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Zhou JX, Li LX, Zhang H, Agborbesong E, Harris PC, Calvet JP, Li X. DNA methyltransferase 1 (DNMT1) promotes cyst growth and epigenetic age acceleration in autosomal dominant polycystic kidney disease. Kidney Int 2024:S0085-2538(24)00336-3. [PMID: 38782200 DOI: 10.1016/j.kint.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 02/28/2024] [Accepted: 04/05/2024] [Indexed: 05/25/2024]
Abstract
Alteration of DNA methylation leads to diverse diseases, and the dynamic changes of DNA methylation (DNAm) on sets of CpG dinucleotides in mammalian genomes are termed "DNAm age" and "epigenetic clocks" that can predict chronological age. However, whether and how dysregulation of DNA methylation promotes cyst progression and epigenetic age acceleration in autosomal dominant polycystic kidney disease (ADPKD) remains elusive. Here, we show that DNA methyltransferase 1 (DNMT1) is upregulated in cystic kidney epithelial cells and tissues and that knockout of Dnmt1 and targeting DNMT1 with hydralazine, a safe demethylating agent, delays cyst growth in Pkd1 mutant kidneys and extends life span of Pkd1 conditional knockout mice. With methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq), DNMT1 chromatin immunoprecipitation (ChIP)-sequencing and RNA-sequencing analysis, we identified two novel DNMT1 targets, PTPRM and PTPN22 (members of the protein tyrosine phosphatase family). PTPRM and PTPN22 function as mediators of DNMT1 and the phosphorylation and activation of PKD associated signaling pathways, including ERK, mTOR and STAT3. With whole genome bisulfide sequencing in kidneys of patients with ADPKD versus normal individuals, we found that the methylation of epigenetic clock associated genes was dysregulated, supporting that epigenetic age is accelerated in the kidneys of patients with ADPKD. Furthermore, five epigenetic clock associated genes, including Hsd17b14, Itpkb, Mbnl1, Rassf5 and Plk2 were identified. Thus, the diverse biological roles of these five genes suggest that their methylation status may not only predict epigenetic age acceleration but also contribute to disease progression in ADPKD.
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Affiliation(s)
- Julie Xia Zhou
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
| | - Linda Xiaoyan Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
| | - Hongbing Zhang
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Ewud Agborbesong
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
| | - Peter C Harris
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
| | - James P Calvet
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905.
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2
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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] [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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3
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Qiao X, Straight B, Ngo D, Hilton CE, Owuor Olungah C, Naugle A, Lalancette C, Needham BL. Severe drought exposure in utero associates to children's epigenetic age acceleration in a global climate change hot spot. Nat Commun 2024; 15:4140. [PMID: 38755138 PMCID: PMC11099019 DOI: 10.1038/s41467-024-48426-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
The goal of this study is to examine the association between in utero drought exposure and epigenetic age acceleration (EAA) in a global climate change hot spot. Calculations of EAA in adults using DNA methylation have been found to accurately predict chronic disease and longevity. However, fewer studies have examined EAA in children, and drought exposure in utero has not been investigated. Additionally, studies of EAA in low-income countries with diverse populations are rare. We assess EAA using epigenetic clocks and two DNAm-based pace-of-aging measurements from whole saliva samples in 104 drought-exposed children and 109 same-sex sibling controls in northern Kenya. We find a positive association between in utero drought exposure and EAA in two epigenetic clocks (Hannum's and GrimAge) and a negative association in the DNAm based telomere length (DNAmTL) clock. The combined impact of drought's multiple deleterious stressors may reduce overall life expectancy through accelerated epigenetic aging.
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Affiliation(s)
- Xi Qiao
- Department of Statistics, Western Michigan University, Kalamazoo, MI, USA
| | - Bilinda Straight
- School of Environment, Geography, & Sustainability, Western Michigan University, Kalamazoo, MI, USA.
| | - Duy Ngo
- Department of Statistics, Western Michigan University, Kalamazoo, MI, USA
| | - Charles E Hilton
- Department of Anthropology, University of North Carolina - Chapel Hill, Chapel Hill, NC, USA
| | - Charles Owuor Olungah
- Department of Anthropology, Gender and African Studies, University of Nairobi, Nairobi, Kenya
| | - Amy Naugle
- Department of Psychology, Western Michigan University, Kalamazoo, MI, USA
| | | | - Belinda L Needham
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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4
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Mayne B, Chandler D, Noune C, Espinoza T, Roberts D, Anderson C, Berry O. Increased scalability and sequencing quality of an epigenetic age prediction assay. PLoS One 2024; 19:e0297006. [PMID: 38743704 PMCID: PMC11093300 DOI: 10.1371/journal.pone.0297006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/22/2023] [Indexed: 05/16/2024] Open
Abstract
Epigenetic ageing in a human context, has been used to better understand the relationship between age and factors such as lifestyle and genetics. In an ecological setting, it has been used to predict the age of individual animals for wildlife management. Despite the importance of epigenetic ageing in a range of research fields, the assays to measure epigenetic ageing are either expensive on a large scale or complex. In this study, we aimed to improve the efficiency and sequencing quality of an existing epigenetic ageing assay for the Australian Lungfish (Neoceratodus forsteri). We used an enzyme-based alternative to bisulfite conversion to reduce DNA fragmentation and evaluated its performance relative to bisulfite conversion. We found the sequencing quality to be 12% higher with the enzymatic alternative compared to bisulfite treatment (p-value < 0.01). This new enzymatic based approach, although currently double the cost of bisulfite treatment can increases the throughput and sequencing quality. We envisage this assay setup being adopted increasingly as the scope and scale of epigenetic ageing research continues to grow.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, Western Australia, Australia
| | - David Chandler
- Australian Genome Research Facility, Perth, WA, Australia
| | | | | | | | - Chloe Anderson
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, Western Australia, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, Western Australia, Australia
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5
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Tarkhov AE, Lindstrom-Vautrin T, Zhang S, Ying K, Moqri M, Zhang B, Tyshkovskiy A, Levy O, Gladyshev VN. Nature of epigenetic aging from a single-cell perspective. NATURE AGING 2024:10.1038/s43587-024-00616-0. [PMID: 38724733 DOI: 10.1038/s43587-024-00616-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/26/2024] [Indexed: 05/15/2024]
Abstract
Age-related changes in DNA methylation (DNAm) form the basis of the most robust predictors of age-epigenetic clocks-but a clear mechanistic understanding of exactly which aspects of aging are quantified by these clocks is lacking. Here, to clarify the nature of epigenetic aging, we juxtapose the dynamics of tissue and single-cell DNAm in mice. We compare these changes during early development with those observed during adult aging in mice, and corroborate our analyses with a single-cell RNA sequencing analysis within the same multiomics dataset. We show that epigenetic aging involves co-regulated changes as well as a major stochastic component, and this is consistent with transcriptional patterns. We further support the finding of stochastic epigenetic aging by direct tissue and single-cell DNAm analyses and modeling of aging DNAm trajectories with a stochastic process akin to radiocarbon decay. Finally, we describe a single-cell algorithm for the identification of co-regulated and stochastic CpG clusters showing consistent transcriptomic coordination patterns. Together, our analyses increase our understanding of the basis of epigenetic clocks and highlight potential opportunities for targeting aging and evaluating longevity interventions.
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Affiliation(s)
- Andrei E Tarkhov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Retro Biosciences Inc., Redwood City, CA, USA.
| | - Thomas Lindstrom-Vautrin
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kejun Ying
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Mahdi Moqri
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Orr Levy
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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6
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Tong H, Dwaraka VB, Chen Q, Luo Q, Lasky-Su JA, Smith R, Teschendorff AE. Quantifying the stochastic component of epigenetic aging. NATURE AGING 2024:10.1038/s43587-024-00600-8. [PMID: 38724732 DOI: 10.1038/s43587-024-00600-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/21/2024] [Indexed: 05/15/2024]
Abstract
DNA methylation clocks can accurately estimate chronological age and, to some extent, also biological age, yet the process by which age-associated DNA methylation (DNAm) changes are acquired appears to be quasi-stochastic, raising a fundamental question: how much of an epigenetic clock's predictive accuracy could be explained by a stochastic process of DNAm change? Here, using DNAm data from sorted immune cells, we build realistic simulation models, subsequently demonstrating in over 22,770 sorted and whole-blood samples from 25 independent cohorts that approximately 66-75% of the accuracy underpinning Horvath's clock could be driven by a stochastic process. This fraction increases to 90% for the more accurate Zhang's clock, but is lower (63%) for the PhenoAge clock, suggesting that biological aging is reflected by nonstochastic processes. Confirming this, we demonstrate that Horvath's age acceleration in males and PhenoAge's age acceleration in severe coronavirus disease 2019 cases and smokers are not driven by an increased rate of stochastic change but by nonstochastic processes. These results significantly deepen our understanding and interpretation of epigenetic clocks.
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Affiliation(s)
- Huige Tong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Qi Luo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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7
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Pruszkowska-Przybylska P, Dupont ME, Jacobsen SB, Smerup M, Tfelt-Hansen J, Morling N, Andersen JD. Evaluation of DNAmAge in paired fresh, frozen, and formalin-fixed paraffin-embedded heart tissues. PLoS One 2024; 19:e0299557. [PMID: 38718072 PMCID: PMC11078437 DOI: 10.1371/journal.pone.0299557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/12/2024] [Indexed: 05/12/2024] Open
Abstract
The continued development in methylome analysis has enabled a more precise assessment of DNA methylation, but treatment of target tissue prior to analysis may affect DNA analysis. Prediction of age based on methylation levels in the genome (DNAmAge) has gained much interest in disease predisposition (biological age estimation), but also in chronological donor age estimation in crime case samples. Various epigenetic clocks were designed to predict the age. However, it remains unknown how the storage of the tissues affects the DNAmAge estimation. In this study, we investigated the storage method impact of DNAmAge by the comparing the DNAmAge of the two commonly used storage methods, freezing and formalin-fixation and paraffin-embedding (FFPE) to DNAmAge of fresh tissue. This was carried out by comparing paired heart tissue samples of fresh tissue, samples stored by freezing and FFPE to chronological age and whole blood samples from the same individuals. Illumina EPIC beadchip array was used for methylation analysis and the DNAmAge was evaluated with the following epigenetic clocks: Horvath, Hannum, Levine, Horvath skin+blood clock (Horvath2), PedBE, Wu, BLUP, EN, and TL. We observed differences in DNAmAge among the storage conditions. FFPE samples showed a lower DNAmAge compared to that of frozen and fresh samples. Additionally, the DNAmAge of the heart tissue was lower than that of the whole blood and the chronological age. This highlights caution when evaluating DNAmAge for FFPE samples as the results were underestimated compared with fresh and frozen tissue samples. Furthermore, the study also emphasizes the need for a DNAmAge model based on heart tissue samples for an accurate age estimation.
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Affiliation(s)
| | - Mikkel Eriksen Dupont
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stine Bøttcher Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Smerup
- Department of Cardiothoracic Surgery, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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Tao X, Zhu Z, Wang L, Li C, Sun L, Wang W, Gong W. Biomarkers of Aging and Relevant Evaluation Techniques: A Comprehensive Review. Aging Dis 2024; 15:977-1005. [PMID: 37611906 PMCID: PMC11081160 DOI: 10.14336/ad.2023.00808-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023] Open
Abstract
The risk of developing chronic illnesses and disabilities is increasing with age. To predict and prevent aging, biomarkers relevant to the aging process must be identified. This paper reviews the known molecular, cellular, and physiological biomarkers of aging. Moreover, we discuss the currently available technologies for identifying these biomarkers, and their applications and potential in aging research. We hope that this review will stimulate further research and innovation in this emerging and fast-growing field.
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Affiliation(s)
- Xue Tao
- Department of Research, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China.
| | - Ziman Zhu
- Beijing Rehabilitation Medicine Academy, Capital Medical University, Beijing, China.
| | - Liguo Wang
- Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
| | - Chunlin Li
- School of Biomedical Engineering, Capital Medical University, Beijing, China.
