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Gomez-Pinilla F, Thapak P. Exercise epigenetics is fueled by cell bioenergetics: Supporting role on brain plasticity and cognition. Free Radic Biol Med 2024; 220:43-55. [PMID: 38677488 PMCID: PMC11144461 DOI: 10.1016/j.freeradbiomed.2024.04.237] [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: 02/29/2024] [Revised: 04/04/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Exercise has the unique aptitude to benefit overall health of body and brain. Evidence indicates that the effects of exercise can be saved in the epigenome for considerable time to elevate the threshold for various diseases. The action of exercise on epigenetic regulation seems central to building an "epigenetic memory" to influence long-term brain function and behavior. As an intrinsic bioenergetic process, exercise engages the function of the mitochondria and redox pathways to impinge upon molecular mechanisms that regulate synaptic plasticity and learning and memory. We discuss how the action of exercise uses mechanisms of bioenergetics to support a "epigenetic memory" with long-term implications for neural and behavioral plasticity. This information is crucial for directing the power of exercise to reduce the burden of neurological and psychiatric disorders.
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Affiliation(s)
- Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Department of Neurosurgery, UCLA Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Pavan Thapak
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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2
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Kaplinsky A, Halperin R, Shlomai G, Tirosh A. Role of epigenetic regulation on catecholamine synthesis in pheochromocytoma and paraganglioma. Cancer 2024. [PMID: 38872410 DOI: 10.1002/cncr.35426] [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: 02/10/2024] [Revised: 04/27/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
INTRODUCTION Pheochromocytomas and paragangliomas (PPGLs) typically secrete catecholamines and their metabolites (metanephrines [MN] and normetanephrine [NMN]). Catecholamines are synthesized by several enzymes: phenylalanine hydroxylase (encoded by PAH), tyrosine hydroxylase (TH), aromatic L-amino acid decarboxylase (DDC), dopamine β-hydroxylase (DBH), and phenylethanolamine N-methyltransferase (PNMT). MN/NMN secretion varies between anatomical and molecular subgroups. The aim of this study was to assess the correlation between DNA methylation of catecholamine synthesis genes and MN/NMN secretion. METHODS Gene promoter methylation of PAH, TH, AADC, DBH, and PNMT were extracted and calculated based on publicly available data. Comparisons and correlation analysis were performed between MN ± NMN (MN/NMN), NMN only, and neither/unknown secretion patterns. Methylation levels and MN/NMN patterns were compared by three genetic alteration subgroups: pseudohypoxia (PH), kinase signaling (KS), and others. RESULTS A total of 178 cases were included. Methylation of PAH CpGs negatively correlated with probability for MN/NMN secretion (p < .05 for all CpGs) and positively with NMN-only secretion. NMN-only secreting tumors had significantly higher promoter methylation of PAH, DBH, and PNMT compared with MN/NMN-secreting tumors. MN/NMN-secreting PPGLs had mainly KS alterations (52.1%), whereas NMN-only PPGLs had PH alterations (41.9%). PPGLs in the PH versus KS group had gene promoter hypermethylation of PAH (p = .002), DBH (p = .02), and PNMT (p = .003). CONCLUSIONS Promoter methylation of genes encoding catecholamine synthesis enzymes is strongly and inversely correlated with MN/NMN patterns in PPGLs. KS and PH-related tumors have distinct methylation patterns. These results imply that methylation is a key regulatory mechanism of catecholamine synthesis in PPGLs.
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Affiliation(s)
- Anna Kaplinsky
- Cancer Center, Ramat Gan, Israel
- Tel Aviv University Faculty of Medicine, Tel-Aviv, Israel
| | - Reut Halperin
- Tel Aviv University Faculty of Medicine, Tel-Aviv, Israel
- Division of Endocrinology, Metabolism, and Diabetes, ENTIRE - Endocrine Neoplasia Translational Research Center, Ramat Gan, Israel
| | - Gadi Shlomai
- Tel Aviv University Faculty of Medicine, Tel-Aviv, Israel
- Internal Medicine D Ward, Sheba Medical Center, Ramat Gan, Israel
| | - Amit Tirosh
- Division of Endocrinology, Metabolism, and Diabetes, ENTIRE - Endocrine Neoplasia Translational Research Center, Ramat Gan, Israel
- Internal Medicine D Ward, Sheba Medical Center, Ramat Gan, Israel
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3
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Mack TM, Raddatz MA, Pershad Y, Nachun DC, Taylor KD, Guo X, Shuldiner AR, O'Connell JR, Kenny EE, Loos RJF, Redline S, Cade BE, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Cho MH, DeMeo DL, Levy D, Johnson AD, Mathias RA, Yanek LR, Heckbert SR, Smith NL, Wiggins KL, Raffield LM, Carson AP, Rotter JI, Rich SS, Manichaikul AW, Gu CC, Chen YDI, Lee WJ, Shoemaker MB, Roden DM, Kooperberg C, Auer PL, Desai P, Blackwell TW, Smith AV, Reiner AP, Jaiswal S, Weinstock JS, Bick AG. Epigenetic and proteomic signatures associate with clonal hematopoiesis expansion rate. NATURE AGING 2024:10.1038/s43587-024-00647-7. [PMID: 38834882 DOI: 10.1038/s43587-024-00647-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 05/08/2024] [Indexed: 06/06/2024]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP), whereby somatic mutations in hematopoietic stem cells confer a selective advantage and drive clonal expansion, not only correlates with age but also confers increased risk of morbidity and mortality. Here, we leverage genetically predicted traits to identify factors that determine CHIP clonal expansion rate. We used the passenger-approximated clonal expansion rate method to quantify the clonal expansion rate for 4,370 individuals in the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) cohort and calculated polygenic risk scores for DNA methylation aging, inflammation-related measures and circulating protein levels. Clonal expansion rate was significantly associated with both genetically predicted and measured epigenetic clocks. No associations were identified with inflammation-related lab values or diseases and CHIP expansion rate overall. A proteome-wide search identified predicted circulating levels of myeloid zinc finger 1 and anti-Müllerian hormone as associated with an increased CHIP clonal expansion rate and tissue inhibitor of metalloproteinase 1 and glycine N-methyltransferase as associated with decreased CHIP clonal expansion rate. Together, our findings identify epigenetic and proteomic patterns associated with the rate of hematopoietic clonal expansion.
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Affiliation(s)
- Taralynn M Mack
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael A Raddatz
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yash Pershad
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daniel C Nachun
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alan R Shuldiner
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, Mount Sinai Hospital, New York City, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Brian E Cade
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeong H Yun
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Levy
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - C Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yii-Der Ida Chen
- Medical Genetics Translational Genomics and Population Sciences (TGPS), Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung City, Taiwan
| | - M Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas W Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Albert V Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alexander G Bick
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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4
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Dormann D, Lemke EA. Adding intrinsically disordered proteins to biological ageing clocks. Nat Cell Biol 2024; 26:851-858. [PMID: 38783141 DOI: 10.1038/s41556-024-01423-w] [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: 12/01/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
Research into how the young and old differ, and which biomarkers reflect the diverse biological processes underlying ageing, is a current and fast-growing field. Biological clocks provide a means to evaluate whether a molecule, cell, tissue or even an entire organism is old or young. Here we summarize established and emerging molecular clocks as timepieces. We emphasize that intrinsically disordered proteins (IDPs) tend to transform into a β-sheet-rich aggregated state and accumulate in non-dividing or slowly dividing cells as they age. We hypothesize that understanding these protein-based molecular ageing mechanisms might provide a conceptual pathway to determining a cell's health age by probing the aggregation state of IDPs, which we term the IDP clock.
