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Olecka M, van Bömmel A, Best L, Haase M, Foerste S, Riege K, Dost T, Flor S, Witte OW, Franzenburg S, Groth M, von Eyss B, Kaleta C, Frahm C, Hoffmann S. Nonlinear DNA methylation trajectories in aging male mice. Nat Commun 2024; 15:3074. [PMID: 38594255 PMCID: PMC11004021 DOI: 10.1038/s41467-024-47316-2] [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: 07/10/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024] Open
Abstract
Although DNA methylation data yields highly accurate age predictors, little is known about the dynamics of this quintessential epigenomic biomarker during lifespan. To narrow the gap, we investigate the methylation trajectories of male mouse colon at five different time points of aging. Our study indicates the existence of sudden hypermethylation events at specific stages of life. Precisely, we identify two epigenomic switches during early-to-midlife (3-9 months) and mid-to-late-life (15-24 months) transitions, separating the rodents' life into three stages. These nonlinear methylation dynamics predominantly affect genes associated with the nervous system and enrich in bivalently marked chromatin regions. Based on groups of nonlinearly modified loci, we construct a clock-like classifier STageR (STage of aging estimatoR) that accurately predicts murine epigenetic stage. We demonstrate the universality of our clock in an independent mouse cohort and with publicly available datasets.
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Affiliation(s)
- Maja Olecka
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Alena van Bömmel
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Lena Best
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Madlen Haase
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Silke Foerste
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Konstantin Riege
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Thomas Dost
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Stefano Flor
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Otto W Witte
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Marco Groth
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Björn von Eyss
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Christiane Frahm
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Steve Hoffmann
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.
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Yanai H, Park B, Koh H, Jang HJ, Vaughan KL, Tanaka-Yano M, Aon M, Blanton M, Messaoudi I, Diaz-Ruiz A, Mattison JA, Beerman I. Short-term periodic restricted feeding elicits metabolome-microbiome signatures with sex dimorphic persistence in primate intervention. Nat Commun 2024; 15:1088. [PMID: 38316796 PMCID: PMC10844192 DOI: 10.1038/s41467-024-45359-z] [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: 08/02/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
Dietary restriction has shown benefits in physiological, metabolic, and molecular signatures associated with aging but is a difficult lifestyle to maintain for most individuals. In mice, a less restrictive diet that allows for cyclical periods of reduced calories mitigates aging phenotypes, yet the effects of such an intervention in a genetically heterogenous, higher-order mammal has not been examined. Here, using middle-aged rhesus macaques matched for age and sex, we show that a regimen of 4 days of low-calorie intake followed by 10 days of ad libitum feeding (4:10 diet) performed in repeating cycles over 12 weeks led to significant loss of weight and fat percentage, despite the free access to food for most of the study duration. We show the 4-day restriction period is sufficient to drive alterations to the serum metabolome characterized by substantial differences in lipid classes. These phenotypes were paralleled by changes in the gut microbiome of restricted monkeys that highlight the involvement of a microbiome-metabolome axis. This regimen shows promising phenotypes, with some sex-dimorphic responses, including residual memory of the diet. As many calorie restriction interventions are difficult to sustain, we propose that this short-term diet may be easier to adhere to and have benefits directly relevant to human aging.
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Affiliation(s)
- Hagai Yanai
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Bongsoo Park
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Hyunwook Koh
- Department of Applied Mathematics & Statistics, The State University of New York, Korea (SUNY Korea), Incheon, South Korea
| | - Hyo Jung Jang
- Department of Applied Mathematics & Statistics, The State University of New York, Korea (SUNY Korea), Incheon, South Korea
| | - Kelli L Vaughan
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Mayuri Tanaka-Yano
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Miguel Aon
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Madison Blanton
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Alberto Diaz-Ruiz
- Laboratory of Cellular and Molecular Gerontology, Precision Nutrition and Aging Program, Institute IMDEA Food (CEI UAM+CSIC), Madrid, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Madrid, Spain
| | - Julie A Mattison
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Isabel Beerman
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA.
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