stable probes. Finally, using highly stable probes in the absence of stress, we identified multiple probes that were hypomethylated in the presence of acute stress, regardless of ELA status. Two hypomethylated probes are located near the transcription start site of the glutathione-disulfide reductase gene (GSR), which has previously been shown to be an integral part of the stress response to environmental toxins. We discuss implications for future studies concerning the reliability and reproducibility of DNA methylation measurements.Abbreviations: DNAm - DNA methylation, CpG - 5'-cytosine-phosphate-guanine-3,' ICC - Interclass correlation coefficient, ELA - Early-life adversity, PBMCs - Peripheral blood mononuclear cells, mQTL - Methylation quantitative trait loci, TSS - Transcription start site, GSR - Glutathione-disulfide reductase gene, TSST - Trier social stress test, PC - Principal component.
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Affiliation(s)
- Abner T. Apsley
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
- Department of Molecular, Cellular and Integrative Biological Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Qiaofeng Ye
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Laura Etzel
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Sarah Wolf
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Waylon J. Hastings
- Department of Psychiatry, Tulane University School of Medicine, New Orleans, LA, USA
| | - Brooke C. Mattern
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Sue Rutherford Siegel
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Idan Shalev
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
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McMurran CE, Wang Y, Mak JKL, Karlsson IK, Tang B, Ploner A, Pedersen NL, Hägg S. Advanced biological ageing predicts future risk for neurological diagnoses and clinical examination findings. Brain 2023; 146:4891-4902. [PMID: 37490842 PMCID: PMC10690013 DOI: 10.1093/brain/awad252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/15/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
Age is a dominant risk factor for some of the most common neurological diseases. Biological ageing encompasses interindividual variation in the rate of ageing and can be calculated from clinical biomarkers or DNA methylation data amongst other approaches. Here, we tested the hypothesis that a biological age greater than one's chronological age affects the risk of future neurological diagnosis and the development of abnormal signs on clinical examination. We analysed data from the Swedish Adoption/Twin Study of Aging (SATSA): a cohort with 3175 assessments of 802 individuals followed-up over several decades. Six measures of biological ageing were generated: two physiological ages (created from bedside clinical measurements and standard blood tests) and four blood methylation age measures. Their effects on future stroke, dementia or Parkinson's disease diagnosis, or development of abnormal clinical signs, were determined using survival analysis, with and without stratification by twin pairs. Older physiological ages were associated with ischaemic stroke risk; for example one standard deviation advancement in baseline PhenoAgePhys or KDMAgePhys residual increased future ischaemic stroke risk by 29.2% [hazard ratio (HR): 1.29, 95% confidence interval (CI) 1.06-1.58, P = 0.012] and 42.9% (HR 1.43, CI 1.18-1.73, P = 3.1 × 10-4), respectively. In contrast, older methylation ages were more predictive of future dementia risk, which was increased by 29.7% (HR 1.30, CI 1.07-1.57, P = 0.007) per standard deviation advancement in HorvathAgeMeth. Older physiological ages were also positively associated with future development of abnormal patellar or pupillary reflexes, and the loss of normal gait. Measures of biological ageing can predict clinically relevant pathology of the nervous system independent of chronological age. This may help to explain variability in disease risk between individuals of the same age and strengthens the case for trials of geroprotective interventions for people with neurological disorders.
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Affiliation(s)
- Christopher E McMurran
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE 171 77, Sweden
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yunzhang Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE 171 77, Sweden
| | - Jonathan K L Mak
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE 171 77, Sweden
| | - Ida K Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE 171 77, Sweden
| | - Bowen Tang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE 171 77, Sweden
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE 171 77, Sweden
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE 171 77, Sweden
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE 171 77, Sweden
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Hecker J, Lee S, Kachroo P, Prokopenko D, Maaser-Hecker A, Lutz SM, Hahn G, Irizarry R, Weiss ST, DeMeo DL, Lange C. A consistent pattern of slide effects in Illumina DNA methylation BeadChip array data. Epigenetics 2023; 18:2257437. [PMID: 37731367 PMCID: PMC11062373 DOI: 10.1080/15592294.2023.2257437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/01/2023] [Indexed: 09/22/2023] Open
Abstract
Background: Recent studies have identified thousands of associations between DNA methylation CpGs and complex diseases/traits, emphasizing the critical role of epigenetics in understanding disease aetiology and identifying biomarkers. However, association analyses based on methylation array data are susceptible to batch/slide effects, which can lead to inflated false positive rates or reduced statistical powerResults: We use multiple DNA methylation datasets based on the popular Illumina Infinium MethylationEPIC BeadChip array to describe consistent patterns and the joint distribution of slide effects across CpGs, confirming and extending previous results. The susceptible CpGs overlap with the Illumina Infinium HumanMethylation450 BeadChip array content.Conclusions: Our findings reveal systematic patterns in slide effects. The observations provide further insights into the characteristics of these effects and can improve existing adjustment approaches.