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Affiliation(s)
- Dorothee Dormann
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
| | - Edward Anton Lemke
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg University, Mainz, Germany.
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5
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Balard A, Baltazar-Soares M, Eizaguirre C, Heckwolf MJ. An epigenetic toolbox for conservation biologists. Evol Appl 2024; 17:e13699. [PMID: 38832081 PMCID: PMC11146150 DOI: 10.1111/eva.13699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Ongoing climatic shifts and increasing anthropogenic pressures demand an efficient delineation of conservation units and accurate predictions of populations' resilience and adaptive potential. Molecular tools involving DNA sequencing are nowadays routinely used for these purposes. Yet, most of the existing tools focusing on sequence-level information have shortcomings in detecting signals of short-term ecological relevance. Epigenetic modifications carry valuable information to better link individuals, populations, and species to their environment. Here, we discuss a series of epigenetic monitoring tools that can be directly applied to various conservation contexts, complementing already existing molecular monitoring frameworks. Focusing on DNA sequence-based methods (e.g. DNA methylation, for which the applications are readily available), we demonstrate how (a) the identification of epi-biomarkers associated with age or infection can facilitate the determination of an individual's health status in wild populations; (b) whole epigenome analyses can identify signatures of selection linked to environmental conditions and facilitate estimating the adaptive potential of populations; and (c) epi-eDNA (epigenetic environmental DNA), an epigenetic-based conservation tool, presents a non-invasive sampling method to monitor biological information beyond the mere presence of individuals. Overall, our framework refines conservation strategies, ensuring a comprehensive understanding of species' adaptive potential and persistence on ecologically relevant timescales.
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Affiliation(s)
- Alice Balard
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | | | - Christophe Eizaguirre
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | - Melanie J Heckwolf
- Department of Ecology Leibniz Centre for Tropical Marine Research Bremen Germany
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6
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Sandalova E, Maier AB. Targeting the epigenetically older individuals for geroprotective trials: the use of DNA methylation clocks. Biogerontology 2024; 25:423-431. [PMID: 37968337 DOI: 10.1007/s10522-023-10077-4] [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: 09/08/2023] [Accepted: 10/15/2023] [Indexed: 11/17/2023]
Abstract
Chronological age is the most important risk factor for the incidence of age-related diseases. The pace of ageing determines the magnitude of that risk and can be expressed as biological age. Targeting fundamental pathways of human aging with geroprotectors has the potential to lower the biological age and therewith prolong the healthspan, the period of life one spends in good health. Target populations for geroprotective interventions should be chosen based on the ageing mechanisms being addressed and the expected effect of the geroprotector on the primary outcome. Biomarkers of ageing, such as DNA methylation age, can be used to select populations for geroprotective interventions and as a surrogate outcome. Here, the use of DNA methylation clocks for selecting target populations for geroprotective intervention is explored.
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Affiliation(s)
- Elena Sandalova
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore, Singapore.
| | - Andrea B Maier
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore, Singapore.
- Department of Human Movement Sciences, @AgeAmsterdam, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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7
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Chien JF, Liu H, Wang BA, Luo C, Bartlett A, Castanon R, Johnson ND, Nery JR, Osteen J, Li J, Altshul J, Kenworthy M, Valadon C, Liem M, Claffey N, O'Connor C, Seeker LA, Ecker JR, Behrens MM, Mukamel EA. Cell-type-specific effects of age and sex on human cortical neurons. Neuron 2024:S0896-6273(24)00360-X. [PMID: 38838671 DOI: 10.1016/j.neuron.2024.05.013] [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: 11/29/2023] [Revised: 03/29/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024]
Abstract
Altered transcriptional and epigenetic regulation of brain cell types may contribute to cognitive changes with advanced age. Using single-nucleus multi-omic DNA methylation and transcriptome sequencing (snmCT-seq) in frontal cortex from young adult and aged donors, we found widespread age- and sex-related variation in specific neuron types. The proportion of inhibitory SST- and VIP-expressing neurons was reduced in aged donors. Excitatory neurons had more profound age-related changes in their gene expression and DNA methylation than inhibitory cells. Hundreds of genes involved in synaptic activity, including EGR1, were less expressed in aged adults. Genes located in subtelomeric regions increased their expression with age and correlated with reduced telomere length. We further mapped cell-type-specific sex differences in gene expression and X-inactivation escape genes. Multi-omic single-nucleus epigenomes and transcriptomes provide new insight into the effects of age and sex on human neurons.
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Affiliation(s)
- Jo-Fan Chien
- Department of Physics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Bang-An Wang
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Rosa Castanon
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Nicholas D Johnson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA; Computational Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Julia Osteen
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Junhao Li
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jordan Altshul
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Mia Kenworthy
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Cynthia Valadon
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Michelle Liem
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Naomi Claffey
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Caz O'Connor
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Luise A Seeker
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA.
| | - M Margarita Behrens
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA; Computational Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037, USA.
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA.
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8
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Quarato ER, Salama NA, Calvi LM. Interplay Between Skeletal and Hematopoietic Cells in the Bone Marrow Microenvironment in Homeostasis and Aging. Curr Osteoporos Rep 2024:10.1007/s11914-024-00874-2. [PMID: 38782850 DOI: 10.1007/s11914-024-00874-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/05/2024] [Indexed: 05/25/2024]
Abstract
PURPOSE OF THE REVIEW In this review, we discuss the most recent scientific advances on the reciprocal regulatory interactions between the skeletal and hematopoietic stem cell niche, focusing on immunomodulation and its interplay with the cell's mitochondrial function, and how this impacts osteoimmune health during aging and disease. RECENT FINDINGS Osteoimmunology investigates interactions between cells that make up the skeletal stem cell niche and immune system. Much work has investigated the complexity of the bone marrow microenvironment with respect to the skeletal and hematopoietic stem cells that regulate skeletal formation and immune health respectively. It has now become clear that these cellular components cooperate to maintain homeostasis and that dysfunction in their interaction can lead to aging and disease. Having a deeper, mechanistic appreciation for osteoimmune regulation will lead to better research perspective and therapeutics with the potential to improve the aging process, skeletal and hematologic regeneration, and disease targeting.
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Affiliation(s)
- Emily R Quarato
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA.
- James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA.
| | - Noah A Salama
- James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA.
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA.
| | - Laura M Calvi
- James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA.
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA.