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China.
| | - Liwei Sun
- School of Biomedical Engineering, Capital Medical University, Beijing, China.
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China.
| | - Wei Wang
- Department of Rehabilitation Radiology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China.
| | - Weijun Gong
- Department of Neurological Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China.
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9
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Zoller J, Horvath S. MammalMethylClock R package: software for DNA methylation-based epigenetic clocks in mammals. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae280. [PMID: 38656974 DOI: 10.1093/bioinformatics/btae280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/16/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
MOTIVATION Epigenetic clocks are prediction methods based on DNA methylation levels in a given species or set of species. Defined as multivariate regression models, these DNA methylation-based biomarkers of age or mortality risk are useful in species conservation efforts and in preclinical studies. RESULTS We present an R package called MammalMethylClock for the construction, assessment, and application of epigenetic clocks in different mammalian species. The R package includes the utility for implementing pre-existing mammalian clocks from the Mammalian Methylation Consortium. AVAILABILITY AND IMPLEMENTATION The source code and documentation manual for MammalMethylClock, and clock coefficient .csv files that are included within this software package, can be found on Zenodo at https://doi.org/10.5281/zenodo.10971037.
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Affiliation(s)
- Joseph Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, United States
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, United States
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, United States
- Altos Labs, San Diego, CA, 92121, United States
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10
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Gerra MC, Dallabona C, Cecchi R. Epigenetic analyses in forensic medicine: future and challenges. Int J Legal Med 2024; 138:701-719. [PMID: 38242965 PMCID: PMC11003920 DOI: 10.1007/s00414-024-03165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
The possibility of using epigenetics in forensic investigation has gradually risen over the last few years. Epigenetic changes with their dynamic nature can either be inherited or accumulated throughout a lifetime and be reversible, prompting investigation of their use across various fields. In forensic sciences, multiple applications have been proposed, such as the discrimination of monozygotic twins, identifying the source of a biological trace left at a crime scene, age prediction, determination of body fluids and tissues, human behavior association, wound healing progression, and determination of the post-mortem interval (PMI). Despite all these applications, not all the studies considered the impact of PMI and post-sampling effects on the epigenetic modifications and the tissue-specificity of the epigenetic marks.This review aims to highlight the substantial forensic significance that epigenetics could support in various forensic investigations. First, basic concepts in epigenetics, describing the main epigenetic modifications and their functions, in particular, DNA methylation, histone modifications, and non-coding RNA, with a particular focus on forensic applications, were covered. For each epigenetic marker, post-mortem stability and tissue-specificity, factors that should be carefully considered in the study of epigenetic biomarkers in the forensic context, have been discussed. The advantages and limitations of using post-mortem tissues have been also addressed, proposing directions for these innovative strategies to analyze forensic specimens.
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Affiliation(s)
- Maria Carla Gerra
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy.
| | - Rossana Cecchi
- Department of Medicine and Surgery, University of Parma, Via Antonio Gramsci 14, 43126, Parma, PR, Italy
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11
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Jin P, Duan X, Li L, Zhou P, Zou C, Xie K. Cellular senescence in cancer: molecular mechanisms and therapeutic targets. MedComm (Beijing) 2024; 5:e542. [PMID: 38660685 PMCID: PMC11042538 DOI: 10.1002/mco2.542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 04/26/2024] Open
Abstract
Aging exhibits several hallmarks in common with cancer, such as cellular senescence, dysbiosis, inflammation, genomic instability, and epigenetic changes. In recent decades, research into the role of cellular senescence on tumor progression has received widespread attention. While how senescence limits the course of cancer is well established, senescence has also been found to promote certain malignant phenotypes. The tumor-promoting effect of senescence is mainly elicited by a senescence-associated secretory phenotype, which facilitates the interaction of senescent tumor cells with their surroundings. Targeting senescent cells therefore offers a promising technique for cancer therapy. Drugs that pharmacologically restore the normal function of senescent cells or eliminate them would assist in reestablishing homeostasis of cell signaling. Here, we describe cell senescence, its occurrence, phenotype, and impact on tumor biology. A "one-two-punch" therapeutic strategy in which cancer cell senescence is first induced, followed by the use of senotherapeutics for eliminating the senescent cells is introduced. The advances in the application of senotherapeutics for targeting senescent cells to assist cancer treatment are outlined, with an emphasis on drug categories, and the strategies for their screening, design, and efficient targeting. This work will foster a thorough comprehension and encourage additional research within this field.
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Affiliation(s)
- Ping Jin
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, School of Life SciencesYunnan UniversityKunmingYunnanChina
| | - Xirui Duan
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Lei Li
- Department of Anorectal SurgeryHospital of Chengdu University of Traditional Chinese Medicine and Chengdu University of Traditional Chinese MedicineChengduChina
| | - Ping Zhou
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Cheng‐Gang Zou
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, School of Life SciencesYunnan UniversityKunmingYunnanChina
| | - Ke Xie
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
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12
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Juhász V, Ország A, Balla D, Szabó L, Sydó N, Kiss O, Csulak E, Babity M, Dohy Z, Skoda R, Becker D, Merkely B, Benczúr A, Vágó H, Kerepesi C. Blood Test-Based Age Acceleration Is Inversely Associated with High-Volume Sports Activity. Med Sci Sports Exerc 2024; 56:868-875. [PMID: 38306315 DOI: 10.1249/mss.0000000000003380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
PURPOSE We develop blood test-based aging clocks and examine how these clocks reflect high-volume sports activity. METHODS We use blood tests and body metrics data of 421 Hungarian athletes and 283 age-matched controls (mean age, 24.1 and 23.9 yr, respectively), the latter selected from a group of healthy Caucasians of the National Health and Nutrition Examination Survey (NHANES) to represent the general population ( n = 11,412). We train two age prediction models (i.e., aging clocks) using the NHANES dataset: the first model relies on blood test parameters only, whereas the second one additionally incorporates body measurements and sex. RESULTS We find lower age acceleration among athletes compared with the age-matched controls with a median value of -1.7 and 1.4 yr, P < 0.0001. BMI is positively associated with age acceleration among the age-matched controls ( r = 0.17, P < 0.01) and the unrestricted NHANES population ( r = 0.11, P < 0.001). We find no association between BMI and age acceleration within the athlete dataset. Instead, age acceleration is positively associated with body fat percentage ( r = 0.21, P < 0.05) and negatively associated with skeletal muscle mass (Pearson r = -0.18, P < 0.05) among athletes. The most important blood test features in age predictions were serum ferritin, mean cell volume, blood urea nitrogen, and albumin levels. CONCLUSIONS We develop and apply blood test-based aging clocks to adult athletes and healthy controls. The data suggest that high-volume sports activity is associated with slowed biological aging. Here, we propose an alternative, promising application of routine blood tests.
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Affiliation(s)
- Vencel Juhász
- Heart and Vascular Centre, Semmelweis University, Budapest, HUNGARY
| | - Anna Ország
- Institute for Computer Science and Control (SZTAKI), Hungarian Research Network (HUN-REN), Budapest, HUNGARY
| | - Dorottya Balla
- Heart and Vascular Centre, Semmelweis University, Budapest, HUNGARY
| | - Liliána Szabó
- Heart and Vascular Centre, Semmelweis University, Budapest, HUNGARY
| | | | | | - Emese Csulak
- Heart and Vascular Centre, Semmelweis University, Budapest, HUNGARY
| | - Máté Babity
- Heart and Vascular Centre, Semmelweis University, Budapest, HUNGARY
| | - Zsófia Dohy
- Heart and Vascular Centre, Semmelweis University, Budapest, HUNGARY
| | - Réka Skoda
- Heart and Vascular Centre, Semmelweis University, Budapest, HUNGARY
| | - Dávid Becker
- Heart and Vascular Centre, Semmelweis University, Budapest, HUNGARY
| | | | - András Benczúr
- Institute for Computer Science and Control (SZTAKI), Hungarian Research Network (HUN-REN), Budapest, HUNGARY
| | | | - Csaba Kerepesi
- Institute for Computer Science and Control (SZTAKI), Hungarian Research Network (HUN-REN), Budapest, HUNGARY
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13
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Künstner A, Schwarting J, Witte HM, Xing P, Bernard V, Stölting S, Lohneis P, Janke F, Salehi M, Chen X, Kusch K, Sültmann H, Chteinberg E, Fischer A, Siebert R, von Bubnoff N, Merz H, Busch H, Feller AC, Gebauer N. Genome-wide DNA methylation-analysis of blastic plasmacytoid dendritic cell neoplasm identifies distinct molecular features. Leukemia 2024; 38:1086-1098. [PMID: 38600314 DOI: 10.1038/s41375-024-02240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) constitutes a rare and aggressive malignancy originating from plasmacytoid dendritic cells (pDCs) with a primarily cutaneous tropism followed by dissemination to the bone marrow and other organs. We conducted a genome-wide analysis of the tumor methylome in an extended cohort of 45 BPDCN patients supplemented by WES and RNA-seq as well as ATAC-seq on selected cases. We determined the BPDCN DNA methylation profile and observed a dramatic loss of DNA methylation during malignant transformation from early and mature DCs towards BPDCN. DNA methylation profiles further differentiate between BPDCN, AML, CMML, and T-ALL exhibiting the most striking global demethylation, mitotic stress, and merely localized DNA hypermethylation in BPDCN resulting in pronounced inactivation of tumor suppressor genes by comparison. DNA methylation-based analysis of the tumor microenvironment by MethylCIBERSORT yielded two, prognostically relevant clusters (IC1 and IC2) with specific cellular composition and mutational spectra. Further, the transcriptional subgroups of BPDCN (C1 and C2) differ by DNA methylation signatures in interleukin/inflammatory signaling genes but also by higher transcription factor activity of JAK-STAT and NFkB signaling in C2 in contrast to an EZH2 dependence in C1-BPDCN. Our integrative characterization of BPDCN offers novel molecular insights and potential diagnostic applications.
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Affiliation(s)
- Axel Künstner
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Julian Schwarting
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Hanno M Witte
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Department of Hematology and Oncology, Federal Armed Forces Hospital Ulm, Oberer Eselsberg 40, 89081, Ulm, Germany
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Veronica Bernard
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Stephanie Stölting
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Philipp Lohneis
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Maede Salehi
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Kathrin Kusch
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Emil Chteinberg
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Nikolas von Bubnoff
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Hartmut Merz
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Alfred C Feller
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Niklas Gebauer
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany.
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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14
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Ingram SJ, Vazquez AY, Klump KL, Hyde LW, Burt SA, Clark SL. Associations of depression and anxiety symptoms in childhood and adolescence with epigenetic aging. J Affect Disord 2024; 352:250-258. [PMID: 38360371 PMCID: PMC11000694 DOI: 10.1016/j.jad.2024.02.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Childhood anxiety and depression symptoms are potential risk factors for accelerated biological aging. In child and adolescent twins, we tested whether these symptoms were associated with DNA methylation (DNAm) aging, a measure of biological aging. METHODS 276 twins (135 pairs, 6 singletons) had DNAm assayed from saliva in middle childhood (mean = 7.8 years). Residuals of five different DNAm age estimates regressed on chronological age were used to indicate accelerated aging. Anxiety and depression symptoms were assessed in middle childhood and early adolescence using the Child Behavior Checklist. Mixed effect regression was used to examine potential relationships between anxiety or depression symptoms, and accelerated DNAm age. MZ twin difference analysis was then utilized to determine if associations were environmentally-driven or due to genetic or shared-environment confounding. RESULTS Anxiety and depression symptoms were not associated with accelerated DNAm aging in middle childhood. In early adolescence, only the Wu clock was significant and indicated that each one symptom increase in anxiety symptoms had an associated age acceleration of 0.03 years (~0.4 months; p = 0.019). MZ twin difference analysis revealed non-significant within-pair effects, suggesting genetic and shared environmental influences. LIMITATIONS Sample is predominantly male and white. Generalizability to other populations may be limited. CONCLUSION Accelerated DNAm aging of the Wu clock in middle childhood is associated with anxiety, but not depression, symptoms in early adolescence. Further, this association may be the result of shared genetic and environmental influences. Accelerated DNAm aging may serve as an early risk factor or predictor of later anxiety symptoms.