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Affiliation(s)
- Julian Hecker
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Sanghun Lee
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin-si, South Korea
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dmitry Prokopenko
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Anna Maaser-Hecker
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sharon M. Lutz
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care and Harvard Medical School, Boston, MA, USA
| | - Georg Hahn
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rafael Irizarry
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Christoph Lange
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Kresovich JK, O’Brien KM, Xu Z, Weinberg CR, Sandler DP, Taylor JA. Changes in methylation-based aging in women who do and do not develop breast cancer. J Natl Cancer Inst 2023; 115:1329-1336. [PMID: 37467056 PMCID: PMC10637033 DOI: 10.1093/jnci/djad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Breast cancer survivors have increased incidence of age-related diseases, suggesting that some survivors may experience faster biological aging. METHODS Among 417 women enrolled in the prospective Sister Study cohort, DNA methylation data were generated on paired blood samples collected an average of 7.7 years apart and used to calculate 3 epigenetic metrics of biological aging (PhenoAgeAccel, GrimAgeAccel, and Dunedin Pace of Aging Calculated from the Epigenome [DunedinPACE]). Approximately half (n = 190) the women sampled were diagnosed and treated for breast cancer between blood draws, whereas the other half (n = 227) remained breast cancer-free. Breast tumor characteristics and treatment information were abstracted from medical records. RESULTS Among women who developed breast cancer, diagnoses occurred an average of 3.5 years after the initial blood draw and 4 years before the second draw. After accounting for covariates and biological aging metrics measured at baseline, women diagnosed and treated for breast cancer had higher biological aging at the second blood draw than women who remained cancer-free as measured by PhenoAgeAccel (standardized mean difference [β] = 0.13, 95% confidence interval [CI) = 0.00 to 0.26), GrimAgeAccel (β = 0.14, 95% CI = 0.03 to 0.25), and DunedinPACE (β = 0.37, 95% CI = 0.24 to 0.50). In case-only analyses assessing associations with different breast cancer therapies, radiation had strong positive associations with biological aging (PhenoAgeAccel: β = 0.39, 95% CI = 0.19 to 0.59; GrimAgeAccel: β = 0.29, 95% CI = 0.10 to 0.47; DunedinPACE: β = 0.25, 95% CI = 0.02 to 0.48). CONCLUSIONS Biological aging is accelerated following a breast cancer diagnosis and treatment. Breast cancer treatment modalities appear to differentially contribute to biological aging.
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Affiliation(s)
- Jacob K Kresovich
- Departments of Cancer Epidemiology & Breast Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Katie M O’Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
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Vladimir K, Perišić MM, Štorga M, Mostashari A, Khanin R. Epigenetics insights from perceived facial aging. Clin Epigenetics 2023; 15:176. [PMID: 37924108 PMCID: PMC10623707 DOI: 10.1186/s13148-023-01590-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023] Open
Abstract
Facial aging is the most visible manifestation of aging. People desire to look younger than others of the same chronological age. Hence, perceived age is often used as a visible marker of aging, while biological age, often estimated by methylation markers, is used as an objective measure of age. Multiple epigenetics-based clocks have been developed for accurate estimation of general biological age and the age of specific organs, including the skin. However, it is not clear whether the epigenetic biomarkers (CpGs) used in these clocks are drivers of aging processes or consequences of aging. In this proof-of-concept study, we integrate data from GWAS on perceived facial aging and EWAS on CpGs measured in blood. By running EW Mendelian randomization, we identify hundreds of putative CpGs that are potentially causal to perceived facial aging with similar numbers of damaging markers that causally drive or accelerate facial aging and protective methylation markers that causally slow down or protect from aging. We further demonstrate that while candidate causal CpGs have little overlap with known epigenetics-based clocks, they affect genes or proteins with known functions in skin aging, such as skin pigmentation, elastin, and collagen levels. Overall, our results suggest that blood methylation markers reflect facial aging processes, and thus can be used to quantify skin aging and develop anti-aging solutions that target the root causes of aging.
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Affiliation(s)
- Klemo Vladimir
- LifeNome Inc., New York, 10018, NY, USA
- Faculty of Electrical Engineering and Computing, University of Zagreb, 10000, Zagreb, Croatia
| | - Marija Majda Perišić
- LifeNome Inc., New York, 10018, NY, USA
- Faculty of Mechanical Engineering and Naval Architecture, University of Zagreb, 10000, Zagreb, Croatia
| | - Mario Štorga
- LifeNome Inc., New York, 10018, NY, USA
- Faculty of Mechanical Engineering and Naval Architecture, University of Zagreb, 10000, Zagreb, Croatia
| | | | - Raya Khanin
- LifeNome Inc., New York, 10018, NY, USA.
- Bioinformatics Core, Memorial Sloan-Kettering Cancer Center, New York, 10065, NY, USA.