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9
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Zhu T, Tong H, Du Z, Beck S, Teschendorff AE. An improved epigenetic counter to track mitotic age in normal and precancerous tissues. Nat Commun 2024; 15:4211. [PMID: 38760334 PMCID: PMC11101651 DOI: 10.1038/s41467-024-48649-8] [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: 09/24/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
The cumulative number of stem cell divisions in a tissue, known as mitotic age, is thought to be a major determinant of cancer-risk. Somatic mutational and DNA methylation (DNAm) clocks are promising tools to molecularly track mitotic age, yet their relationship is underexplored and their potential for cancer risk prediction in normal tissues remains to be demonstrated. Here we build and validate an improved pan-tissue DNAm counter of total mitotic age called stemTOC. We demonstrate that stemTOC's mitotic age proxy increases with the tumor cell-of-origin fraction in each of 15 cancer-types, in precancerous lesions, and in normal tissues exposed to major cancer risk factors. Extensive benchmarking against 6 other mitotic counters shows that stemTOC compares favorably, specially in the preinvasive and normal-tissue contexts. By cross-correlating stemTOC to two clock-like somatic mutational signatures, we confirm the mitotic-like nature of only one of these. Our data points towards DNAm as a promising molecular substrate for detecting mitotic-age increases in normal tissues and precancerous lesions, and hence for developing cancer-risk prediction strategies.
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Affiliation(s)
- Tianyu Zhu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for 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, China
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for 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, China
| | - Zhaozhen Du
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for 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, China
| | - Stephan Beck
- Medical Genomics Group, UCL Cancer Institute, University College London, 72 Huntley Street, WC1E 6BT, London, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for 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, China.
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10
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Szakállas N, Barták BK, Valcz G, Nagy ZB, Takács I, Molnár B. Can long-read sequencing tackle the barriers, which the next-generation could not? A review. Pathol Oncol Res 2024; 30:1611676. [PMID: 38818014 PMCID: PMC11137202 DOI: 10.3389/pore.2024.1611676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points. The appearance of new sequencing techniques was essential to get more interpretable genomic data. In contrast to the previous short-reads, longer lengths can provide a better insight into the potential health threatening genetic abnormalities. Long-reads offer more accurate variant identification and genome assembly methods, indicating advances in nucleotide deflect-related studies. In this review, we introduce the historical background of sequencing technologies and show their benefits and limits, as well. Furthermore, we highlight the differences between short- and long-read approaches, including their unique advances and difficulties in methodologies and evaluation. Additionally, we provide a detailed description of the corresponding bioinformatics and the current applications.
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Affiliation(s)
- Nikolett Szakállas
- Department of Biological Physics, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
| | - Barbara K. Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Gábor Valcz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary
| | - Zsófia B. Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
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11
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Li SJ, Gao X, Wang ZH, Li J, Zeng LT, Dang YM, Ma YQ, Zhang LQ, Wang QY, Zhang YM, Liu HL, Qi RM, Cai JP. Cell-free DNA methylation patterns in aging and their association with inflamm-aging. Epigenomics 2024:1-17. [PMID: 38869474 DOI: 10.1080/17501911.2024.2340958] [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: 02/13/2024] [Accepted: 04/05/2024] [Indexed: 06/14/2024] Open
Abstract
Aim: Liquid biopsies analyzing cell-free DNA (cfDNA) methylation in plasma offer a noninvasive diagnostic for diseases, with the potential of aging biomarkers underexplored. Methods: Utilizing enzymatic methyl-seq (EM-seq), this study assessed cfDNA methylation patterns in aging with blood from 35 healthy individuals. Results: It found aging signatures, including higher cfDNA levels and variations in fragment sizes, plus approximately 2000 age-related differentially methylated CpG sites. A biological age predictive model based on 48 CpG sites showed a strong correlation with chronological age, verified by two datasets. Age-specific epigenetic shifts linked to inflammation were revealed through differentially methylated regions profiling and Olink proteomics. Conclusion: These findings suggest cfDNA methylation as a potential aging biomarker and might exacerbate immunoinflammatory reactivity in older individuals.
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Affiliation(s)
- Si-Jia Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, PR China
| | - Xin Gao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, PR China
| | - Zi-Hui Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, PR China
| | - Jin Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Lv-Tao Zeng
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Ya-Min Dang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, PR China
| | - Ya-Qing Ma
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Li-Qun Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Qing-Yu Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Ying-Min Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Hong-Lei Liu
- School of Biomedical Engineering, Capital Medical University, 100730, PR China
| | - Ruo-Mei Qi
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, PR China
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, PR China
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12
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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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13
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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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14
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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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15
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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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16
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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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17
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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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18
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Palma FR, Coelho DR, Pulakanti K, Sakiyama MJ, Huang Y, Ogata FT, Danes JM, Meyer A, Furdui CM, Spitz DR, Gomes AP, Gantner BN, Rao S, Backman V, Bonini MG. Histone H3.1 is a chromatin-embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multidrug resistance. Cell Rep 2024; 43:113897. [PMID: 38493478 DOI: 10.1016/j.celrep.2024.113897] [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: 06/26/2023] [Revised: 01/08/2024] [Accepted: 02/16/2024] [Indexed: 03/19/2024] Open
Abstract
Chromatin structure is regulated through posttranslational modifications of histone variants that modulate transcription. Although highly homologous, histone variants display unique amino acid sequences associated with specific functions. Abnormal incorporation of histone variants contributes to cancer initiation, therapy resistance, and metastasis. This study reports that, among its biologic functions, histone H3.1 serves as a chromatin redox sensor that is engaged by mitochondrial H2O2. In breast cancer cells, the oxidation of H3.1Cys96 promotes its eviction and replacement by H3.3 in specific promoters. We also report that this process facilitates the opening of silenced chromatin domains and transcriptional activation of epithelial-to-mesenchymal genes associated with cell plasticity. Scavenging nuclear H2O2 or amino acid substitution of H3.1(C96S) suppresses plasticity, restores sensitivity to chemotherapy, and induces remission of metastatic lesions. Hence, it appears that increased levels of H2O2 produced by mitochondria of breast cancer cells directly promote redox-regulated H3.1-dependent chromatin remodeling involved in chemoresistance and metastasis.