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Affiliation(s)
- Sarah J Ingram
- Interdisciplinary Graduate Program in Genetics, Department of Psychiatry & Behavioral Sciences, Texas A&M University, United States of America
| | - Alexandra Y Vazquez
- Department of Psychology, Michigan State University, United States of America
| | - Kelly L Klump
- Department of Psychology, Michigan State University, United States of America
| | - Luke W Hyde
- Department of Psychology, University of Michigan, United States of America
| | - S Alexandra Burt
- Department of Psychology, Michigan State University, United States of America
| | - Shaunna L Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, United States of America.
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15
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Graves AJ, Danoff JS, Kim M, Brindley SR, Skyberg AM, Giamberardino SN, Lynch ME, Straka BC, Lillard TS, Gregory SG, Connelly JJ, Morris JP. Accelerated epigenetic age is associated with whole-brain functional connectivity and impaired cognitive performance in older adults. Sci Rep 2024; 14:9646. [PMID: 38671048 PMCID: PMC11053089 DOI: 10.1038/s41598-024-60311-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/21/2024] [Indexed: 04/28/2024] Open
Abstract
While chronological age is a strong predictor for health-related risk factors, it is an incomplete metric that fails to fully characterize the unique aging process of individuals with different genetic makeup, neurodevelopment, and environmental experiences. Recent advances in epigenomic array technologies have made it possible to generate DNA methylation-based biomarkers of biological aging, which may be useful in predicting a myriad of cognitive abilities and functional brain network organization across older individuals. It is currently unclear which cognitive domains are negatively correlated with epigenetic age above and beyond chronological age, and it is unknown if functional brain organization is an important mechanism for explaining these associations. In this study, individuals with accelerated epigenetic age (i.e. AgeAccelGrim) performed worse on tasks that spanned a wide variety of cognitive faculties including both fluid and crystallized intelligence (N = 103, average age = 68.98 years, 73 females, 30 males). Additionally, fMRI connectome-based predictive models suggested a mediating mechanism of functional connectivity on epigenetic age acceleration-cognition associations primarily in medial temporal lobe and limbic structures. This research highlights the important role of epigenetic aging processes on the development and maintenance of healthy cognitive capacities and function of the aging brain.
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Affiliation(s)
| | | | - Minah Kim
- University of Virginia, Charlottesville, USA
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16
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Teschendorff AE. On epigenetic stochasticity, entropy and cancer risk. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230054. [PMID: 38432318 PMCID: PMC10909509 DOI: 10.1098/rstb.2023.0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 09/26/2023] [Indexed: 03/05/2024] Open
Abstract
Epigenetic changes are known to accrue in normal cells as a result of ageing and cumulative exposure to cancer risk factors. Increasing evidence points towards age-related epigenetic changes being acquired in a quasi-stochastic manner, and that they may play a causal role in cancer development. Here, I describe the quasi-stochastic nature of DNA methylation (DNAm) changes in ageing cells as well as in normal cells at risk of neoplastic transformation, discussing the implications of this stochasticity for developing cancer risk prediction strategies, and in particular, how it may require a conceptual paradigm shift in how we select cancer risk markers. I also describe the mounting evidence that a significant proportion of DNAm changes in ageing and cancer development are related to cell proliferation, reflecting tissue-turnover and the opportunity this offers for predicting cancer risk via the development of epigenetic mitotic-like clocks. Finally, I describe how age-associated DNAm changes may be causally implicated in cancer development via an irreversible suppression of tissue-specific transcription factors that increases epigenetic and transcriptomic entropy, promoting a more plastic yet aberrant cancer stem-cell state. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, People's Republic of China
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17
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Mäkinen VP, Ala-Korpela M. Influence of age and sex on longitudinal metabolic profiles and body weight trajectories in the UK Biobank. Int J Epidemiol 2024; 53:dyae055. [PMID: 38641429 PMCID: PMC11031410 DOI: 10.1093/ije/dyae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/04/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Accurate characterization of how age influences body weight and metabolism at different stages of life is important for understanding ageing processes. Here, we explore observational longitudinal associations between metabolic health and weight from the fifth to the seventh decade of life, using carefully adjusted statistical designs. METHODS Body measures and biochemical data from blood and urine (220 measures) across two visits were available from 10 104 UK Biobank participants. Participants were divided into stable (within ±4% per decade), weight loss and weight gain categories. Final subgroups were metabolically matched at baseline (48% women, follow-up 4.3 years, ages 41-70; n = 3368 per subgroup) and further stratified by the median age of 59.3 years and sex. RESULTS Pulse pressure, haemoglobin A1c and cystatin-C tracked ageing consistently (P < 0.0001). In women under 59, age-associated increases in citrate, pyruvate, alkaline phosphatase and calcium were observed along with adverse changes across lipoprotein measures, fatty acid species and liver enzymes (P < 0.0001). Principal component analysis revealed a qualitative sex difference in the temporal relationship between body weight and metabolism: weight loss was not associated with systemic metabolic improvement in women, whereas both age strata converged consistently towards beneficial (weight loss) or adverse (weight gain) phenotypes in men. CONCLUSIONS We report longitudinal ageing trends for 220 metabolic measures in absolute concentrations, many of which have not been described for older individuals before. Our results also revealed a fundamental dynamic sex divergence that we speculate is caused by menopause-driven metabolic deterioration in women.
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Affiliation(s)
- Ville-Petteri Mäkinen
- Systems Epidemiology, Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Mika Ala-Korpela
- Systems Epidemiology, Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
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18
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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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19
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Ori APS, Olde Loohuis LM, Guintivano J, Hannon E, Dempster E, St Clair D, Bass NJ, McQuillin A, Mill J, Sullivan PF, Kahn RS, Horvath S, Ophoff RA. Meta-analysis of epigenetic aging in schizophrenia reveals multifaceted relationships with age, sex, illness duration, and polygenic risk. Clin Epigenetics 2024; 16:53. [PMID: 38589929 PMCID: PMC11003125 DOI: 10.1186/s13148-024-01660-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/16/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND The study of biological age acceleration may help identify at-risk individuals and reduce the rising global burden of age-related diseases. Using DNA methylation (DNAm) clocks, we investigated biological aging in schizophrenia (SCZ), a mental illness that is associated with an increased prevalence of age-related disabilities and morbidities. In a whole blood DNAm sample of 1090 SCZ cases and 1206 controls across four European cohorts, we performed a meta-analysis of differential aging using three DNAm clocks (i.e., Hannum, Horvath, and Levine). To dissect how DNAm aging contributes to SCZ, we integrated information on duration of illness and SCZ polygenic risk, as well as stratified our analyses by chronological age and biological sex. RESULTS We found that blood-based DNAm aging is significantly altered in SCZ independent from duration of the illness since onset. We observed sex-specific and nonlinear age effects that differed between clocks and point to possible distinct age windows of altered aging in SCZ. Most notably, intrinsic cellular age (Horvath clock) is decelerated in SCZ cases in young adulthood, while phenotypic age (Levine clock) is accelerated in later adulthood compared to controls. Accelerated phenotypic aging was most pronounced in women with SCZ carrying a high polygenic burden with an age acceleration of + 3.82 years (CI 2.02-5.61, P = 1.1E-03). Phenotypic aging and SCZ polygenic risk contributed additively to the illness and together explained up to 14.38% of the variance in disease status. CONCLUSIONS Our study contributes to the growing body of evidence of altered DNAm aging in SCZ and points to intrinsic age deceleration in younger adulthood and phenotypic age acceleration in later adulthood in SCZ. Since increased phenotypic age is associated with increased risk of all-cause mortality, our findings indicate that specific and identifiable patient groups are at increased mortality risk as measured by the Levine clock. Our study did not find that DNAm aging could be explained by the duration of illness of patients, but we did observe age- and sex-specific effects that warrant further investigation. Finally, our results show that combining genetic and epigenetic predictors can improve predictions of disease outcomes and may help with disease management in schizophrenia.
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Affiliation(s)
- Anil P S Ori
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Gonda Center, Room 4357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-176, USA.
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
| | - Loes M Olde Loohuis
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Gonda Center, Room 4357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-176, USA
| | - Jerry Guintivano
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma Dempster
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - David St Clair
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| | - Nick J Bass
- Division of Psychiatry, University College London, London, UK
| | | | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Rene S Kahn
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Gonda Center, Room 4357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-176, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands.
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20
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Stangis MM, Chen Z, Min J, Glass SE, Jackson JO, Radyk MD, Hoi XP, Brennen WN, Yu M, Dinh HQ, Coffey RJ, Shrubsole MJ, Chan KS, Grady WM, Yegnasubramanian S, Lyssiotis CA, Maitra A, Halberg RB, Dey N, Lau KS. The Hallmarks of Precancer. Cancer Discov 2024; 14:683-689. [PMID: 38571435 DOI: 10.1158/2159-8290.cd-23-1550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Research on precancers, as defined as at-risk tissues and early lesions, is of high significance given the effectiveness of early intervention. We discuss the need for risk stratification to prevent overtreatment, an emphasis on the role of genetic and epigenetic aging when considering risk, and the importance of integrating macroenvironmental risk factors with molecules and cells in lesions and at-risk normal tissues for developing effective intervention and health policy strategies.
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Affiliation(s)
- Mary M Stangis
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Gastroenterology Division, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Zhengyi Chen
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jimin Min
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah E Glass
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jordan O Jackson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Megan D Radyk
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Xen Ping Hoi
- Department of Urology, Houston Methodist Research Institute, Houston, Texas
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas
| | - W Nathaniel Brennen
- Genitourinary Cancer Disease Division, Department of Oncology, Johns Hopkins Medicine, Baltimore, Maryland
- Department of Pharmacology and Molecular Sciences, Johns Hopkins Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins Medicine, Baltimore, Maryland
| | - Ming Yu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Division of Gastroenterology, Hepatology, & Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Martha J Shrubsole
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Keith S Chan
- Department of Urology, Houston Methodist Research Institute, Houston, Texas
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas
| | - William M Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Srinivasan Yegnasubramanian
- Genitourinary Cancer Disease Division, Department of Oncology, Johns Hopkins Medicine, Baltimore, Maryland
- Molecular Radiation Science Division, Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, Maryland
- Kidney-Urologic Pathology Division, Department of Pathology, Johns Hopkins Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
- Division of Gastroenterology, Internal Medicine, University of Washington, Seattle, Washington
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
| | - Anirban Maitra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Richard B Halberg
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Gastroenterology Division, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Neelendu Dey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
| | - Ken S Lau
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
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21
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Salontaji K, Haftorn KL, Sanders F, Page CM, Walton E, Felix JF, Bekkhus M, Bohlin J, Tiemeier H, Cecil CAM. Gestational epigenetic age and ADHD symptoms in childhood: a prospective, multi-cohort study. Mol Psychiatry 2024:10.1038/s41380-024-02544-2. [PMID: 38561466 DOI: 10.1038/s41380-024-02544-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Epigenetic age acceleration (EAA), defined as the difference between chronological age and epigenetically predicted age, was calculated from multiple gestational epigenetic clocks (Bohlin, EPIC overlap, and Knight) using DNA methylation levels from cord blood in three large population-based birth cohorts: the Generation R Study (The Netherlands), the Avon Longitudinal Study of Parents and Children (United Kingdom), and the Norwegian Mother, Father and Child Cohort Study (Norway). We hypothesized that a lower EAA associates prospectively with increased ADHD symptoms. We tested our hypotheses in these three cohorts and meta-analyzed the results (n = 3383). We replicated previous research on the association between gestational age (GA) and ADHD. Both clinically measured gestational age as well as epigenetic age measures at birth were negatively associated with ADHD symptoms at ages 5-7 years (clinical GA: β = -0.04, p < 0.001, Bohlin: β = -0.05, p = 0.01; EPIC overlap: β = -0.05, p = 0.01; Knight: β = -0.01, p = 0.26). Raw EAA (difference between clinical and epigenetically estimated gestational age) was positively associated with ADHD in our main model, whereas residual EAA (raw EAA corrected for clinical gestational age) was not associated with ADHD symptoms across cohorts. Overall, findings support a link between lower gestational age (either measured clinically or using epigenetic-derived estimates) and ADHD symptoms. Epigenetic age acceleration does not, however, add unique information about ADHD risk independent of clinically estimated gestational age at birth.