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40
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Harvanek ZM, Boks MP, Vinkers CH, Higgins-Chen AT. The Cutting Edge of Epigenetic Clocks: In Search of Mechanisms Linking Aging and Mental Health. Biol Psychiatry 2023; 94:694-705. [PMID: 36764569 PMCID: PMC10409884 DOI: 10.1016/j.biopsych.2023.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Individuals with psychiatric disorders are at increased risk of age-related diseases and early mortality. Recent studies demonstrate that this link between mental health and aging is reflected in epigenetic clocks, aging biomarkers based on DNA methylation. The reported relationships between epigenetic clocks and mental health are mostly correlational, and the mechanisms are poorly understood. Here, we review recent progress concerning the molecular and cellular processes underlying epigenetic clocks as well as novel technologies enabling further studies of the causes and consequences of epigenetic aging. We then review the current literature on how epigenetic clocks relate to specific aspects of mental health, such as stress, medications, substance use, health behaviors, and symptom clusters. We propose an integrated framework where mental health and epigenetic aging are each broken down into multiple distinct processes, which are then linked to each other, using stress and schizophrenia as examples. This framework incorporates the heterogeneity and complexity of both mental health conditions and aging, may help reconcile conflicting results, and provides a basis for further hypothesis-driven research in humans and model systems to investigate potentially causal mechanisms linking aging and mental health.
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Affiliation(s)
- Zachary M Harvanek
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Marco P Boks
- Department of Psychiatry, University Medical Center Utrecht Brain Center, University of Utrecht, Utrecht, the Netherlands
| | - Christiaan H Vinkers
- Department of Psychiatry, Amsterdam University Medical Center, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Mood, Anxiety, Psychosis, Sleep & Stress program, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Albert T Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut; Department of Pathology, Yale University School of Medicine, New Haven, Connecticut.
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Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea IV, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A, Abdel-Mohsen M. Distinct Intestinal Microbial Signatures Linked to Accelerated Biological Aging in People with HIV. Res Sq 2023:rs.3.rs-3492242. [PMID: 37961645 PMCID: PMC10635386 DOI: 10.21203/rs.3.rs-3492242/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background People with HIV (PWH), even with controlled viral replication through antiretroviral therapy (ART), experience persistent inflammation. This is partly due to intestinal microbial dysbiosis and translocation. Such ongoing inflammation may lead to the development of non-AIDS-related aging-associated comorbidities. However, there remains uncertainty regarding whether HIV affects the biological age of the intestines and whether microbial dysbiosis and translocation influence the biological aging process in PWH on ART. To fill this knowledge gap, we utilized a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PWH on ART and their matched HIV-negative counterparts. Results Despite having similar chronological ages, PWH on ART exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to HIV-negative controls. Investigating the relationship between microbial translocation and biological aging, PWH on ART had decreased levels of tight junction proteins in the colon and ileum, along with increased microbial translocation. This increased intestinal permeability correlated with faster intestinal and systemic biological aging, as well as increased systemic inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PWH on ART had higher abundance of specific pro-inflammatory bacterial genera, such as Catenibacterium and Prevotella. These bacteria significantly correlated with accelerated local and systemic biological aging. Conversely, the intestines of PWH on ART had lower abundance of bacterial genera known for producing short-chain fatty acids and exhibiting anti-inflammatory properties, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria taxa were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbial-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid and oleic acid. Conclusions We identified a specific microbial composition and microbiome-related metabolic pathways that are intertwined with both intestinal and systemic biological aging in PWH on ART. A deeper understanding of the mechanisms underlying these connections could potentially offer strategies to counteract premature aging and its associated health complications in PWH.
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Chen Q, Dwaraka VB, Carreras-Gallo N, Mendez K, Chen Y, Begum S, Kachroo P, Prince N, Went H, Mendez T, Lin A, Turner L, Moqri M, Chu SH, Kelly RS, Weiss ST, Rattray NJ, Gladyshev VN, Karlson E, Wheelock C, Mathé EA, Dahlin A, McGeachie MJ, Smith R, Lasky-Su JA. OMICmAge: An integrative multi-omics approach to quantify biological age with electronic medical records. bioRxiv 2023:2023.10.16.562114. [PMID: 37904959 PMCID: PMC10614756 DOI: 10.1101/2023.10.16.562114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Biological aging is a multifactorial process involving complex interactions of cellular and biochemical processes that is reflected in omic profiles. Using common clinical laboratory measures in ~30,000 individuals from the MGB-Biobank, we developed a robust, predictive biological aging phenotype, EMRAge, that balances clinical biomarkers with overall mortality risk and can be broadly recapitulated across EMRs. We then applied elastic-net regression to model EMRAge with DNA-methylation (DNAm) and multiple omics, generating DNAmEMRAge and OMICmAge, respectively. Both biomarkers demonstrated strong associations with chronic diseases and mortality that outperform current biomarkers across our discovery (MGB-ABC, n=3,451) and validation (TruDiagnostic, n=12,666) cohorts. Through the use of epigenetic biomarker proxies, OMICmAge has the unique advantage of expanding the predictive search space to include epigenomic, proteomic, metabolomic, and clinical data while distilling this in a measure with DNAm alone, providing opportunities to identify clinically-relevant interconnections central to the aging process.