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Affiliation(s)
- Flavio R Palma
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Diego R Coelho
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Kirthi Pulakanti
- Versiti Blood Research Institute of Wisconsin, and Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marcelo J Sakiyama
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Yunping Huang
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Fernando T Ogata
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Jeanne M Danes
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Alison Meyer
- Versiti Blood Research Institute of Wisconsin, and Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Douglas R Spitz
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52245, USA
| | - Ana P Gomes
- Molecular Oncology Program, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Benjamin N Gantner
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sridhar Rao
- Versiti Blood Research Institute of Wisconsin, and Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL 60208, USA
| | - Marcelo G Bonini
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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19
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Yeung-Luk BH, Wally A, Swaby C, Jauregui S, Lee E, Zhang R, Chen D, Luk SH, Upadya N, Tieng E, Wilmsen K, Sherman E, Sudhakar D, Luk M, Shrivastav AK, Cao S, Ghosh B, Christenson SA, Huang YJ, Ortega VE, Biswal S, Tang WY, Sidhaye VK. Epigenetic Reprogramming Drives Epithelial Disruption in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2024; 70:165-177. [PMID: 37976469 PMCID: PMC10914773 DOI: 10.1165/rcmb.2023-0147oc] [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: 04/25/2023] [Accepted: 11/17/2023] [Indexed: 11/19/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) remains a major public health challenge that contributes greatly to mortality and morbidity worldwide. Although it has long been recognized that the epithelium is altered in COPD, there has been little focus on targeting it to modify the disease course. Therefore, mechanisms that disrupt epithelial cell function in patients with COPD are poorly understood. In this study, we sought to determine whether epigenetic reprogramming of the cell-cell adhesion molecule E-cadherin, encoded by the CDH1 gene, disrupts epithelial integrity. By reducing these epigenetic marks, we can restore epithelial integrity and rescue alveolar airspace destruction. We used differentiated normal and COPD-derived primary human airway epithelial cells, genetically manipulated mouse tracheal epithelial cells, and mouse and human precision-cut lung slices to assess the effects of epigenetic reprogramming. We show that the loss of CDH1 in COPD is due to increased DNA methylation site at the CDH1 enhancer D through the downregulation of the ten-eleven translocase methylcytosine dioxygenase (TET) enzyme TET1. Increased DNA methylation at the enhancer D region decreases the enrichment of RNA polymerase II binding. Remarkably, treatment of human precision-cut slices derived from patients with COPD with the DNA demethylation agent 5-aza-2'-deoxycytidine decreased cell damage and reduced air space enlargement in the diseased tissue. Here, we present a novel mechanism that targets epigenetic modifications to reverse the tissue remodeling in human COPD lungs and serves as a proof of concept for developing a disease-modifying target.
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Affiliation(s)
| | - Ara Wally
- Department of Environmental Health and Engineering and
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Carter Swaby
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Sofia Jauregui
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Esther Lee
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Rachel Zhang
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Daniel Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Sean H. Luk
- Department of Environmental Health and Engineering and
| | - Nisha Upadya
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Ethan Tieng
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Kai Wilmsen
- Department of Environmental Health and Engineering and
| | - Ethan Sherman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Dheeksha Sudhakar
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Matthew Luk
- Department of Environmental Health and Engineering and
| | - Abhishek Kumar Shrivastav
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | - Shuo Cao
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | | | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | - Yvonne J. Huang
- Department of Medicine, University of Michigan, Ann Arbor, Michigan; and
| | | | - Shyam Biswal
- Department of Environmental Health and Engineering and
| | - Wan-yee Tang
- Department of Environmental Health and Engineering and
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Venkataramana K. Sidhaye
- Department of Environmental Health and Engineering and
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
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20
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Chen J, Zhang H, Yi X, Dou Q, Yang X, He Y, Chen J, Chen K. Cellular senescence of renal tubular epithelial cells in acute kidney injury. Cell Death Discov 2024; 10:62. [PMID: 38316761 PMCID: PMC10844256 DOI: 10.1038/s41420-024-01831-9] [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: 11/19/2023] [Revised: 01/14/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024] Open
Abstract
Cellular senescence represents an irreversible state of cell-cycle arrest during which cells secrete senescence-associated secretory phenotypes, including inflammatory factors and chemokines. Additionally, these cells exhibit an apoptotic resistance phenotype. Cellular senescence serves a pivotal role not only in embryonic development, tissue regeneration, and tumor suppression but also in the pathogenesis of age-related degenerative diseases, malignancies, metabolic diseases, and kidney diseases. The senescence of renal tubular epithelial cells (RTEC) constitutes a critical cellular event in the progression of acute kidney injury (AKI). RTEC senescence inhibits renal regeneration and repair processes and, concurrently, promotes the transition of AKI to chronic kidney disease via the senescence-associated secretory phenotype. The mechanisms underlying cellular senescence are multifaceted and include telomere shortening or damage, DNA damage, mitochondrial autophagy deficiency, cellular metabolic disorders, endoplasmic reticulum stress, and epigenetic regulation. Strategies aimed at inhibiting RTEC senescence, targeting the clearance of senescent RTEC, or promoting the apoptosis of senescent RTEC hold promise for enhancing the renal prognosis of AKI. This review primarily focuses on the characteristics and mechanisms of RTEC senescence, and the impact of intervening RTEC senescence on the prognosis of AKI, aiming to provide a foundation for understanding the pathogenesis and providing potentially effective approaches for AKI treatment.
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Affiliation(s)
- Juan Chen
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Huhai Zhang
- Department of Nephrology, Southwest Hospital, Army Medical University, 400042, Chongqing, China
| | - Xiangling Yi
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Qian Dou
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Xin Yang
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Yani He
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Jia Chen
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China.
| | - Kehong Chen
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China.
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, China.
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21
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Perez K, Parras A, Picó S, Rechsteiner C, Haghani A, Brooke R, Mrabti C, Schoenfeldt L, Horvath S, Ocampo A. DNA repair-deficient premature aging models display accelerated epigenetic age. Aging Cell 2024; 23:e14058. [PMID: 38140713 PMCID: PMC10861193 DOI: 10.1111/acel.14058] [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: 04/07/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Several premature aging mouse models have been developed to study aging and identify interventions that can delay age-related diseases. Yet, it is still unclear whether these models truly recapitulate natural aging. Here, we analyzed DNA methylation in multiple tissues of four previously reported mouse models of premature aging (Ercc1, LAKI, Polg, and Xpg). We estimated DNA methylation (DNAm) age of these samples using the Horvath clock. The most pronounced increase in DNAm age could be observed in Ercc1 mice, a strain which exhibits a deficit in DNA nucleotide excision repair. Similarly, we detected an increase in epigenetic age in fibroblasts isolated from patients with progeroid syndromes associated with mutations in DNA excision repair genes. These findings highlight that mouse models with deficiencies in DNA repair, unlike other premature aging models, display accelerated epigenetic age, suggesting a strong connection between DNA damage and epigenetic dysregulation during aging.
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Affiliation(s)
- Kevin Perez
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
| | - Alberto Parras
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
| | - Sara Picó
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Cheyenne Rechsteiner
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | | | - Robert Brooke
- Epigenetic Clock Development FoundationTorranceCaliforniaUSA
| | - Calida Mrabti
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Lucas Schoenfeldt
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
| | - Steve Horvath
- Altos LabsSan DiegoCaliforniaUSA
- Epigenetic Clock Development FoundationTorranceCaliforniaUSA
- Human Genetics, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Alejandro Ocampo
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
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22
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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: 2] [Impact Index Per Article: 2.0] [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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23
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Prosz A, Pipek O, Börcsök J, Palla G, Szallasi Z, Spisak S, Csabai I. Biologically informed deep learning for explainable epigenetic clocks. Sci Rep 2024; 14:1306. [PMID: 38225268 PMCID: PMC10789766 DOI: 10.1038/s41598-023-50495-5] [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: 01/17/2023] [Accepted: 12/20/2023] [Indexed: 01/17/2024] Open
Abstract
Ageing is often characterised by progressive accumulation of damage, and it is one of the most important risk factors for chronic disease development. Epigenetic mechanisms including DNA methylation could functionally contribute to organismal aging, however the key functions and biological processes may govern ageing are still not understood. Although age predictors called epigenetic clocks can accurately estimate the biological age of an individual based on cellular DNA methylation, their models have limited ability to explain the prediction algorithm behind and underlying key biological processes controlling ageing. Here we present XAI-AGE, a biologically informed, explainable deep neural network model for accurate biological age prediction across multiple tissue types. We show that XAI-AGE outperforms the first-generation age predictors and achieves similar results to deep learning-based models, while opening up the possibility to infer biologically meaningful insights of the activity of pathways and other abstract biological processes directly from the model.