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Affiliation(s)
- Kristina Salontaji
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Centre, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Kristine L Haftorn
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Faye Sanders
- Department of Psychology, University of Bath, Bath, United Kingdom
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Physical Health and Ageing, Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Esther Walton
- Department of Psychology, University of Bath, Bath, United Kingdom
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mona Bekkhus
- Promenta research centre, Department of Psychology, University of Oslo, Oslo, Norway
| | - Jon Bohlin
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department for methods development and analysis, section for modeling and bioinformatics, Division for infectious diseases, Norwegian Institute of Public Health, Oslo, Norway
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Centre, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Medicine, Boston, MA, USA
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Centre, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.
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22
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Yang X, Li R, Yang X, Zhou Y, Liu Y, Han JDJ. Coordinate-wise monotonic transformations enable privacy-preserving age estimation with 3D face point cloud. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2518-8. [PMID: 38573362 DOI: 10.1007/s11427-023-2518-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/25/2023] [Indexed: 04/05/2024]
Abstract
The human face is a valuable biomarker of aging, but the collection and use of its image raise significant privacy concerns. Here we present an approach for facial data masking that preserves age-related features using coordinate-wise monotonic transformations. We first develop a deep learning model that estimates age directly from non-registered face point clouds with high accuracy and generalizability. We show that the model learns a highly indistinguishable mapping using faces treated with coordinate-wise monotonic transformations, indicating that the relative positioning of facial information is a low-level biomarker of facial aging. Through visual perception tests and computational 3D face verification experiments, we demonstrate that transformed faces are significantly more difficult to perceive for human but not for machines, except when only the face shape information is accessible. Our study leads to a facial data protection guideline that has the potential to broaden public access to face datasets with minimized privacy risks.
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Affiliation(s)
- Xinyu Yang
- School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China
| | - Runhan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China
| | - Xindi Yang
- Beijing Key Lab of Traffic Data Analysis and Mining, School of Computer and Information Technology, Beijing Jiaotong University, Beijing, 100044, China
| | - Yong Zhou
- Clinical Research Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yi Liu
- Beijing Key Lab of Traffic Data Analysis and Mining, School of Computer and Information Technology, Beijing Jiaotong University, Beijing, 100044, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
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23
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Jin K, McCoy BM, Goldman EA, Usova V, Tkachev V, Chitsazan AD, Kakebeen A, Jeffery U, Creevy KE, Wills A, Snyder‐Mackler N, Promislow DEL. DNA methylation and chromatin accessibility predict age in the domestic dog. Aging Cell 2024; 23:e14079. [PMID: 38263575 PMCID: PMC11019125 DOI: 10.1111/acel.14079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Across mammals, the epigenome is highly predictive of chronological age. These "epigenetic clocks," most of which have been built using DNA methylation (DNAm) profiles, have gained traction as biomarkers of aging and organismal health. While the ability of DNAm to predict chronological age has been repeatedly demonstrated, the ability of other epigenetic features to predict age remains unclear. Here, we use two types of epigenetic information-DNAm, and chromatin accessibility as measured by ATAC-seq-to develop age predictors in peripheral blood mononuclear cells sampled from a population of domesticated dogs. We measured DNAm and ATAC-seq profiles for 71 dogs, building separate predictive clocks from each, as well as the combined dataset. We also use fluorescence-assisted cell sorting to quantify major lymphoid populations for each sample. We found that chromatin accessibility can accurately predict chronological age (R2 ATAC = 26%), though less accurately than the DNAm clock (R2 DNAm = 33%), and the clock built from the combined datasets was comparable to both (R2 combined = 29%). We also observed various populations of CD62L+ T cells significantly correlated with dog age. Finally, we found that all three clocks selected features that were in or near at least two protein-coding genes: BAIAP2 and SCARF2, both previously implicated in processes related to cognitive or neurological impairment. Taken together, these results highlight the potential of chromatin accessibility as a complementary epigenetic resource for modeling and investigating biologic age.
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Affiliation(s)
- Kelly Jin
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Brianah M. McCoy
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | | | - Viktoria Usova
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Victor Tkachev
- Division of Pediatric Hematology/OncologyBoston Children's HospitalBostonMassachusettsUSA
- Dana Farber Cancer InstituteBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Alex D. Chitsazan
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Anneke Kakebeen
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Unity Jeffery
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Kate E. Creevy
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Andrea Wills
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Noah Snyder‐Mackler
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Daniel E. L. Promislow
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
- Department of BiologyUniversity of WashingtonSeattleWashingtonUSA
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24
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Lian J, Vardhanabhuti V. Metabolic biomarkers using nuclear magnetic resonance metabolomics assay for the prediction of aging-related disease risk and mortality: a prospective, longitudinal, observational, cohort study based on the UK Biobank. GeroScience 2024; 46:1515-1526. [PMID: 37648937 PMCID: PMC10828466 DOI: 10.1007/s11357-023-00918-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
The identification of metabolic biomarkers for aging-related diseases and mortality is of significant interest in the field of longevity. In this study, we investigated the associations between nuclear magnetic resonance (NMR) metabolomics biomarkers and aging-related diseases as well as mortality using the UK Biobank dataset. We analyzed NMR samples from approximately 110,000 participants and used multi-head machine learning classification models to predict the incidence of aging-related diseases. Cox regression models were then applied to assess the relevance of NMR biomarkers to the risk of death due to aging-related diseases. Additionally, we conducted survival analyses to evaluate the potential improvements of NMR in predicting survival and identify the biomarkers most strongly associated with negative health outcomes by dividing participants into health, disease, and death groups for all age groups. Our analysis revealed specific metabolomics profiles that were associated with the incidence of age-related diseases, and the most significant biomarker was intermediate density lipoprotein cholesteryl (IDL-CE). In addition, NMR biomarkers could provide additional contributions to relevant mortality risk prediction when combined with conventional risk factors, by improving the C-index from 0.813 to 0.833, with 17 NMR biomarkers significantly contributing to disease-related death, such as monounsaturated fatty acids (MUFA), linoleic acid (LA), glycoprotein acetyls (GlycA), and omega-3. Moreover, the value of free cholesterol in very large HDL particles (XL-HDL-FC) in the healthy control group demonstrated significantly higher values than the disease and death group across all age groups. This study highlights the potential of NMR metabolomics profiling as a valuable tool for identifying metabolic biomarkers associated with aging-related diseases and mortality risk, which could have practical implications for aging-related disease risk and mortality prediction.
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Affiliation(s)
- Jie Lian
- Department of Diagnostic Radiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Room 406, Block K, Queen Mary Hospital, Pokfulam Road, Hong Kong, SAR, China
| | - Varut Vardhanabhuti
- Department of Diagnostic Radiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Room 406, Block K, Queen Mary Hospital, Pokfulam Road, Hong Kong, SAR, China.
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25
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Tzemah-Shahar R, Turjeman S, Sharon E, Gamliel G, Hochner H, Koren O, Agmon M. Signs of aging in midlife: physical function and sex differences in microbiota. GeroScience 2024; 46:1477-1488. [PMID: 37610596 PMCID: PMC10828485 DOI: 10.1007/s11357-023-00905-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Microbiota composition has been linked to physical activity, health measures, and biological age, but a shared profile has yet to be shown. The aim of this study was to examine the associations between microbiota composition and measures of function, such as a composite measure of physical capacity, and biological age in midlife, prior to onset of age-related diseases. Seventy healthy midlife individuals (age 44.58 ± 0.18) were examined cross-sectionally, and their gut-microbiota profile was characterized from stool samples using 16SrRNA gene sequencing. Biological age was measured using the Klemera-Doubal method and a composition of blood and physiological biomarkers. Physical capacity was calculated based on sex-standardized functional tests. We demonstrate that the women had significantly richer microbiota, p = 0.025; however, microbiota diversity was not linked with chronological age, biological age, or physical capacity for either women or men. Men had slightly greater β-diversity; however, β-diversity was positively associated with biological age and with physical capacity for women only (p = 0.01 and p = 0.04; respectively). For women, an increase in abundance of Roseburia faecis and Collinsella aerofaciens, as well as genus Ruminococcus and Dorea, was significantly associated with higher biological age and lower physical capacity; an increase in abundance of Akkermansia muciniphila and genera Bacteroides and Alistipes was associated with younger biological age and increased physical capacity. Differentially abundant taxa were also associated with non-communicable diseases. These findings suggest that microbiota composition is a potential mechanism linking physical capacity and health status; personalized probiotics may serve as a new means to support health-promoting interventions in midlife. Investigating additional factors underlying this link may facilitate the development of a more accurate method to estimate the rate of aging.
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Affiliation(s)
- Roy Tzemah-Shahar
- Faculty of Social Welfare and Health Sciences, University of Haifa, Abba Khoushy Ave 199, 3498838, Haifa, Israel
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Efrat Sharon
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Gila Gamliel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Hagit Hochner
- Epidemiology Unit, Hebrew University School of Public Health, Jerusalem, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Maayan Agmon
- Faculty of Social Welfare and Health Sciences, University of Haifa, Abba Khoushy Ave 199, 3498838, Haifa, Israel.
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26
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Aroke EN, Srinivasasainagendra V, Kottae P, Quinn TL, Wiggins AM, Hobson J, Kinnie K, Stoudmire T, Tiwari HK, Goodin BR. The Pace of Biological Aging Predicts Nonspecific Chronic Low Back Pain Severity. THE JOURNAL OF PAIN 2024; 25:974-983. [PMID: 37907115 PMCID: PMC10960701 DOI: 10.1016/j.jpain.2023.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/15/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023]
Abstract
This study aimed to determine if and how the pace of biological aging was associated with nonspecific chronic low back pain (cLBP) and compare what measure of epigenetic age acceleration most strongly predicts cLBP outcomes. We used the Dunedin Pace of Aging from the Epigenome (DunedinPACE), Horvath's, Hannum's, and PhenoAge clocks to determine the pace of biological aging in 69 cLBP, and 49 pain-free controls (PFCs) adults, ages 18 to 85 years. On average, participants with cLBP had higher DunedinPACE (P < .001) but lower Horvath (P = .04) and Hannum (P = .02) accelerated epigenetic age than PFCs. There was no significant difference in PhenoAge acceleration between the cLBP and PFC groups (P = .97). DunedinPACE had the largest effect size (Cohen's d = .78) on group differences. In univariate regressions, a unit increase in DunedinPACE score was associated with 265.98 times higher odds of cLBP than the PFC group (P < .001). After controlling for sex, race, and body mass index (BMI), the odds ratio of cLBP to PFC group was 149.62 (P < .001). Furthermore, among participants with cLBP, DunedinPACE scores positively correlated with pain severity (rs = .385, P = .001) and interference (rs = .338, P = .005). Epigenetic age acceleration from Horvath, Hannum, and PhenoAge clocks were not significant predictors of cLBP. The odds of a faster pace of biological aging are higher among adults with cLBP, and this was associated with greater pain severity and disability. Future interventions to slow the pace of biological aging may improve cLBP outcomes. PERSPECTIVE: Accelerated epigenetic aging is common among adults with nonspecific cLBP. Higher DunedinPACE scores positively correlate with pain severity and interference, and better predict cLBP than other DNA methylation clocks. Interventions to slow the pace of biological aging may be viable targets for improving pain outcomes.