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Affiliation(s)
- Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Kevin Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Yulu Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Sofina Begum
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicole Prince
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Aaron Lin
- TruDiagnostic, Inc., Lexington, KY USA
| | | | - Mahdi Moqri
- Division of Genetics, Dept. of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Su H. Chu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Rachel S. Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicholas J.W Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde, Glasgow, UK
| | - Vadim N. Gladyshev
- Division of Genetics, Dept. of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Karlson
- Department of Personalized Medicine, Mass General Brigham and Harvard Medical School, Boston, MA, USA
| | - Craig Wheelock
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Ewy A. Mathé
- Division of Preclinical Innovation, National Center for Advancing Translational Science, National Institutes of Health, Rockville, MD, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michae J. McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Jessica A. Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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Crochemore C, Chica C, Garagnani P, Lattanzi G, Horvath S, Sarasin A, Franceschi C, Bacalini MG, Ricchetti M. Epigenomic signature of accelerated ageing in progeroid Cockayne syndrome. Aging Cell 2023; 22:e13959. [PMID: 37688320 PMCID: PMC10577576 DOI: 10.1111/acel.13959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/16/2023] [Accepted: 07/31/2023] [Indexed: 09/10/2023] Open
Abstract
Cockayne syndrome (CS) and UV-sensitive syndrome (UVSS) are rare genetic disorders caused by mutation of the DNA repair and multifunctional CSA or CSB protein, but only CS patients display a progeroid and neurodegenerative phenotype, providing a unique conceptual and experimental paradigm. As DNA methylation (DNAm) remodelling is a major ageing marker, we performed genome-wide analysis of DNAm of fibroblasts from healthy, UVSS and CS individuals. Differential analysis highlighted a CS-specific epigenomic signature (progeroid-related; not present in UVSS) enriched in three categories: developmental transcription factors, ion/neurotransmitter membrane transporters and synaptic neuro-developmental genes. A large fraction of CS-specific DNAm changes were associated with expression changes in CS samples, including in previously reported post-mortem cerebella. The progeroid phenotype of CS was further supported by epigenomic hallmarks of ageing: the prediction of DNAm of repetitive elements suggested an hypomethylation of Alu sequences in CS, and the epigenetic clock returned a marked increase in CS biological age respect to healthy and UVSS cells. The epigenomic remodelling of accelerated ageing in CS displayed both commonalities and differences with other progeroid diseases and regular ageing. CS shared DNAm changes with normal ageing more than other progeroid diseases do, and included genes functionally validated for regular ageing. Collectively, our results support the existence of an epigenomic basis of accelerated ageing in CS and unveil new genes and pathways that are potentially associated with the progeroid/degenerative phenotype.
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Affiliation(s)
- Clément Crochemore
- Institut Pasteur, Université Paris Cité, Molecular Mechanisms of Pathological and Physiological Ageing Unit, UMR3738 CNRSParisFrance
- Institut Pasteur, Team Stability of Nuclear and Mitochondrial DNA, Stem Cells and Development, UMR3738 CNRSParisFrance
- Sup'BiotechVillejuifFrance
| | - Claudia Chica
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HubParisFrance
| | - Paolo Garagnani
- IRCCS Azienda Ospedaliero‐Universitaria di BolognaBolognaItaly
- Department of Medical and Surgical Sciences (DIMEC)University of BolognaBolognaItaly
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli‐Sforza”, Unit of BolognaBolognaItaly
- IRCCS Istituto Ortopedico RizzoliBolognaItaly
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of MedicineUniversity of CaliforniaLos AngelesUSA
- Department of Biostatistics Fielding School of Public HealthUniversity of CaliforniaLos AngelesUSA
| | - Alain Sarasin
- Laboratory of Genetic Stability and Oncogenesis, Institut de Cancérologie Gustave RoussyUniversity Paris‐SudVillejuifFrance
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and MechanicsLobachevsky UniversityNizhniy NovgorodRussia
| | | | - Miria Ricchetti
- Institut Pasteur, Université Paris Cité, Molecular Mechanisms of Pathological and Physiological Ageing Unit, UMR3738 CNRSParisFrance
- Institut Pasteur, Team Stability of Nuclear and Mitochondrial DNA, Stem Cells and Development, UMR3738 CNRSParisFrance
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44
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Mastrotheodoros S, Boks MP, Rousseau C, Meeus W, Branje S. Negative parenting, epigenetic age, and psychological problems: prospective associations from adolescence to young adulthood. J Child Psychol Psychiatry 2023; 64:1446-1461. [PMID: 37203368 DOI: 10.1111/jcpp.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Epigenetic clocks are based on DNA methylation levels of several genomic loci and have been developed as indices of biological aging. Studies examining the effects of stressful environmental exposures have shown that stress is associated with differences between epigenetic age and chronological age (i.e., Epigenetic Age acceleration, EA). This pre-registered longitudinal study examined the long-term effects of negative parenting and psychological problems throughout adolescence (ages 13-17 years) on EA in late adolescence (age 17 years) and EA changes from late adolescence to young adulthood (age 25 years). Further, it examined how (change in) EA is related to changes in psychological problems from adolescence to young adulthood. METHODS We used data from a sample of 434 participants followed from age 13 to age 25, with saliva collected at ages 17 and 25. We estimated EA using four commonly used epigenetic clocks and analyzed the data using Structural Equation Modeling. RESULTS While negative parenting was not related to EA nor change in EA, (change in) EA was related to developmental indices such as externalizing problems and self-concept clarity. CONCLUSIONS Declining psychological well-being during young adulthood was preceded by EA.