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Affiliation(s)
- Aurel Prosz
- Danish Cancer Institute, Copenhagen, Denmark
| | - Orsolya Pipek
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Judit Börcsök
- Danish Cancer Institute, Copenhagen, Denmark
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Gergely Palla
- Department of Biological Physics, ELTE Eötvös Loránd University, Budapest, Hungary
- Health Services Management Training Centre, Semmelweis University, Budapest, Hungary
| | | | - Sandor Spisak
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
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24
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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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25
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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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26
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Lee JM, Park SU, Lee SD, Lee HY. Application of array-based age prediction models to post-mortem tissue samples. Forensic Sci Int Genet 2024; 68:102940. [PMID: 37857127 DOI: 10.1016/j.fsigen.2023.102940] [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: 05/23/2023] [Revised: 09/03/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
Since DNA methylation at specific CpG sites exhibits a strong age association, researchers have developed numerous age prediction models based on the methylation BeadChip array. These models harness epigenetic clocks that hold the potential to narrow down the search range for unknown suspects and unidentified victims. This study collected 180 post-mortem tissue samples comprising nine tissue types (blood, brain, heart, lung, liver, kidney, muscle, epidermis, and dermis) from autopsies of 20 Koreans aged 18-78. Subsequently, DNA methylation profiling was conducted using the Infinium MethylationEPIC array. We tested several array-based age prediction models using the data obtained from various tissues. The pan-tissue clock exhibited a moderately accurate prediction across all nine tissue types (MAE = 8.7 years, r = 0.88). Notably, the DNAm ages of the Hannum clock, the skin & blood clock, and the Zhang clock strongly correlated with the actual age in blood samples (MAE < approximately 5 years, r > 0.9). PhenoAge yielded an MAE of 10.1 years and an r-value of 0.92. The muscle-specific epigenetic clock, the MEAT package, demonstrated high prediction accuracy in muscle samples (MAE = 4.7 years, r = 0.93). Those previously reported array-based age prediction models were mainly constructed in Europeans but performed well in Koreans. In addition, tests involving various quantities of DNA and fragmented DNA have shown that DNA quantity and quality affected methylation measurements and age prediction results. However, robust age prediction models exist under low amounts of DNA and fragmented DNA conditions.
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Affiliation(s)
- Jeong Min Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Un Park
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea.
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27
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Ananthamohan K, Stelzer JE, Sadayappan S. Hypertrophic cardiomyopathy in MYBPC3 carriers in aging. THE JOURNAL OF CARDIOVASCULAR AGING 2024; 4:9. [PMID: 38406555 PMCID: PMC10883298 DOI: 10.20517/jca.2023.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Hypertrophic cardiomyopathy (HCM) is characterized by abnormal thickening of the myocardium, leading to arrhythmias, heart failure, and elevated risk of sudden cardiac death, particularly among the young. This inherited disease is predominantly caused by mutations in sarcomeric genes, among which those in the cardiac myosin binding protein-C3 (MYBPC3) gene are major contributors. HCM associated with MYBPC3 mutations usually presents in the elderly and ranges from asymptomatic to symptomatic forms, affecting numerous cardiac functions and presenting significant health risks with a spectrum of clinical manifestations. Regulation of MYBPC3 expression involves various transcriptional and translational mechanisms, yet the destiny of mutant MYBPC3 mRNA and protein in late-onset HCM remains unclear. Pathogenesis related to MYBPC3 mutations includes nonsense-mediated decay, alternative splicing, and ubiquitin-proteasome system events, leading to allelic imbalance and haploinsufficiency. Aging further exacerbates the severity of HCM in carriers of MYBPC3 mutations. Advancements in high-throughput omics techniques have identified crucial molecular events and regulatory disruptions in cardiomyocytes expressing MYBPC3 variants. This review assesses the pathogenic mechanisms that promote late-onset HCM through the lens of transcriptional, post-transcriptional, and post-translational modulation of MYBPC3, underscoring its significance in HCM across carriers. The review also evaluates the influence of aging on these processes and MYBPC3 levels during HCM pathogenesis in the elderly. While pinpointing targets for novel medical interventions to conserve cardiac function remains challenging, the emergence of personalized omics offers promising avenues for future HCM treatments, particularly for late-onset cases.
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Affiliation(s)
- Kalyani Ananthamohan
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Julian E. Stelzer
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 45267, USA
| | - Sakthivel Sadayappan
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH 45267, USA
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28
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Voisin S, Seale K, Jacques M, Landen S, Harvey NR, Haupt LM, Griffiths LR, Ashton KJ, Coffey VG, Thompson JM, Doering TM, Lindholm ME, Walsh C, Davison G, Irwin R, McBride C, Hansson O, Asplund O, Heikkinen AE, Piirilä P, Pietiläinen KH, Ollikainen M, Blocquiaux S, Thomis M, Coletta DK, Sharples AP, Eynon N. Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle. Aging Cell 2024; 23:e13859. [PMID: 37128843 PMCID: PMC10776126 DOI: 10.1111/acel.13859] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
Exercise training prevents age-related decline in muscle function. Targeting epigenetic aging is a promising actionable mechanism and late-life exercise mitigates epigenetic aging in rodent muscle. Whether exercise training can decelerate, or reverse epigenetic aging in humans is unknown. Here, we performed a powerful meta-analysis of the methylome and transcriptome of an unprecedented number of human skeletal muscle samples (n = 3176). We show that: (1) individuals with higher baseline aerobic fitness have younger epigenetic and transcriptomic profiles, (2) exercise training leads to significant shifts of epigenetic and transcriptomic patterns toward a younger profile, and (3) muscle disuse "ages" the transcriptome. Higher fitness levels were associated with attenuated differential methylation and transcription during aging. Furthermore, both epigenetic and transcriptomic profiles shifted toward a younger state after exercise training interventions, while the transcriptome shifted toward an older state after forced muscle disuse. We demonstrate that exercise training targets many of the age-related transcripts and DNA methylation loci to maintain younger methylome and transcriptome profiles, specifically in genes related to muscle structure, metabolism, and mitochondrial function. Our comprehensive analysis will inform future studies aiming to identify the best combination of therapeutics and exercise regimes to optimize longevity.