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Affiliation(s)
- Edwin N. Aroke
- School of Nursing, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Pooja Kottae
- Department of Computer Science, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tammie L. Quinn
- Department of Psychology, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Asia M. Wiggins
- Department of Psychology, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joanna Hobson
- Department of Psychology, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kiari Kinnie
- School of Nursing, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tonya Stoudmire
- School of Nursing, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K. Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Burel R. Goodin
- Department of Anesthesiology, School of Medicine, Washington University, St Louis, USA
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27
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Okada D. Application of a mathematical model to clarify the statistical characteristics of a pan-tissue DNA methylation clock. GeroScience 2024; 46:2001-2015. [PMID: 37787856 PMCID: PMC10828133 DOI: 10.1007/s11357-023-00949-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023] Open
Abstract
DNA methylation clocks estimate biological age based on DNA methylation profiles. This study developed a mathematical model to describe DNA methylation aging and the establishment of a pan-tissue DNA methylation clock. The model simulates the aging dynamics of DNA methylation profiles based on passive demethylation as well as the process of cross-sectional bulk data acquisition. As a result, this study identified two conditions under which the pan-tissue DNA methylation clock can successfully predict biological age: one condition is that the target tissues are sufficiently well represented in the training dataset, and the other condition is that the target sample contains cell subsets that are common among different tissues. When either of these conditions is met, the clock performs well. It is also suggested that the epigenetic age of all samples in the target tissue tends to be either over or underestimated when biological age prediction fails. The model can reveal the statistical characteristics of DNA methylation clocks.
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Affiliation(s)
- Daigo Okada
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, 53 Syogoin-Kawaramachi, Sakyo-ku, Kyoto, Kyoto, 606-8507, Japan.
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28
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Nwanaji-Enwerem JC. Considering the role of epigenetic mitotic indices in oral cancer screening and risk stratification. Oral Dis 2024. [PMID: 38525676 DOI: 10.1111/odi.14940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/16/2023] [Accepted: 03/12/2024] [Indexed: 03/26/2024]
Affiliation(s)
- Jamaji C Nwanaji-Enwerem
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, Georgia, USA
- Department of Emergency Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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29
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Brink K, Thomas CL, Jones A, Chan TW, Mallon EB. Exploring the ageing methylome in the model insect, Nasonia vitripennis. BMC Genomics 2024; 25:305. [PMID: 38519892 PMCID: PMC10958858 DOI: 10.1186/s12864-024-10211-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The ageing process is a multifaceted phenomenon marked by the gradual deterioration of cellular and organismal functions, accompanied by an elevated susceptibility to diseases. The intricate interplay between genetic and environmental factors complicates research, particularly in complex mammalian models. In this context, simple invertebrate organisms have been pivotal, but the current models lack detectable DNA methylation limiting the exploration of this critical epigenetic ageing mechanism. This study introduces Nasonia vitripennis, the jewel wasp, as an innovative invertebrate model for investigating the epigenetics of ageing. Leveraging its advantages as a model organism and possessing a functional DNA methylation system, Nasonia emerges as a valuable addition to ageing research. RESULTS Whole-genome bisulfite sequencing unveiled dynamic alterations in DNA methylation, with differentially methylated CpGs between distinct time points in both male and female wasps. These changes were associated with numerous genes, enriching for functions related to telomere maintenance, histone methylation, and mRNA catabolic processes. Additionally, other CpGs were found to be variably methylated at each timepoint. Sex-specific effects on epigenetic entropy were observed, indicating differential patterns in the loss of epigenetic stability over time. Constructing an epigenetic clock containing 19 CpGs revealed a robust correlation between epigenetic age and chronological age. CONCLUSIONS Nasonia vitripennis emerges as a promising model for investigating the epigenetics of ageing, shedding light on the intricate dynamics of DNA methylation and their implications for age-related processes. This research not only expands the repertoire of ageing models but also opens avenues for deeper exploration of epigenetic mechanisms in the context of ageing.
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Affiliation(s)
- K Brink
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK
| | - C L Thomas
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK
| | - A Jones
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstrabe, Muenster, Germany
| | - T W Chan
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, UK
| | - E B Mallon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK.
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30
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Graf GHJ, Aiello AE, Caspi A, Kothari M, Liu H, Moffitt TE, Muennig PA, Ryan CP, Sugden K, Belsky DW. Educational Mobility, Pace of Aging, and Lifespan Among Participants in the Framingham Heart Study. JAMA Netw Open 2024; 7:e240655. [PMID: 38427354 PMCID: PMC10907927 DOI: 10.1001/jamanetworkopen.2024.0655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/04/2024] [Indexed: 03/02/2024] Open
Abstract
Importance People who complete more education live longer lives with better health. New evidence suggests that these benefits operate through a slowed pace of biological aging. If so, measurements of the pace of biological aging could offer intermediate end points for studies of how interventions to promote education will affect healthy longevity. Objective To test the hypothesis that upward educational mobility is associated with a slower pace of biological aging and increased longevity. Design, Setting, and Participants This prospective cohort study analyzed data from 3 generations of participants in the Framingham Heart Study: (1) the original cohort, enrolled beginning in 1948; (2) the Offspring cohort, enrolled beginning in 1971; and (3) the Gen3 cohort, enrolled beginning in 2002. A 3-generation database was constructed to quantify intergenerational educational mobility. Mobility data were linked with blood DNA-methylation data collected from the Offspring cohort in 2005 to 2008 (n = 1652) and the Gen3 cohort in 2009 to 2011 (n = 1449). Follow-up is ongoing. Data analysis was conducted from June 2022 to November 2023 using data obtained from the National Institutes of Health database of Genotypes and Phenotypes (dbGaP). Exposure Educational mobility was measured by comparing participants' educational outcomes with those of their parents. Main Outcomes and Measures The pace of biological aging was measured from whole-blood DNA-methylation data using the DunedinPACE epigenetic clock. For comparison purposes, the analysis was repeated using 4 other epigenetic clocks. Survival follow-up was conducted through 2019. Results This study analyzed data from 3101 participants from the Framingham Heart Study; 1652 were in the Offspring cohort (mean [SD] age, 65.57 [9.22] years; 764 [46.2%] male) and 1449 were in the Gen3 cohort (mean [SD] age, 45.38 [7.83] years; 691 [47.7%] male). Participants who were upwardly mobile in educational terms tended to have slower pace of aging in later life (r = -0.18 [95% CI, -0.23 to -0.13]; P < .001). This pattern of association was similar across generations and held in within-family sibling comparisons. There were 402 Offspring cohort participants who died over the follow-up period. Upward educational mobility was associated with lower mortality risk (hazard ratio, 0.89 [95% CI, 0.81 to 0.98]; P = .01). Slower pace of aging accounted for approximately half of this association. Conclusions and Relevance This cohort study's findings support the hypothesis that interventions to promote educational attainment may slow the pace of biological aging and promote longevity. Epigenetic clocks have potential as near-term outcome measures of intervention effects on healthy aging. Experimental evidence is needed to confirm findings.
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Affiliation(s)
- Gloria H. J. Graf
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York
- Robert N. Butler Columbia Aging Center, New York, New York
| | - Allison E. Aiello
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York
- Robert N. Butler Columbia Aging Center, New York, New York
| | - Avshalom Caspi
- Department of Psychology & Neuroscience, Duke University, Durham, North Carolina
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, North Carolina
- PROMENTA, University of Oslo, Oslo, Norway
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, & Neuroscience, King’s College London, London, United Kingdom
| | - Meeraj Kothari
- Robert N. Butler Columbia Aging Center, New York, New York
| | - Hexuan Liu
- School of Criminal Justice, University of Cincinnati, Cincinnati, Ohio
- Institute for Interdisciplinary Data Science, University of Cincinnati, Cincinnati, Ohio
| | - Terrie E. Moffitt
- Department of Psychology & Neuroscience, Duke University, Durham, North Carolina
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, North Carolina
- PROMENTA, University of Oslo, Oslo, Norway
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, & Neuroscience, King’s College London, London, United Kingdom
| | - Peter A. Muennig
- Department of Health Policy and Management, Columbia University Mailman School of Public Health, New York, New York
| | - Calen P. Ryan
- Robert N. Butler Columbia Aging Center, New York, New York
| | - Karen Sugden
- Department of Psychology & Neuroscience, Duke University, Durham, North Carolina
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Daniel W. Belsky
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York
- Robert N. Butler Columbia Aging Center, New York, New York
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31
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Kapadia CD, Goodell MA. Tissue mosaicism following stem cell aging: blood as an exemplar. NATURE AGING 2024; 4:295-308. [PMID: 38438628 DOI: 10.1038/s43587-024-00589-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024]
Abstract
Loss of stem cell regenerative potential underlies aging of all tissues. Somatic mosaicism, the emergence of cellular patchworks within tissues, increases with age and has been observed in every organ yet examined. In the hematopoietic system, as in most tissues, stem cell aging through a variety of mechanisms occurs in lockstep with the emergence of somatic mosaicism. Here, we draw on insights from aging hematopoiesis to illustrate fundamental principles of stem cell aging and somatic mosaicism. We describe the generalizable changes intrinsic to aged stem cells and their milieu that provide the backdrop for somatic mosaicism to emerge. We discuss genetic and nongenetic mechanisms that can result in tissue somatic mosaicism and existing methodologies to detect such clonal outgrowths. Finally, we propose potential avenues to modify mosaicism during aging, with the ultimate aim of increasing tissue resiliency.
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Affiliation(s)
- Chiraag D Kapadia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
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32
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Zhang Z, Reynolds SR, Stolrow HG, Chen JQ, Christensen BC, Salas LA. Deciphering the role of immune cell composition in epigenetic age acceleration: Insights from cell-type deconvolution applied to human blood epigenetic clocks. Aging Cell 2024; 23:e14071. [PMID: 38146185 DOI: 10.1111/acel.14071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/27/2023] Open
Abstract
Aging is a significant risk factor for various human disorders, and DNA methylation clocks have emerged as powerful tools for estimating biological age and predicting health-related outcomes. Methylation data from blood DNA has been a focus of more recently developed DNA methylation clocks. However, the impact of immune cell composition on epigenetic age acceleration (EAA) remains unclear as only some clocks incorporate partial cell type composition information when analyzing EAA. We investigated associations of 12 immune cell types measured by cell-type deconvolution with EAA predicted by six widely-used DNA methylation clocks in data from >10,000 blood samples. We observed significant associations of immune cell composition with EAA for all six clocks tested. Across the clocks, nine or more of the 12 cell types tested exhibited significant associations with EAA. Higher memory lymphocyte subtype proportions were associated with increased EAA, and naïve lymphocyte subtypes were associated with decreased EAA. To demonstrate the potential confounding of EAA by immune cell composition, we applied EAA in rheumatoid arthritis. Our research maps immune cell type contributions to EAA in human blood and offers opportunities to adjust for immune cell composition in EAA studies to a significantly more granular level. Understanding associations of EAA with immune profiles has implications for the interpretation of epigenetic age and its relevance in aging and disease research. Our detailed map of immune cell type contributions serves as a resource for studies utilizing epigenetic clocks across diverse research fields, including aging-related diseases, precision medicine, and therapeutic interventions.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Quantitative Biomedical Sciences Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
| | - Samuel R Reynolds
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Hannah G Stolrow
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Ji-Qing Chen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Molecular and Cellular Biology Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Quantitative Biomedical Sciences Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
- Molecular and Cellular Biology Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Quantitative Biomedical Sciences Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
- Molecular and Cellular Biology Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
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33
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Campisi M, Cannella L, Pavanello S. Cosmic chronometers: Is spaceflight a catalyst for biological ageing? Ageing Res Rev 2024; 95:102227. [PMID: 38346506 DOI: 10.1016/j.arr.2024.102227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/05/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Astronauts returning from space missions often exhibit health issues mirroring age-related conditions, suggesting spaceflight as a potential driver of biological ageing and age-related diseases. To unravel the underlying mechanisms of these conditions, this comprehensive review explores the impact of the space "exposome" on the twelve hallmarks of ageing. Through a meticulous analysis encompassing both space environments and terrestrial analogs, we aim to decipher how different conditions influence ageing hallmarks. Utilizing PubMed, we identified 189 studies and 60 meet screening criteria. Research on biological ageing in space has focused on genomic instability, chronic inflammation, and deregulated nutrient sensing. Spaceflight consistently induces genomic instability, linked to prolonged exposure to ionizing radiation, triggers pro-inflammatory and immune alterations, resembling conditions in isolated simulations. Nutrient sensing pathways reveal increased systemic insulin-like growth-factor-1. Microbiome studies indicate imbalances favoring opportunistic species during spaceflight. Telomere dynamics present intriguing patterns, with lengthening during missions and rapid shortening upon return. Despite a pro-ageing trend, some protective mechanisms emerge. Countermeasures, encompassing dietary adjustments, prebiotics, postbiotics, symbiotics, tailored exercises, meditation, and anti-inflammatory supplements, exhibit potential. Spaceflight's impact on ageing is intricate, with diverse findings challenging established beliefs. Multidisciplinary studies provide guidance for future research in this field.