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Affiliation(s)
- Stefanos Mastrotheodoros
- Department of Youth and Family, Utrecht University, Utrecht, The Netherlands
- Department of Psychology, University of Crete, Rethymno, Greece
| | - Marco P Boks
- Department of Psychiatry, Brain Center University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Céline Rousseau
- Department of Psychiatry, Brain Center University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Wim Meeus
- Department of Youth and Family, Utrecht University, Utrecht, The Netherlands
| | - Susan Branje
- Department of Youth and Family, Utrecht University, Utrecht, The Netherlands
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45
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Yaskolka Meir A, Keller M, Hoffmann A, Rinott E, Tsaban G, Kaplan A, Zelicha H, Hagemann T, Ceglarek U, Isermann B, Shelef I, Blüher M, Stumvoll M, Li J, Haange SB, Engelmann B, Rolle-Kampczyk U, von Bergen M, Hu FB, Stampfer MJ, Kovacs P, Liang L, Shai I. The effect of polyphenols on DNA methylation-assessed biological age attenuation: the DIRECT PLUS randomized controlled trial. BMC Med 2023; 21:364. [PMID: 37743489 PMCID: PMC10519069 DOI: 10.1186/s12916-023-03067-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/31/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND Epigenetic age is an estimator of biological age based on DNA methylation; its discrepancy from chronologic age warrants further investigation. We recently reported that greater polyphenol intake benefitted ectopic fats, brain function, and gut microbiota profile, corresponding with elevated urine polyphenols. The effect of polyphenol-rich dietary interventions on biological aging is yet to be determined. METHODS We calculated different biological aging epigenetic clocks of different generations (Horvath2013, Hannum2013, Li2018, Horvath skin and blood2018, PhenoAge2018, PCGrimAge2022), their corresponding age and intrinsic age accelerations, and DunedinPACE, all based on DNA methylation (Illumina EPIC array; pre-specified secondary outcome) for 256 participants with abdominal obesity or dyslipidemia, before and after the 18-month DIRECT PLUS randomized controlled trial. Three interventions were assigned: healthy dietary guidelines, a Mediterranean (MED) diet, and a polyphenol-rich, low-red/processed meat Green-MED diet. Both MED groups consumed 28 g walnuts/day (+ 440 mg/day polyphenols). The Green-MED group consumed green tea (3-4 cups/day) and Mankai (Wolffia globosa strain) 500-ml green shake (+ 800 mg/day polyphenols). Adherence to the Green-MED diet was assessed by questionnaire and urine polyphenols metabolomics (high-performance liquid chromatography quadrupole time of flight). RESULTS Baseline chronological age (51.3 ± 10.6 years) was significantly correlated with all methylation age (mAge) clocks with correlations ranging from 0.83 to 0.95; p < 2.2e - 16 for all. While all interventions did not differ in terms of changes between mAge clocks, greater Green-Med diet adherence was associated with a lower 18-month relative change (i.e., greater mAge attenuation) in Li and Hannum mAge (beta = - 0.41, p = 0.004 and beta = - 0.38, p = 0.03, respectively; multivariate models). Greater Li mAge attenuation (multivariate models adjusted for age, sex, baseline mAge, and weight loss) was mostly affected by higher intake of Mankai (beta = - 1.8; p = 0.061) and green tea (beta = - 1.57; p = 0.0016) and corresponded with elevated urine polyphenols: hydroxytyrosol, tyrosol, and urolithin C (p < 0.05 for all) and urolithin A (p = 0.08), highly common in green plants. Overall, participants undergoing either MED-style diet had ~ 8.9 months favorable difference between the observed and expected Li mAge at the end of the intervention (p = 0.02). CONCLUSIONS This study showed that MED and green-MED diets with increased polyphenols intake, such as green tea and Mankai, are inversely associated with biological aging. To the best of our knowledge, this is the first clinical trial to indicate a potential link between polyphenol intake, urine polyphenols, and biological aging. TRIAL REGISTRATION ClinicalTrials.gov, NCT03020186.
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Affiliation(s)
- Anat Yaskolka Meir
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Maria Keller
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany
| | - Anne Hoffmann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
| | - Ehud Rinott
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel
| | - Gal Tsaban
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel
- Soroka University Medical Center, 84101, Be'er Sheva, Israel
| | - Alon Kaplan
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel
| | - Hila Zelicha
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel
| | - Tobias Hagemann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Ilan Shelef
- Soroka University Medical Center, 84101, Be'er Sheva, Israel
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany
| | - Michael Stumvoll
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany
| | - Jun Li
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and, Harvard Medical School, Boston, MA, 02115, USA
| | - Sven-Bastian Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH, 04318, Leipzig, Germany
| | - Beatrice Engelmann
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH, 04318, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH, 04318, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH, 04318, Leipzig, Germany
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, 04103, Leipzig, Germany
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Meir J Stampfer
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany.
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA, 02115, USA.
| | - Iris Shai
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel.