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Affiliation(s)
- Sarah Voisin
- Institute for Health and Sport (iHeS)Victoria UniversityFootscrayVictoriaAustralia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Kirsten Seale
- Institute for Health and Sport (iHeS)Victoria UniversityFootscrayVictoriaAustralia
| | - Macsue Jacques
- Institute for Health and Sport (iHeS)Victoria UniversityFootscrayVictoriaAustralia
| | - Shanie Landen
- Institute for Health and Sport (iHeS)Victoria UniversityFootscrayVictoriaAustralia
| | - Nicholas R. Harvey
- Faculty of Health Sciences and MedicineBond UniversityGold CoastQueenslandAustralia
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Larisa M. Haupt
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
- ARC Training Centre for Cell and Tissue Engineering TechnologiesQueensland University of Technology (QUT)BrisbaneQueenslandAustralia
- Max Planck Queensland Centre for the Materials Sciences of Extracellular MatricesBrisbaneQueenslandAustralia
| | - Lyn R. Griffiths
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Kevin J. Ashton
- Faculty of Health Sciences and MedicineBond UniversityGold CoastQueenslandAustralia
| | - Vernon G. Coffey
- Faculty of Health Sciences and MedicineBond UniversityGold CoastQueenslandAustralia
| | | | - Thomas M. Doering
- School of Health, Medical and Applied SciencesCentral Queensland UniversityRockhamptonQueenslandAustralia
| | - Malene E. Lindholm
- Department of Medicine, School of MedicineStanford UniversityStanfordCaliforniaUSA
| | - Colum Walsh
- Genomic Medicine Research Group, School of Biomedical SciencesUlster UniversityColeraineUK
| | - Gareth Davison
- Sport and Exercise Sciences Research InstituteUlster UniversityBelfastUK
| | - Rachelle Irwin
- Genomic Medicine Research Group, School of Biomedical SciencesUlster UniversityColeraineUK
| | - Catherine McBride
- Sport and Exercise Sciences Research InstituteUlster UniversityBelfastUK
| | - Ola Hansson
- Department of Clinical Sciences, Genomics, Diabetes and Endocrinology Unit, Lund University Diabetes CenterLund UniversityLundSweden
- Institute for Molecular Medicine Finland (FIMM)Helsinki UniversityHelsinkiFinland
| | - Olof Asplund
- Department of Clinical Sciences, Genomics, Diabetes and Endocrinology Unit, Lund University Diabetes CenterLund UniversityLundSweden
| | - Aino E. Heikkinen
- Institute for Molecular Medicine Finland (FIMM)Helsinki UniversityHelsinkiFinland
| | - Päivi Piirilä
- Unit of Clinical PhysiologyHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Kirsi H. Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- HealthyWeightHub, Endocrinology, Abdominal CenterHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM)Helsinki UniversityHelsinkiFinland
- Minerva Foundation Institute for Medical ResearchHelsinkiFinland
| | - Sara Blocquiaux
- Department of Movement Sciences, Physical Activity, Sports and Health Research GroupKU LeuvenLeuvenBelgium
| | - Martine Thomis
- Department of Movement Sciences, Physical Activity, Sports and Health Research GroupKU LeuvenLeuvenBelgium
| | - Dawn K. Coletta
- Department of Medicine, Division of EndocrinologyUniversity of ArizonaTucsonArizonaUSA
- UA Center for Disparities in Diabetes Obesity and MetabolismUniversity of ArizonaTucsonArizonaUSA
- Department of PhysiologyUniversity of ArizonaTucsonArizonaUSA
| | - Adam P. Sharples
- Institute of Physical PerformanceNorwegian School of Sport SciencesOsloNorway
| | - Nir Eynon
- Institute for Health and Sport (iHeS)Victoria UniversityFootscrayVictoriaAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoriaAustralia
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29
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Jankowski CM, Konigsberg IR, Wilson MP, Sun J, Brown TT, Julian CG, Erlandson KM. Skeletal muscle DNA methylation: Effects of exercise and HIV. Aging Cell 2024; 23:e14025. [PMID: 37920126 PMCID: PMC10776118 DOI: 10.1111/acel.14025] [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: 04/04/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 11/04/2023] Open
Abstract
Aging, human immunodeficiency virus (HIV) infection, and antiretroviral therapy modify the epigenetic profile and function of cells and tissues, including skeletal muscle (SkM). In some cells, accelerated epigenetic aging begins very soon after the initial HIV infection, potentially setting the stage for the early onset of frailty. Exercise imparts epigenetic modifications in SkM that may underpin some health benefits, including delayed frailty, in people living with HIV (PWH). In this first report of exercise-related changes in SkM DNA methylation among PWH, we investigated the impact of 24 weeks of aerobic and resistance exercise training on SkM (vastus lateralis) DNA methylation profiles and epigenetic age acceleration (EAA) in older, virally suppressed PWH (n = 12) and uninfected controls (n = 18), and associations of EAA with physical function at baseline. We identified 983 differentially methylated positions (DMPs) in PWH and controls at baseline and 237 DMPs after training. The influence of HIV serostatus on SkM methylation was more pronounced than that of exercise training. There was little overlap in the genes associated with the probes most significantly differentiated by exercise training within each group. Baseline EAA (mean ± SD) was similar between PWH (-0.4 ± 2.5 years) and controls (0.2 ± 2.6 years), and the exercise effect was not significant (p = 0.79). EAA and physical function at baseline were not significantly correlated (all p ≥ 0.10). This preliminary investigation suggests HIV-specific epigenetic adaptations in SkM with exercise training but confirmation in a larger study that includes transcriptomic analysis is warranted.
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Affiliation(s)
| | - Iain R. Konigsberg
- Department of Biomedical InformaticsUniversity of Colorado Anschutz Medical CampusColoradoAuroraUSA
| | - Melissa P. Wilson
- Division of Infectious Diseases, Department of MedicineUniversity of Colorado Anschutz Medical CampusColoradoAuroraUSA
| | - Jing Sun
- Department of EpidemiologyJohns Hopkins Bloomberg School of Public HealthMarylandBaltimoreUSA
| | - Todd T. Brown
- Division of Endocrinology, Diabetes, & Metabolism, Department of MedicineJohns Hopkins UniversityMarylandBaltimoreUSA
| | - Colleen G. Julian
- Department of Biomedical InformaticsUniversity of Colorado Anschutz Medical CampusColoradoAuroraUSA
| | - Kristine M. Erlandson
- Division of Infectious Diseases, Department of MedicineUniversity of Colorado Anschutz Medical CampusColoradoAuroraUSA
- Division of Geriatric Medicine, Department of MedicineUniversity of Colorado Anschutz Medical CampusColoradoAuroraUSA
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Ali H, Shahzil M, Moond V, Shahzad M, Thandavaram A, Sehar A, Waseem H, Siddiqui T, Dahiya DS, Patel P, Tillmann H. Non-Pharmacological Approach to Diet and Exercise in Metabolic-Associated Fatty Liver Disease: Bridging the Gap between Research and Clinical Practice. J Pers Med 2024; 14:61. [PMID: 38248762 PMCID: PMC10817352 DOI: 10.3390/jpm14010061] [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: 12/01/2023] [Revised: 12/23/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
This review provides a practical and comprehensive overview of non-pharmacological interventions for metabolic-associated fatty liver disease (MASLD), focusing on dietary and exercise strategies. It highlights the effectiveness of coffee consumption, intermittent fasting, and Mediterranean and ketogenic diets in improving metabolic and liver health. The review emphasizes the importance of combining aerobic and resistance training as a critical approach to reducing liver fat and increasing insulin sensitivity. Additionally, it discusses the synergy between diet and exercise in enhancing liver parameters and the role of gut microbiota in MASLD. The paper underscores the need for a holistic, individualized approach, integrating diet, exercise, gut health, and patient motivation. It also highlights the long-term benefits and minimal risks of lifestyle interventions compared to the side effects of pharmacological and surgical options. The review calls for personalized treatment strategies, continuous patient education, and further research to optimize therapeutic outcomes in MASLD management.