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Affiliation(s)
- Manuela Campisi
- Occupational Medicine, Department of Cardio-Thoraco-Vascular Sciences and Public Health, University of Padua, Padua, Italy
| | - Luana Cannella
- Occupational Medicine, Department of Cardio-Thoraco-Vascular Sciences and Public Health, University of Padua, Padua, Italy
| | - Sofia Pavanello
- Occupational Medicine, Department of Cardio-Thoraco-Vascular Sciences and Public Health, University of Padua, Padua, Italy.
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34
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Lee E, Carreras-Gallo N, Lopez L, Turner L, Lin A, Mendez TL, Went H, Tomusiak A, Verdin E, Corley M, Ndhlovu L, Smith R, Dwaraka VB. Exploring the effects of Dasatinib, Quercetin, and Fisetin on DNA methylation clocks: a longitudinal study on senolytic interventions. Aging (Albany NY) 2024; 16:3088-3106. [PMID: 38393697 DOI: 10.18632/aging.205581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/19/2024] [Indexed: 02/25/2024]
Abstract
Senolytics, small molecules targeting cellular senescence, have emerged as potential therapeutics to enhance health span. However, their impact on epigenetic age remains unstudied. This study aimed to assess the effects of Dasatinib and Quercetin (DQ) senolytic treatment on DNA methylation (DNAm), epigenetic age, and immune cell subsets. In a Phase I pilot study, 19 participants received DQ for 6 months, with DNAm measured at baseline, 3 months, and 6 months. Significant increases in epigenetic age acceleration were observed in first-generation epigenetic clocks and mitotic clocks at 3 and 6 months, along with a notable decrease in telomere length. However, no significant differences were observed in second and third-generation clocks. Building upon these findings, a subsequent investigation evaluated the combination of DQ with Fisetin (DQF), a well-known antioxidant and antiaging senolytic molecule. After one year, 19 participants (including 10 from the initial study) received DQF for 6 months, with DNAm assessed at baseline and 6 months. Remarkably, the addition of Fisetin to the treatment resulted in non-significant increases in epigenetic age acceleration, suggesting a potential mitigating effect of Fisetin on the impact of DQ on epigenetic aging. Furthermore, our analyses unveiled notable differences in immune cell proportions between the DQ and DQF treatment groups, providing a biological basis for the divergent patterns observed in the evolution of epigenetic clocks. These findings warrant further research to validate and comprehensively understand the implications of these combined interventions.
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Affiliation(s)
- Edwin Lee
- Institute For Hormonal Balance, Orlando, FL 32819, USA
| | | | | | | | - Aaron Lin
- TruDiagnostic, Lexington, KY 40503, USA
| | | | | | - Alan Tomusiak
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA 94945, USA
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35
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Ruprecht NA, Singhal S, Schaefer K, Panda O, Sens D, Singhal SK. A Review: Multi-Omics Approach to Studying the Association between Ionizing Radiation Effects on Biological Aging. BIOLOGY 2024; 13:98. [PMID: 38392316 PMCID: PMC10886797 DOI: 10.3390/biology13020098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Multi-omics studies have emerged as powerful tools for tailoring individualized responses to various conditions, capitalizing on genome sequencing technologies' increasing affordability and efficiency. This paper delves into the potential of multi-omics in deepening our understanding of biological age, examining the techniques available in light of evolving technology and computational models. The primary objective is to review the relationship between ionizing radiation and biological age, exploring a wide array of functional, physiological, and psychological parameters. This comprehensive review draws upon an extensive range of sources, including peer-reviewed journal articles, government documents, and reputable websites. The literature review spans from fundamental insights into radiation effects to the latest developments in aging research. Ionizing radiation exerts its influence through direct mechanisms, notably single- and double-strand DNA breaks and cross links, along with other critical cellular events. The cumulative impact of DNA damage forms the foundation for the intricate process of natural aging, intersecting with numerous diseases and pivotal biomarkers. Furthermore, there is a resurgence of interest in ionizing radiation research from various organizations and countries, reinvigorating its importance as a key contributor to the study of biological age. Biological age serves as a vital reference point for the monitoring and mitigation of the effects of various stressors, including ionizing radiation. Ionizing radiation emerges as a potent candidate for modeling the separation of biological age from chronological age, offering a promising avenue for tailoring protocols across diverse fields, including the rigorous demands of space exploration.
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Affiliation(s)
- Nathan A Ruprecht
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND 58202, USA
| | - Sonalika Singhal
- Department of Pathology, University of North Dakota, Grand Forks, ND 58202, USA
| | - Kalli Schaefer
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND 58202, USA
| | - Om Panda
- Department of Public Health, University of California Irvine, Irvine, CA 92697, USA
| | - Donald Sens
- Department of Pathology, University of North Dakota, Grand Forks, ND 58202, USA
| | - Sandeep K Singhal
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND 58202, USA
- Department of Pathology, University of North Dakota, Grand Forks, ND 58202, USA
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36
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Zhang K, Fu R, Liu R, Su Z. Circulating cell-free DNA-based multi-cancer early detection. Trends Cancer 2024; 10:161-174. [PMID: 37709615 DOI: 10.1016/j.trecan.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023]
Abstract
Patients benefit considerably from early detection of cancer. Existing single-cancer tests have various limitations, which could be effectively addressed by circulating cell-free DNA (cfDNA)-based multi-cancer early detection (MCED). With sensitive detection and accurate localization of multiple cancer types at a very low and fixed false-positive rate (FPR), MCED has great potential to revolutionize early cancer detection. Herein, we review state-of-the-art approaches for cfDNA-based MCED and their limitations and discuss both technical and clinical challenges in the development and application of MCED tests. Given the constant improvements in technology and understanding of cancer biology, we propose that a cfDNA-based targeted sequencing assay that integrates multimodal features should be optimized for MCED.
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Affiliation(s)
- Kai Zhang
- Department of Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, Chaoyang District, Beijing 100021, China
| | - Ruiqing Fu
- Singlera Genomics Ltd, Shanghai 201203, China
| | - Rui Liu
- Singlera Genomics Ltd, Shanghai 201203, China
| | - Zhixi Su
- Singlera Genomics Ltd, Shanghai 201203, China.
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37
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Kordowitzki P, Graczyk S, Haghani A, Klutstein M. Oocyte Aging: A Multifactorial Phenomenon in A Unique Cell. Aging Dis 2024; 15:5-21. [PMID: 37307833 PMCID: PMC10796106 DOI: 10.14336/ad.2023.0527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 05/27/2023] [Indexed: 06/14/2023] Open
Abstract
The oocyte is considered to be the largest cell in mammalian species. Women hoping to become pregnant face a ticking biological clock. This is becoming increasingly challenging as an increase in life expectancy is accompanied by the tendency to conceive at older ages. With advancing maternal age, the fertilized egg will exhibit lower quality and developmental competence, which contributes to increased chances of miscarriage due to several causes such as aneuploidy, oxidative stress, epigenetics, or metabolic disorders. In particular, heterochromatin in oocytes and with it, the DNA methylation landscape undergoes changes. Further, obesity is a well-known and ever-increasing global problem as it is associated with several metabolic disorders. More importantly, both obesity and aging negatively affect female reproduction. However, among women, there is immense variability in age-related decline of oocytes' quantity, developmental competence, or quality. Herein, the relevance of obesity and DNA-methylation will be discussed as these aspects have a tremendous effect on female fertility, and it is a topic of continuous and widespread interest that has yet to be fully addressed for the mammalian oocyte.
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Affiliation(s)
- Pawel Kordowitzki
- Department of Preclinical and Basic Sciences, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.
| | - Szymon Graczyk
- Department of Preclinical and Basic Sciences, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego, CA, USA.
| | - Michael Klutstein
- Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
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38
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Zoller JA, Parasyraki E, Lu AT, Haghani A, Niehrs C, Horvath S. DNA methylation clocks for clawed frogs reveal evolutionary conservation of epigenetic aging. GeroScience 2024; 46:945-960. [PMID: 37270437 PMCID: PMC10828168 DOI: 10.1007/s11357-023-00840-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023] Open
Abstract
To address how conserved DNA methylation-based epigenetic aging is in diverse branches of the tree of life, we generated DNA methylation data from African clawed frogs (Xenopus laevis) and Western clawed frogs (Xenopus tropicalis) and built multiple epigenetic clocks. Dual species clocks were developed that apply to both humans and frogs (human-clawed frog clocks), supporting that epigenetic aging processes are evolutionary conserved outside mammals. Highly conserved positively age-related CpGs are located in neural-developmental genes such as uncx, tfap2d as well as nr4a2 implicated in age-associated disease. We conclude that signatures of epigenetic aging are evolutionary conserved between frogs and mammals and that the associated genes relate to neural processes, altogether opening opportunities to employ Xenopus as a model organism to study aging.
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Affiliation(s)
- Joseph A Zoller
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.
- German Cancer Research Center (DKFZ), Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Steve Horvath
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego, CA, USA.
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39
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Wang Y, Grant OA, Zhai X, Mcdonald-Maier KD, Schalkwyk LC. Insights into ageing rates comparison across tissues from recalibrating cerebellum DNA methylation clock. GeroScience 2024; 46:39-56. [PMID: 37597113 PMCID: PMC10828477 DOI: 10.1007/s11357-023-00871-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/07/2023] [Indexed: 08/21/2023] Open
Abstract
DNA methylation (DNAm)-based age clocks have been studied extensively as a biomarker of human ageing and a risk factor for age-related diseases. Despite different tissues having vastly different rates of proliferation, it is still largely unknown whether they age at different rates. It was previously reported that the cerebellum ages slowly; however, this claim was drawn from a single clock using a relatively small sample size and so warrants further investigation. We collected the largest cerebellum DNAm dataset (N = 752) to date. We found the respective epigenetic ages are all severely underestimated by six representative DNAm age clocks, with the underestimation effects more pronounced in the four clocks whose training datasets do not include brain-related tissues. We identified 613 age-associated CpGs in the cerebellum, which accounts for only 14.5% of the number found in the middle temporal gyrus from the same population (N = 404). From the 613 cerebellum age-associated CpGs, we built a highly accurate age prediction model for the cerebellum named CerebellumClockspecific (Pearson correlation=0.941, MAD=3.18 years). Ageing rate comparisons based on the two tissue-specific clocks constructed on the 201 overlapping age-associated CpGs support the cerebellum has younger DNAm age. Nevertheless, we built BrainCortexClock to prove a single DNAm clock is able to unbiasedly estimate DNAm ages of both cerebellum and cerebral cortex, when they are adequately and equally represented in the training dataset. Comparing ageing rates across tissues using DNA methylation multi-tissue clocks is flawed. The large underestimation of age prediction for cerebellums by previous clocks mainly reflects the improper usage of these age clocks. There exist strong and consistent ageing effects on the cerebellar methylome, and we suggest the smaller number of age-associated CpG sites in cerebellum is largely attributed to its extremely low average cell replication rates.