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Faculty of Medicine, Leipzig University, Leipzig, 04103, Germany.
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Owen BM, Phie J, Huynh J, Needham S, Fraser C. Evaluation of quantitative biomarkers of aging in human PBMCs. Front Aging 2023; 4:1260502. [PMID: 37780865 PMCID: PMC10540680 DOI: 10.3389/fragi.2023.1260502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
Functional decline with age contributes significantly to the burden of disease in developed countries. There is growing interest in the development of therapeutic interventions which slow or even reverse aging. Time and cost constraints prohibit the testing of a large number of interventions for health and lifespan extension in model organisms. Cell-based models of aging could enable high throughput testing of potential interventions. Despite extensive reports in the literature of cell properties that correlate with donor age, few are robustly observed across different laboratories. This casts doubt on the extent that aging signatures are captured in cultured cells. We tested molecular changes previously reported to correlate with donor age in peripheral blood mononuclear cells (PBMCs) and evaluated their suitability for inclusion in a panel of functional aging measures. The tested measures spanned several pathways implicated in aging including epigenetic changes, apoptosis, proteostasis, and intracellular communication. Surprisingly, only two markers correlated with donor age. DNA methylation age accurately predicted donor age confirming this is a robust aging biomarker. Additionally, the apoptotic marker CD95 correlated with donor age but only within subsets of PBMCs. To demonstrate cellular rejuvenation in response to a treatment will require integration of multiple read-outs of cell function. However, building a panel of measures to detect aging in cells is challenging and further research is needed to identify robust predictors of age in humans.
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Bourdon C, Etain B, Spano L, Belzeaux R, Leboyer M, Delahaye-Duriez A, Ibrahim EC, Lutz PE, Gard S, Schwan R, Polosan M, Courtet P, Passerieux C, Bellivier F, Marie-Claire C. Accelerated aging in bipolar disorders: An exploratory study of six epigenetic clocks. Psychiatry Res 2023; 327:115373. [PMID: 37542794 DOI: 10.1016/j.psychres.2023.115373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
Bipolar disorder (BD) is a chronic and severe psychiatric disorder associated with significant medical morbidity and reduced life expectancy. In this study, we assessed accelerated epigenetic aging in individuals with BD using various DNA methylation (DNAm)-based markers. For this purpose, we used five epigenetic clocks (Horvath, Hannum, EN, PhenoAge, and GrimAge) and a DNAm-based telomere length clock (DNAmTL). DNAm profiles were obtained using Infinium MethylationEPIC Arrays from whole-blood samples of 184 individuals with BD. We also estimated blood cell counts based on DNAm levels for adjustment. Significant correlations between chronological age and each epigenetic age estimated using the six different clocks were observed. Following adjustment for blood cell counts, we found that the six epigenetic AgeAccels (age accelerations) were significantly associated with the body mass index. GrimAge AgeAccel was significantly associated with male sex, smoking status and childhood maltreatment. DNAmTL AgeAccel was significantly associated with smoking status. Overall, this study showed that distinct epigenetic clocks are sensitive to different aspects of aging process in BD. Further investigations with comprehensive epigenetic clock analyses and large samples are required to confirm our findings of potential determinants of an accelerated epigenetic aging in BD.
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Affiliation(s)
- Céline Bourdon
- Université Paris Cité, Inserm, Optimisation Thérapeutique en Neuropsychopharmacologie, F-75006 Paris, France.
| | - Bruno Etain
- Université Paris Cité, Inserm, Optimisation Thérapeutique en Neuropsychopharmacologie, F-75006 Paris, France; Département de Psychiatrie et de Médecine Addictologique, Hôpitaux Lariboisière-Fernand Widal, GHU APHP.Nord - Université de Paris, Paris, F-75010, France; Fondation Fondamental, F-94010, Créteil, France
| | - Luana Spano
- Université Paris Cité, Inserm, Optimisation Thérapeutique en Neuropsychopharmacologie, F-75006 Paris, France
| | - Raoul Belzeaux
- Pôle Universitaire de Psychiatrie, CHU de Montpellier, France; Pôle de Psychiatrie, Assistance Publique Hôpitaux de Marseille, INT-UMR7289, CNRS Aix-Marseille Université, Marseille, France; Université Paris Est Créteil, INSERM U955, IMRB, Translational Neuro-Psychiatry, Créteil, France
| | - Marion Leboyer
- Fondation Fondamental, F-94010, Créteil, France; Université Paris Est Créteil, INSERM U955, IMRB, Translational Neuro-Psychiatry, Créteil, France; AP-HP, Hôpitaux Universitaires Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision en Psychiatrie (FHU ADAPT), Créteil, France
| | | | - El Chérif Ibrahim
- Aix-Marseille Univ, CNRS, INT, Inst Neurosci Timone, 13005 Marseille, France
| | - Pierre-Eric Lutz