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Affiliation(s)
- Hassam Ali
- Department of Gastroenterology, Hepatology & Nutrition, ECU Health Medical Center, Brody School of Medicine, Greenville, NC 27834, USA
- Division of Gastroenterology, Hepatology & Nutrition, East Carolina University, Greenville, NC 27834, USA
| | - Muhammad Shahzil
- Department of Internal Medicine, Weiss Memorial Hospital, Chicago, IL 60640, USA;
| | - Vishali Moond
- Department of Internal Medicine, Saint Peter’s University Hospital, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - Maria Shahzad
- Department of Internal Medicine, Jacobi Medical Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Abhay Thandavaram
- Department of Internal Medicine, Kamineni Academy of Medical Sciences and Research Centre, Hyderabad 500068, Telangana, India
| | - Alina Sehar
- Department of Internal Medicine, University of Alabama at Birmingham-Huntsville Campus, Huntsville, AL 35801, USA
| | - Haniya Waseem
- Department of Internal Medicine, Advent Health Tampa, Tampa, FL 33613, USA
| | - Taha Siddiqui
- Department of Internal Medicine, Mather Hospital, Hofstra University Zucker School of Medicine, Port Jefferson, NY 11777, USA;
| | - Dushyant Singh Dahiya
- Division of Gastroenterology, Hepatology & Motility, The University of Kansas School of Medicine, Kansas City, KS 66103, USA
| | - Pratik Patel
- Department of Gastroenterology, Mather Hospital, Hofstra University Zucker School of Medicine, Port Jefferson, NY 11777, USA
| | - Hans Tillmann
- Department of Gastroenterology, Hepatology & Nutrition, ECU Health Medical Center, Brody School of Medicine, Greenville, NC 27834, USA
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31
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Dutta S, Goodrich JM, Dolinoy DC, Ruden DM. Biological Aging Acceleration Due to Environmental Exposures: An Exciting New Direction in Toxicogenomics Research. Genes (Basel) 2023; 15:16. [PMID: 38275598 PMCID: PMC10815440 DOI: 10.3390/genes15010016] [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: 11/27/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Biological clock technologies are designed to assess the acceleration of biological age (B-age) in diverse cell types, offering a distinctive opportunity in toxicogenomic research to explore the impact of environmental stressors, social challenges, and unhealthy lifestyles on health impairment. These clocks also play a role in identifying factors that can hinder aging and promote a healthy lifestyle. Over the past decade, researchers in epigenetics have developed testing methods that predict the chronological and biological age of organisms. These methods rely on assessing DNA methylation (DNAm) levels at specific CpG sites, RNA levels, and various biomolecules across multiple cell types, tissues, and entire organisms. Commonly known as 'biological clocks' (B-clocks), these estimators hold promise for gaining deeper insights into the pathways contributing to the development of age-related disorders. They also provide a foundation for devising biomedical or social interventions to prevent, reverse, or mitigate these disorders. This review article provides a concise overview of various epigenetic clocks and explores their susceptibility to environmental stressors.
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Affiliation(s)
- Sudipta Dutta
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (J.M.G.); (D.C.D.)
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (J.M.G.); (D.C.D.)
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Douglas M. Ruden
- C. S. Mott Center for Human Health and Development, Department of Obstetrics and Gynecology, Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA
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Lin SY, Xia W, Kim AK, Chen D, Schleyer S, Choi L, Wang Z, Hamilton JP, Luu H, Hann HW, Chang TT, Hu CT, Woodard A, Gade TP, Su YH. Novel urine cell-free DNA methylation markers for hepatocellular carcinoma. Sci Rep 2023; 13:21585. [PMID: 38062093 PMCID: PMC10703769 DOI: 10.1038/s41598-023-48500-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
An optimized hepatocellular carcinoma (HCC)-targeted methylation next generation sequencing assay was developed to discover HCC-associated methylation markers directly from urine for HCC screening. Urine cell-free DNA (ucfDNA) isolated from a discovery cohort of 31 non-HCC and 30 HCC was used for biomarker discovery, identifying 29 genes with differentially methylated regions (DMRs). Methylation-specific qPCR (MSqPCR) assays were developed to verify the selected DMRs corresponding to 8 genes (GRASP, CCND2, HOXA9, BMP4, VIM, EMX1, SFRP1, and ECE). Using archived ucfDNA, methylation of GRASP, HOXA9, BMP4, and ECE1, were found to be significantly different (p < 0.05) between HCC and non-HCC patients. The four markers together with previously reported GSTP1 and RASSF1A markers were assessed as a 6-marker panel in an independent training cohort of 87 non-HCC and 78 HCC using logistic regression modeling. AUROC of 0.908 (95% CI, 0.8656-0.9252) was identified for the 6-marker panel with AFP, which was significantly higher than AFP-alone (AUROC 0.841 (95% CI, 0.778-0.904), p = 0.0026). Applying backward selection method, a 4-marker panel was found to exhibit similar performance to the 6-marker panel with AFP having 80% sensitivity compared to 29.5% by AFP-alone at a specificity of 85%. This study supports the potential use of methylated transrenal ucfDNA for HCC screening.
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Affiliation(s)
| | - Wei Xia
- JBS Science, Inc., Doylestown, PA, USA
| | - Amy K Kim
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dion Chen
- JBS Science, Inc., Doylestown, PA, USA
- ClinPharma Consulting, Inc., Phoenixville, PA, USA
| | | | - Lin Choi
- JBS Science, Inc., Doylestown, PA, USA
| | | | - James P Hamilton
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harry Luu
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hie-Won Hann
- Department of Medicine, Division of Gastroenterology and Hepatology, Thomas Jefferson University Hospital, Philadelphia, PA, USA
| | - Ting-Tsung Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Tan Hu
- Division of Gastroenterology, Department of Internal Medicine, Hualien Tzu-Chi Hospital, Buddhist Tzu-Chi Medical Foundation, Hualien, Taiwan
| | - Abashai Woodard
- Department of Radiology, University of Pennsylvania College of Medicine, Philadelphia, PA, USA
| | - Terence P Gade
- Department of Radiology, University of Pennsylvania College of Medicine, Philadelphia, PA, USA
| | - Ying-Hsiu Su
- The Baruch S. Blumberg Institute, 805 Old Easton Rd, Doylestown, PA, USA.