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Affiliation(s)
- Yucheng Wang
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ, UK
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Olivia A Grant
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- Institute of Social and Economic Research, University of Essex, Colchester, CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Xiaojun Zhai
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ, UK.
| | - Klaus D Mcdonald-Maier
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ, UK
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40
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Cao B, Xue Y, Liu D. The association between methylmalonic acid, a biomarker of mitochondria dysfunction, and phenotypic age acceleration: A population-based study. Arch Gerontol Geriatr 2024; 117:105176. [PMID: 37713936 DOI: 10.1016/j.archger.2023.105176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/16/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023]
Abstract
Phenotypic age acceleration (PAA) is a sensitive marker of biological aging. Circulating methylmalonic acid (MMA) is a novel biomarker of mitochondrial dysfunction and has been associated with age-related disorders. Our study aimed to investigate to what extent circulating MMA was associated with PAA, and whether the association was independent of vitamin B12 status and renal function in the general population. We analyzed cross-sectional data from 13,023 participants across a wide age range (mean age: 38.9 years, range: 12 - 85 years, 51.1% women) from the US National Health and Nutrition Examination Survey (NHANES). PAA was calculated based on the published algorithm. Linear regression models were performed to assess the association between circulating MAA and PAA. Only 31% of the variation in MMA levels was explained by age, sex, race/ethnicity, social economic status, vitamin B12 status, and renal function. Per unit increase in circulating MAA (1.0 nmol/L) was associated with 1.59 years increase in PAA (β = 1.59, 95% CI: 1.17, 2.00, p < 0.001) after adjusting for multiple confounders. Importantly, PAA increased with circulating MMA levels independent of vitamin B12, creatine, and homocysteine levels. The association was more pronounced in subgroups of age ≥ 65 years, women, underweight, vitamin B12 < 400 μmol/L, and homocysteine ≥ 10 μmol/L. The association was much stronger among participants with cardiovascular diseases (CVDs) than without CVDs. In conclusion, our current population-based study showed that mitochondria-derived circulating MMA was associated with increased phenotypic age acceleration in the general population.
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Affiliation(s)
- Bing Cao
- School of Psychology and Key Laboratory of Cognition and Personality (Ministry of Education), Southwest University, Chongqing, 400715, China
| | - Yu Xue
- Department of Clinical Nutrition, West China Hospital, Sichuan University, No.37 Guoxue Lane, Chengdu, Sichuan, China
| | - Dan Liu
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
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41
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Griffin PT, Kane AE, Trapp A, Li J, Arnold M, Poganik JR, Conway RJ, McNamara MS, Meer MV, Hoffman N, Amorim JA, Tian X, MacArthur MR, Mitchell SJ, Mueller AL, Carmody C, Vera DL, Kerepesi C, Ying K, Noren Hooten N, Mitchell JR, Evans MK, Gladyshev VN, Sinclair DA. TIME-seq reduces time and cost of DNA methylation measurement for epigenetic clock construction. NATURE AGING 2024; 4:261-274. [PMID: 38200273 DOI: 10.1038/s43587-023-00555-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/05/2023] [Indexed: 01/12/2024]
Abstract
Epigenetic 'clocks' based on DNA methylation have emerged as the most robust and widely used aging biomarkers, but conventional methods for applying them are expensive and laborious. Here we develop tagmentation-based indexing for methylation sequencing (TIME-seq), a highly multiplexed and scalable method for low-cost epigenetic clocks. Using TIME-seq, we applied multi-tissue and tissue-specific epigenetic clocks in over 1,800 mouse DNA samples from eight tissue and cell types. We show that TIME-seq clocks are accurate and robust, enriched for polycomb repressive complex 2-regulated loci, and benchmark favorably against conventional methods despite being up to 100-fold less expensive. Using dietary treatments and gene therapy, we find that TIME-seq clocks reflect diverse interventions in multiple tissues. Finally, we develop an economical human blood clock (R > 0.96, median error = 3.39 years) in 1,056 demographically representative individuals. These methods will enable more efficient epigenetic clock measurement in larger-scale human and animal studies.
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Affiliation(s)
- Patrick T Griffin
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Alice E Kane
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
- Institute for Systems Biology, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexandre Trapp
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jien Li
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Matthew Arnold
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Jesse R Poganik
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ryan J Conway
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Maeve S McNamara
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Margarita V Meer
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Noah Hoffman
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - João A Amorim
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Xiao Tian
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael R MacArthur
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Sarah J Mitchell
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
- Ludwig Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Amber L Mueller
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
- Cell Metabolism, Cell Press, Cambridge, MA, USA
| | - Colleen Carmody
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Daniel L Vera
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Csaba Kerepesi
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
- Institute for Computer Science and Control, Eötvös Loránd Research Network, Budapest, Hungary
| | - Kejun Ying
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - James R Mitchell
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Michele K Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - David A Sinclair
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA.
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Macip CC, Hasan R, Hoznek V, Kim J, Lu YR, Metzger LE, Sethna S, Davidsohn N. Gene Therapy-Mediated Partial Reprogramming Extends Lifespan and Reverses Age-Related Changes in Aged Mice. Cell Reprogram 2024; 26:24-32. [PMID: 38381405 PMCID: PMC10909732 DOI: 10.1089/cell.2023.0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Aging is a complex progression of changes best characterized as the chronic dysregulation of cellular processes leading to deteriorated tissue and organ function. Although aging cannot currently be prevented, its impact on life- and healthspan in the elderly can potentially be minimized by interventions that aim to return these cellular processes to optimal function. Recent studies have demonstrated that partial reprogramming using the Yamanaka factors (or a subset; OCT4, SOX2, and KLF4; OSK) can reverse age-related changes in vitro and in vivo. However, it is still unknown whether the Yamanaka factors (or a subset) are capable of extending the lifespan of aged wild-type (WT) mice. In this study, we show that systemically delivered adeno-associated viruses, encoding an inducible OSK system, in 124-week-old male mice extend the median remaining lifespan by 109% over WT controls and enhance several health parameters. Importantly, we observed a significant improvement in frailty scores indicating that we were able to improve the healthspan along with increasing the lifespan. Furthermore, in human keratinocytes expressing exogenous OSK, we observed significant epigenetic markers of age reversal, suggesting a potential reregulation of genetic networks to a younger potentially healthier state. Together, these results may have important implications for the development of partial reprogramming interventions to reverse age-associated diseases in the elderly.
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Affiliation(s)
| | | | | | - Jihyun Kim
- Rejuvenate Bio, San Diego, California, USA
| | - Yuancheng Ryan Lu
- Department of Biology, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
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Laubach ZM, Bozack A, Aris IM, Slopen N, Tiemeier H, Hivert MF, Cardenas A, Perng W. Maternal prenatal social experiences and offspring epigenetic age acceleration from birth to mid-childhood. Ann Epidemiol 2024; 90:28-34. [PMID: 37839726 PMCID: PMC10842218 DOI: 10.1016/j.annepidem.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
PURPOSE Investigate associations of maternal social experiences with offspring epigenetic age acceleration (EAA) from birth through mid-childhood among 205 mother-offspring dyads of minoritized racial and ethnic groups. METHODS We used linear regression to examine associations of maternal experiences of racial bias or discrimination (0 = none, 1-2 = intermediate, or 3+ = high), social support (tertile 1 = low, 2 = intermediate, 3 = high), and socioeconomic status index (tertile 1 = low, 2 = intermediate, 3 = high) during the prenatal period with offspring EAA according to Horvath's Pan-Tissue, Horvath's Skin and Blood, and Intrinsic EAA clocks at birth, 3 years, and 7 years. RESULTS In comparison to children of women who did not experience any racial bias or discrimination, those whose mothers reported highest levels of racial bias or discrimination had lower Pan-Tissue clock EAA in early (-0.50 years; 90% CI: -0.91, -0.09) and mid-childhood (-0.75 years; -1.41, -0.08). We observed similar associations for the Skin and Blood clock and Intrinsic EAA. Maternal experiences of discrimination were not associated with Pan-Tissue EAA at birth. Neither maternal social support nor socioeconomic status predicted offspring EAA. CONCLUSIONS Children whose mothers experienced higher racial bias or discrimination exhibited slower EAA. Future studies are warranted to confirm these findings and establish associations of early-life EAA with long-term health outcomes.
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Affiliation(s)
- Zachary M Laubach
- Department of Ecology and Evolutionary Biology (EBIO), University of Colorado Boulder
| | - Anne Bozack
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA
| | - Izzuddin M Aris
- Division of Chronic Disease Research Across the Lifecourse (CORAL), Department of Population Medicine, Harvard Medical School, Boston, MA
| | - Natalie Slopen
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Henning Tiemeier
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse (CORAL), Department of Population Medicine, Harvard Medical School, Boston, MA; Diabetes Unit, Massachusetts General Hospital, Boston, MA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA
| | - Wei Perng
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD Center), Department of Epidemiology, Colorado School of Public Health, Aurora, CO.
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Lozupone M, Solfrizzi V, Sardone R, Dibello V, Castellana F, Zupo R, Lampignano L, Bortone I, Daniele A, Panza F. The epigenetics of frailty. Epigenomics 2024; 16:189-202. [PMID: 38112012 DOI: 10.2217/epi-2023-0279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
The conceptual change of frailty, from a physical to a biopsychosocial phenotype, expanded the field of frailty, including social and behavioral domains with critical interaction between different frailty models. Environmental exposures - including physical exercise, psychosocial factors and diet - may play a role in the frailty pathophysiology. Complex underlying mechanisms involve the progressive interactions of genetics with epigenetics and of multimorbidity with environmental factors. Here we review the literature on possible mechanisms explaining the association between epigenetic hallmarks (i.e., global DNA methylation, DNA methylation age acceleration and microRNAs) and frailty, considered as biomarkers of aging. Frailty could be considered the result of environmental epigenetic factors on biological aging, caused by conflicting DNA methylation age and chronological age.
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Affiliation(s)
- Madia Lozupone
- Department of Translational Biomedicine & Neuroscience 'DiBraiN', University of Bari Aldo Moro, Bari, Italy
| | - Vincenzo Solfrizzi
- Cesare Frugoni Internal & Geriatric Medicine & Memory Unit, University of Bari Aldo Moro, Bari, Italy
| | | | - Vittorio Dibello
- Cesare Frugoni Internal & Geriatric Medicine & Memory Unit, University of Bari Aldo Moro, Bari, Italy
- Department of Orofacial Pain & Dysfunction, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam & Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Fabio Castellana
- Cesare Frugoni Internal & Geriatric Medicine & Memory Unit, University of Bari Aldo Moro, Bari, Italy
| | - Roberta Zupo
- Cesare Frugoni Internal & Geriatric Medicine & Memory Unit, University of Bari Aldo Moro, Bari, Italy
| | | | - Ilaria Bortone
- Department of Translational Biomedicine & Neuroscience 'DiBraiN', University of Bari Aldo Moro, Bari, Italy
| | - Antonio Daniele
- Department of Neuroscience, Catholic University of Sacred Heart, Rome, Italy
- Neurology Unit, IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy
| | - Francesco Panza
- Cesare Frugoni Internal & Geriatric Medicine & Memory Unit, University of Bari Aldo Moro, Bari, Italy
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Carlberg C, Velleuer E. Vitamin D and Aging: Central Role of Immunocompetence. Nutrients 2024; 16:398. [PMID: 38337682 PMCID: PMC10857325 DOI: 10.3390/nu16030398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/24/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
The pro-hormone vitamin D3 is an important modulator of both innate and adaptive immunity since its biologically active metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) regulates via the transcription factor VDR (vitamin D receptor) the epigenome and transcriptome of human immune cells and controls in this way the expression of hundreds of vitamin D target genes. Since the myeloid linage of hematopoiesis is epigenetically programmed by VDR in concert with the pioneer factors PU.1 (purine-rich box 1) and CEBPα (CCAAT/enhancer binding protein α), monocytes, macrophages, and dendritic cells are the most vitamin D-sensitive immune cell types. The central role of the immune system in various aging-related diseases suggests that immunocompetence describes not only the ability of an individual to resist pathogens and parasites but also to contest non-communicative diseases and the process of aging itself. In this review, we argue that the individual-specific responsiveness to vitamin D relates to a person's immunocompetence via the epigenetic programming function of VDR and its ligand 1,25(OH)2D3 during hematopoiesis as well as in the periphery. This may provide a mechanism explaining how vitamin D protects against major common diseases and, in parallel, promotes healthy aging.