- Centre National de la Recherche Scientifique, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives UPR3212, F-67000 Strasbourg, France
| | - Sébastien Gard
- Fondation Fondamental, F-94010, Créteil, France; Pôle de Psychiatrie Générale et Universitaire, Centre Hospitalier Charles Perrens, Bordeaux, France
| | - Raymund Schwan
- Fondation Fondamental, F-94010, Créteil, France; Université de Lorraine, Centre Psychothérapique de Nancy, Inserm U1254, Nancy, France
| | - Mircea Polosan
- Fondation Fondamental, F-94010, Créteil, France; Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble, Institut Neurosciences, Grenoble, France
| | - Philippe Courtet
- Fondation Fondamental, F-94010, Créteil, France; IGF, Univ. Montpellier France, CNRS, INSERM, Montpellier, France; Department of Emergency Psychiatry and Acute Care, Lapeyronie Hospital, CHU Montpellier, Montpellier, France
| | - Christine Passerieux
- Fondation Fondamental, F-94010, Créteil, France; Centre Hospitalier de Versailles, Service Universitaire de Psychiatrie d'adulte et d'addictologie, Le Chesnay, France; DisAP-DevPsy-CESP, INSERM UMR1018, Université de Versailles Saint-Quentin-En-Yvelines, Université Paris-Saclay, Villejuif, France
| | - Frank Bellivier
- Université Paris Cité, Inserm, Optimisation Thérapeutique en Neuropsychopharmacologie, F-75006 Paris, France; Département de Psychiatrie et de Médecine Addictologique, Hôpitaux Lariboisière-Fernand Widal, GHU APHP.Nord - Université de Paris, Paris, F-75010, France; Fondation Fondamental, F-94010, Créteil, France
| | - Cynthia Marie-Claire
- Université Paris Cité, Inserm, Optimisation Thérapeutique en Neuropsychopharmacologie, F-75006 Paris, France
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Bobba-Alves N, Sturm G, Lin J, Ware SA, Karan KR, Monzel AS, Bris C, Procaccio V, Lenaers G, Higgins-Chen A, Levine M, Horvath S, Santhanam BS, Kaufman BA, Hirano M, Epel E, Picard M. Cellular allostatic load is linked to increased energy expenditure and accelerated biological aging. Psychoneuroendocrinology 2023; 155:106322. [PMID: 37423094 PMCID: PMC10528419 DOI: 10.1016/j.psyneuen.2023.106322] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/08/2023] [Accepted: 06/10/2023] [Indexed: 07/11/2023]
Abstract
Stress triggers anticipatory physiological responses that promote survival, a phenomenon termed allostasis. However, the chronic activation of energy-dependent allostatic responses results in allostatic load, a dysregulated state that predicts functional decline, accelerates aging, and increases mortality in humans. The energetic cost and cellular basis for the damaging effects of allostatic load have not been defined. Here, by longitudinally profiling three unrelated primary human fibroblast lines across their lifespan, we find that chronic glucocorticoid exposure increases cellular energy expenditure by ∼60%, along with a metabolic shift from glycolysis to mitochondrial oxidative phosphorylation (OxPhos). This state of stress-induced hypermetabolism is linked to mtDNA instability, non-linearly affects age-related cytokines secretion, and accelerates cellular aging based on DNA methylation clocks, telomere shortening rate, and reduced lifespan. Pharmacologically normalizing OxPhos activity while further increasing energy expenditure exacerbates the accelerated aging phenotype, pointing to total energy expenditure as a potential driver of aging dynamics. Together, our findings define bioenergetic and multi-omic recalibrations of stress adaptation, underscoring increased energy expenditure and accelerated cellular aging as interrelated features of cellular allostatic load.
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Affiliation(s)
- Natalia Bobba-Alves
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
| | - Sarah A Ware
- Department of Medicine, Vascular Medicine Institute and Center for Metabolic and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kalpita R Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Anna S Monzel
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Céline Bris
- Department of Genetics, Angers Hospital, Angers, France; MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Guy Lenaers
- Department of Genetics, Angers Hospital, Angers, France; MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France; Department of Neurology, Angers Hospital, Angers, France
| | - Albert Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven CT, United States
| | - Morgan Levine
- Altos Labs, San Diego Institute of Science, San Diego, CA United States
| | - Steve Horvath
- Altos Labs, San Diego Institute of Science, San Diego, CA United States
| | - Balaji S Santhanam
- Departments of Biological Sciences, Systems Biology, and Biochemistry and Molecular Biophysics, Institute for Cancer Dynamics, Columbia University, New York, NY, United States
| | - Brett A Kaufman
- Department of Medicine, Vascular Medicine Institute and Center for Metabolic and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Michio Hirano
- Department of Neurology, Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, United States
| | - Elissa Epel
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States; Department of Neurology, Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, United States; New York State Psychiatric Institute, New York, NY, United States.