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Affiliation(s)
- Carsten Carlberg
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, PL-10-748 Olsztyn, Poland
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Eunike Velleuer
- Department for Cytopathology, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany;
- Department for Pediatric Hemato-Oncology, Helios Children’s Hospital, D-47805 Krefeld, Germany
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46
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Merrill SM, Letourneau N, Giesbrecht GF, Edwards K, MacIsaac JL, Martin JW, MacDonald AM, Kinniburgh DW, Kobor MS, Dewey D, England-Mason G, The APrON Study Team. Sex-Specific Associations between Prenatal Exposure to Di(2-ethylhexyl) Phthalate, Epigenetic Age Acceleration, and Susceptibility to Early Childhood Upper Respiratory Infections. EPIGENOMES 2024; 8:3. [PMID: 38390895 PMCID: PMC10885049 DOI: 10.3390/epigenomes8010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Di(2-ethylhexyl) phthalate (DEHP) is a common plasticizer that can affect immune system development and susceptibility to infection. Aging processes (measured as epigenetic age acceleration (EAA)) may mediate the immune-related effects of prenatal exposure to DEHP. This study's objective was to examine associations between prenatal DEHP exposure, EAA at three months of age, and the number of upper respiratory infections (URIs) from 12 to 18 months of age using a sample of 69 maternal-child pairs from a Canadian pregnancy cohort. Blood DNA methylation data were generated using the Infinium HumanMethylation450 BeadChip; EAA was estimated using Horvath's pan-tissue clock. Robust regressions examined overall and sex-specific associations. Higher prenatal DEHP exposure (B = 6.52, 95% CI = 1.22, 11.81) and increased EAA (B = 2.98, 95% CI = 1.64, 4.32) independently predicted more URIs. In sex-specific analyses, some similar effects were noted for boys, and EAA mediated the association between prenatal DEHP exposure and URIs. In girls, higher prenatal DEHP exposure was associated with decreased EAA, and no mediation was noted. Higher prenatal DEHP exposure may be associated with increased susceptibility to early childhood URIs, particularly in boys, and aging biomarkers such as EAA may be a biological mechanism. Larger cohort studies examining the potential developmental immunotoxicity of phthalates are needed.
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Affiliation(s)
- Sarah M Merrill
- Department of Psychiatry and Human Behavior, The Warren Alpert Medical School at Brown University, Providence, RI 02903, USA
- Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V6H 0B3, Canada
| | - Nicole Letourneau
- Faculty of Nursing, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Hotchkiss Brain Institute, Calgary, AB T2N 4N1, Canada
| | - Gerald F Giesbrecht
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Psychology, Faculty of Arts, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Karlie Edwards
- Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V6H 0B3, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V6H 0B3, Canada
| | - Jonathan W Martin
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, 106 91 Stockholm, Sweden
| | - Amy M MacDonald
- Alberta Centre for Toxicology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - David W Kinniburgh
- Alberta Centre for Toxicology, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Michael S Kobor
- Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V6H 0B3, Canada
- Program in Child and Brain Development, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
| | - Deborah Dewey
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Hotchkiss Brain Institute, Calgary, AB T2N 4N1, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Gillian England-Mason
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - The APrON Study Team
- University of Calgary, Calgary, AB T2N 1N4, Canada
- University of Alberta, Edmonton, AB T6G 2R3, Canada
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Gopu V, Camacho FR, Toma R, Torres PJ, Cai Y, Krishnan S, Rajagopal S, Tily H, Vuyisich M, Banavar G. An accurate aging clock developed from large-scale gut microbiome and human gene expression data. iScience 2024; 27:108538. [PMID: 38230258 PMCID: PMC10790003 DOI: 10.1016/j.isci.2023.108538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/18/2021] [Accepted: 11/20/2023] [Indexed: 01/18/2024] Open
Abstract
Accurate measurement of the biological markers of the aging process could provide an "aging clock" measuring predicted longevity and enable the quantification of the effects of specific lifestyle choices on healthy aging. Using machine learning techniques, we demonstrate that chronological age can be predicted accurately from (1) the expression level of human genes in capillary blood and (2) the expression level of microbial genes in stool samples. The latter uses a very large metatranscriptomic dataset, stool samples from 90,303 individuals, which arguably results in a higher quality microbiome-aging model than prior work. Our analysis suggests associations between biological age and lifestyle/health factors, e.g., people on a paleo diet or with IBS tend to have higher model-predicted ages and people on a vegetarian diet tend to have lower model-predicted ages. We delineate the key pathways of systems-level biological decline based on the age-specific features of our model.
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Affiliation(s)
- Vishakh Gopu
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | | | - Ryan Toma
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | - Pedro J. Torres
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | - Ying Cai
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | - Subha Krishnan
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | | | - Hal Tily
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | - Momchilo Vuyisich
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | - Guruduth Banavar
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
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48
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Bienkowska A, Raddatz G, Söhle J, Kristof B, Völzke H, Gallinat S, Lyko F, Kaderali L, Winnefeld M, Grönniger E, Falckenhayn C. Development of an epigenetic clock to predict visual age progression of human skin. FRONTIERS IN AGING 2024; 4:1258183. [PMID: 38274286 PMCID: PMC10809641 DOI: 10.3389/fragi.2023.1258183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024]
Abstract
Aging is a complex process characterized by the gradual decline of physiological functions, leading to increased vulnerability to age-related diseases and reduced quality of life. Alterations in DNA methylation (DNAm) patterns have emerged as a fundamental characteristic of aged human skin, closely linked to the development of the well-known skin aging phenotype. These changes have been correlated with dysregulated gene expression and impaired tissue functionality. In particular, the skin, with its visible manifestations of aging, provides a unique model to study the aging process. Despite the importance of epigenetic age clocks in estimating biological age based on the correlation between methylation patterns and chronological age, a second-generation epigenetic age clock, which correlates DNAm patterns with a particular phenotype, specifically tailored to skin tissue is still lacking. In light of this gap, we aimed to develop a novel second-generation epigenetic age clock explicitly designed for skin tissue to facilitate a deeper understanding of the factors contributing to individual variations in age progression. To achieve this, we used methylation patterns from more than 370 female volunteers and developed the first skin-specific second-generation epigenetic age clock that accurately predicts the skin aging phenotype represented by wrinkle grade, visual facial age, and visual age progression, respectively. We then validated the performance of our clocks on independent datasets and demonstrated their broad applicability. In addition, we integrated gene expression and methylation data from independent studies to identify potential pathways contributing to skin age progression. Our results demonstrate that our epigenetic age clock, VisAgeX, specifically predicting visual age progression, not only captures known biological pathways associated with skin aging, but also adds novel pathways associated with skin aging.
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Affiliation(s)
- Agata Bienkowska
- Beiersdorf AG, Research and Development, Hamburg, Germany
- Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Jörn Söhle
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Boris Kristof
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Henry Völzke
- Institute for Community Medicine, SHIP/KEF, University Medicine Greifswald, Greifswald, Germany
| | | | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Lars Kaderali
- Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Marc Winnefeld
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Elke Grönniger
- Beiersdorf AG, Research and Development, Hamburg, Germany
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49
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Marcante B, Delicati A, Onofri M, Tozzo P, Caenazzo L. Estimation of Human Chronological Age from Buccal Swab Samples through a DNA Methylation Analysis Approach of a Five-Locus Multiple Regression Model. Int J Mol Sci 2024; 25:935. [PMID: 38256009 PMCID: PMC10815300 DOI: 10.3390/ijms25020935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Recent advancements in forensic genetics have facilitated the extraction of additional characteristics from unidentified samples. This study delves into the predictive potential of a five-gene (ELOVL2, FHL2, KLF14, C1orf132, and TRIM59) methylation rate analysis for human age estimation using buccal swabs collected from 60 Italian volunteers. The methylation levels of specific CpG sites in the five genes were analyzed through bisulfite conversion, single-base extension, and capillary electrophoresis. A multivariate linear regression model was crafted on the training set, then the test set was employed to validate the predictive model. The multivariate predictive model revealed a mean absolute deviation of 3.49 years in the test set of our sample. While limitations include a modest sample size, the study provides valuable insights into the potential of buccal swab-based age prediction, aiding in criminal investigations where accurate age determination is crucial. Our results also highlight that it is necessary to investigate the effectiveness of predictive models specific to biological tissues and individual populations, since models already proven effective for other populations or different tissues did not show the same effectiveness in our study.
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Affiliation(s)
- Beatrice Marcante
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35122 Padova, Italy; (B.M.); (A.D.); (P.T.)
| | - Arianna Delicati
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35122 Padova, Italy; (B.M.); (A.D.); (P.T.)
| | - Martina Onofri
- Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy;
| | - Pamela Tozzo
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35122 Padova, Italy; (B.M.); (A.D.); (P.T.)
| | - Luciana Caenazzo
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35122 Padova, Italy; (B.M.); (A.D.); (P.T.)
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50
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Lê BM, Hatch D, Yang Q, Shah N, Luyster FS, Garrett ME, Tanabe P, Ashley-Koch AE, Knisely MR. Characterizing epigenetic aging in an adult sickle cell disease cohort. Blood Adv 2024; 8:47-55. [PMID: 37967379 PMCID: PMC10784677 DOI: 10.1182/bloodadvances.2023011188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
ABSTRACT Sickle cell disease (SCD) affects ∼100 000 predominantly African American individuals in the United States, causing significant cellular damage, increased disease complications, and premature death. However, the contribution of epigenetic factors to SCD pathophysiology remains relatively unexplored. DNA methylation (DNAm), a primary epigenetic mechanism for regulating gene expression in response to the environment, is an important driver of normal cellular aging. Several DNAm epigenetic clocks have been developed to serve as a proxy for cellular aging. We calculated the epigenetic ages of 89 adults with SCD (mean age, 30.64 years; 60.64% female) using 5 published epigenetic clocks: Horvath, Hannum, PhenoAge, GrimAge, and DunedinPACE. We hypothesized that in chronic disease, such as SCD, individuals would demonstrate epigenetic age acceleration, but the results differed depending on the clock used. Recently developed clocks more consistently demonstrated acceleration (GrimAge, DunedinPACE). Additional demographic and clinical phenotypes were analyzed to explore their association with epigenetic age estimates. Chronological age was significantly correlated with epigenetic age in all clocks (Horvath, r = 0.88; Hannum, r = 0.89; PhenoAge, r = 0.85; GrimAge, r = 0.88; DunedinPACE, r = 0.34). The SCD genotype was associated with 2 clocks (PhenoAge, P = .02; DunedinPACE, P < .001). Genetic ancestry, biological sex, β-globin haplotypes, BCL11A rs11886868, and SCD severity were not associated. These findings, among the first to interrogate epigenetic aging in adults with SCD, demonstrate epigenetic age acceleration with recently developed epigenetic clocks but not older-generation clocks. Further development of epigenetic clocks may improve their predictive ability and utility for chronic diseases such as SCD.
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Affiliation(s)
- Brandon M. Lê
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | | | - Qing Yang
- School of Nursing, Duke University, Durham, NC
| | - Nirmish Shah
- Department of Medicine, Division of Pediatric Hematology/Oncology, Duke University, Durham, NC
| | | | - Melanie E. Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | | | | | - Allison E. Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
- Department of Medicine, Duke University Medical Center, Durham, NC
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