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49
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Moqri M, Herzog C, Poganik JR, Justice J, Belsky DW, Higgins-Chen A, Moskalev A, Fuellen G, Cohen AA, Bautmans I, Widschwendter M, Ding J, Fleming A, Mannick J, Han JDJ, Zhavoronkov A, Barzilai N, Kaeberlein M, Cummings S, Kennedy BK, Ferrucci L, Horvath S, Verdin E, Maier AB, Snyder MP, Sebastiano V, Gladyshev VN. Biomarkers of aging for the identification and evaluation of longevity interventions. Cell 2023; 186:3758-3775. [PMID: 37657418 PMCID: PMC11088934 DOI: 10.1016/j.cell.2023.08.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
With the rapid expansion of aging biology research, the identification and evaluation of longevity interventions in humans have become key goals of this field. Biomarkers of aging are critically important tools in achieving these objectives over realistic time frames. However, the current lack of standards and consensus on the properties of a reliable aging biomarker hinders their further development and validation for clinical applications. Here, we advance a framework for the terminology and characterization of biomarkers of aging, including classification and potential clinical use cases. We discuss validation steps and highlight ongoing challenges as potential areas in need of future research. This framework sets the stage for the development of valid biomarkers of aging and their ultimate utilization in clinical trials and practice.
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Affiliation(s)
- Mahdi Moqri
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Obstetrics and Gynecology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening Institute, Universität Innsbruck, Innsbruck, Austria
| | - Jesse R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jamie Justice
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Daniel W Belsky
- Department of Epidemiology, Butler Columbia Aging Center, Mailman School of Public Health, Columbia University, New York, NY, USA
| | | | - Alexey Moskalev
- Institute of Biogerontology, Lobachevsky University, Nizhny Novgorod, Russia
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany; School of Medicine, University College Dublin, Dublin, Ireland
| | - Alan A Cohen
- Department of Environmental Health Sciences, Butler Columbia Aging Center, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Ivan Bautmans
- Gerontology Department, Vrije Universiteit Brussel, Brussels, Belgium; Frailty in Ageing Research Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening Institute, Universität Innsbruck, Innsbruck, Austria; Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, UK; Department of Women's and Children's Health, Division of Obstetrics and Gynaecology, Karolinska Institutet, Stockholm, Sweden
| | - Jingzhong Ding
- Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | | | - Jing-Dong Jackie Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology, Peking University, Beijing, China
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Nir Barzilai
- Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Steven Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Brian K Kennedy
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | | | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Andrea B Maier
- Department of Human Movement Sciences, @AgeAmsterdam, Amsterdam Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore, Singapore
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA.
| | - Vittorio Sebastiano
- Department of Obstetrics and Gynecology, School of Medicine, Stanford University, Stanford, CA, USA.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Minteer CJ, Thrush K, Gonzalez J, Niimi P, Rozenblit M, Rozowsky J, Liu J, Frank M, McCabe T, Sehgal R, Higgins-Chen AT, Hofstatter E, Pusztai L, Beckman K, Gerstein M, Levine ME. More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome. Sci Adv 2023; 9:eadf4163. [PMID: 37467337 PMCID: PMC10355820 DOI: 10.1126/sciadv.adf4163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/15/2023] [Indexed: 07/21/2023]
Abstract
Aging is a leading risk factor for cancer. While it is proposed that age-related accumulation of somatic mutations drives this relationship, it is likely not the full story. We show that aging and cancer share a common epigenetic replication signature, which we modeled using DNA methylation from extensively passaged immortalized human cells in vitro and tested on clinical tissues. This signature, termed CellDRIFT, increased with age across multiple tissues, distinguished tumor from normal tissue, was escalated in normal breast tissue from cancer patients, and was transiently reset upon reprogramming. In addition, within-person tissue differences were correlated with predicted lifetime tissue-specific stem cell divisions and tissue-specific cancer risk. Our findings suggest that age-related replication may drive epigenetic changes in cells and could push them toward a more tumorigenic state.
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Affiliation(s)
| | - Kyra Thrush
- Department of Pathology, Yale School of Medicine,
New Haven, CT, USA
- San Diego Institute of Science, Altos Labs, San
Diego, CA, USA
| | - John Gonzalez
- Department of Pathology, Yale School of Medicine,
New Haven, CT, USA
| | - Peter Niimi
- Department of Pathology, Yale School of Medicine,
New Haven, CT, USA
- San Diego Institute of Science, Altos Labs, San
Diego, CA, USA
| | - Mariya Rozenblit
- Department of Internal Medicine, Section of
Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Joel Rozowsky
- Department of Molecular Biophysics and
Biochemistry, Yale University, New Haven, CT, USA
| | - Jason Liu
- Department of Molecular Biophysics and
Biochemistry, Yale University, New Haven, CT, USA
| | - Mor Frank
- Department of Molecular Biophysics and
Biochemistry, Yale University, New Haven, CT, USA
| | - Thomas McCabe
- Department of Pathology, Yale School of Medicine,
New Haven, CT, USA
| | - Raghav Sehgal
- Department of Pathology, Yale School of Medicine,
New Haven, CT, USA
| | | | - Erin Hofstatter
- Department of Internal Medicine, Section of
Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Lajos Pusztai
- Department of Internal Medicine, Section of
Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Kenneth Beckman
- Biomedical Genomics Center, University of
Minnesota, Minneapolis, MN, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and
Biochemistry, Yale University, New Haven, CT, USA
| | - Morgan E. Levine
- Department of Pathology, Yale School of Medicine,
New Haven, CT, USA
- San Diego Institute of Science, Altos Labs, San
Diego, CA, USA
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