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Li D, Ju F, Wang H, Fan C, Jacob JC, Gul S, Zaliani A, Wartmann T, Polidori MC, Bruns CJ, Zhao Y. Combination of the biomarkers for aging and cancer? - Challenges and current status. Transl Oncol 2023; 38:101783. [PMID: 37716258 PMCID: PMC10514562 DOI: 10.1016/j.tranon.2023.101783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
The proportion of patients diagnosed with cancer has been shown to rise with the increasing aging global population. Advanced age is a major risk factor for morbidity and mortality in older adults. As individuals experience varying health statuses, particularly with age, it poses a challenge for medical professionals in the cancer field to obtain standardized treatment outcomes. Hence, relying solely on chronological age and disease-related parameters is inadequate for clinical decision-making for elderly patients. With functional, multimorbidity-related, and psychosocial changes that occur with aging, oncologic diseases may develop and be treated differently from younger patients, leading to unique challenges in treatment efficacy and tolerance. To overcome this challenge, personalized therapy using biomarkers has emerged as a promising solution. Various categories of biomarkers, including inflammatory, hematological, metabolic, endocrine, and DNA modification-related indicators, may display features related to both cancer and aging, aiding in the development of innovative therapeutic approaches for patients with cancer in old age. Furthermore, physical functional measurements as non-molecular phenotypic biomarkers are being investigated for their potential complementary role in structured multidomain strategies to combat age-related diseases such as cancer. This review provides insight into the current developments, recent discoveries, and significant challenges in cancer and aging biomarkers, with a specific focus on their application in advanced age.
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Affiliation(s)
- Dai Li
- Department of General, Visceral, Tumor and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany; Department of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Feng Ju
- Department of General, Visceral, Tumor and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany
| | - Han Wang
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Chunfu Fan
- Medical faculty, University of Cologne, Germany
| | | | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology, Schnackenburgallee 114, d-22525 Hamburg, Germany; Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hamburg Site, Schnackenburgallee 114, d-22525 Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology, Schnackenburgallee 114, d-22525 Hamburg, Germany; Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hamburg Site, Schnackenburgallee 114, d-22525 Hamburg, Germany
| | - Thomas Wartmann
- Department of General, Visceral und Vascular Surgery, Otto von Guericke University, Magdeburg, Leipziger Str. 44, Magdeburg, 39120, Germany
| | - Maria Cristina Polidori
- Ageing Clinical Research, Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress-Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne Germany
| | - Christiane J Bruns
- Department of General, Visceral, Tumor and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany; Center for Integrated Oncology (CIO) Aachen, Bonn, Cologne and Düsseldorf, Cologne, Germany
| | - Yue Zhao
- Department of General, Visceral, Tumor and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany.
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Hamlat EJ, Neilands TB, Laraia B, Zhang J, Lu AT, Lin J, Horvath S, Epel ES. Early life adversity predicts an accelerated cellular aging phenotype through early timing of puberty. Psychol Med 2023; 53:7720-7728. [PMID: 37325994 PMCID: PMC11131158 DOI: 10.1017/s0033291723001629] [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] [Indexed: 06/17/2023]
Abstract
BACKGROUND The current study examined if early adversity was associated with accelerated biological aging, and if effects were mediated by the timing of puberty. METHODS In early mid-life, 187 Black and 198 White (Mage = 39.4, s.d.age = 1.2) women reported on early abuse and age at first menstruation (menarche). Women provided saliva and blood to assess epigenetic aging, telomere length, and C-reactive protein. Using structural equation modeling, we created a latent variable of biological aging using epigenetic aging, telomere length, and C-reactive protein as indicators, and a latent variable of early abuse using indicators of abuse/threat events before age 13, physical abuse, and sexual abuse. We estimated the indirect effects of early abuse and of race on accelerated aging through age at menarche. Race was used as a proxy for adversity in the form of systemic racism. RESULTS There was an indirect effect of early adversity on accelerated aging through age at menarche (b = 0.19, 95% CI 0.03-0.44), in that women who experienced more adversity were younger at menarche, which was associated with greater accelerated aging. There was also an indirect effect of race on accelerated aging through age at menarche (b = 0.25, 95% CI 0.04-0.52), in that Black women were younger at menarche, which led to greater accelerated aging. CONCLUSIONS Early abuse and being Black in the USA may both induce a phenotype of accelerated aging. Early adversity may begin to accelerate aging during childhood, in the form of early pubertal timing.
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Affiliation(s)
- Elissa J. Hamlat
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
| | - Torsten B. Neilands
- Division of Prevention Science | Department of Medicine, University of California, San Francisco, CA, USA
| | - Barbara Laraia
- School of Public Health, University of California, Berkeley, CA, USA
| | - Joshua Zhang
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Ake T. Lu
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Steve Horvath
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Department of Biostatistics, University of California, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Elissa S. Epel
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
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35
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Stöger R, Choi M, Begum K, Leeman G, Emes RD, Melamed P, Bentley GR. Childhood environment influences epigenetic age and methylation concordance of a CpG clock locus in British-Bangladeshi migrants. Epigenetics 2023; 18:2153511. [PMID: 36495138 PMCID: PMC9980690 DOI: 10.1080/15592294.2022.2153511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Migration from one location to another often comes with a change in environmental conditions. Here, we analysed features of DNA methylation in young, adult British-Bangladeshi women who experienced different environments during their childhoods: a) migrants, who grew up in Bangladesh with exposure to comparatively higher pathogen loads and poorer health care, and b) second-generation British-Bangladeshis, born to Bangladeshi parents, who grew up in the UK. We used buccal DNA to estimate DNA methylation-based age (DNAm age) from 14 migrants and 11 second-generation migrants, aged 18-35 years. 'AgeAccel,' a measure of DNAm age, independent of chronological age, showed that the group of women who spent their childhood in Bangladesh had higher AgeAccel (P = 0.028), compared to their UK peers. Since epigenetic clocks have been proposed to be associated with maintenance processes of epigenetic systems, we evaluated the preference for concordant DNA methylation at the luteinizing hormone/choriogonadotropin receptor (LHCGR/LHR) locus, which harbours one of the CpGs contributing to Horvath's epigenetic clock. Measurements on both strands of individual, double-stranded DNA molecules indicate higher stability of DNA methylation states at this LHCGR/LHR locus in samples of women who grew up in Bangladesh. Together, our two independent analytical approaches imply that childhood environments may induce subtle changes that are detectable long after exposure occurred, which might reflect altered activity of the epigenetic maintenance system or a difference in the proportion of cell types in buccal tissue. This exploratory work supports our earlier findings that adverse childhood environments lead to phenotypic life history trade-offs.
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Affiliation(s)
- Reinhard Stöger
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Minseung Choi
- School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Gregory Leeman
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK.,Advanced Data Analysis Centre, University of Nottingham, Nottingham, UK
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Gillian R Bentley
- Department of Anthropology, Durham University, Durham, UK.,Wolfson Research Institute for Health and Wellbeing, Durham University, Durham, UK
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36
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Yang T, Xiao Y, Cheng Y, Huang J, Wei Q, Li C, Shang H. Epigenetic clocks in neurodegenerative diseases: a systematic review. J Neurol Neurosurg Psychiatry 2023; 94:1064-1070. [PMID: 36963821 DOI: 10.1136/jnnp-2022-330931] [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: 12/11/2022] [Accepted: 03/03/2023] [Indexed: 03/26/2023]
Abstract
BACKGROUND Biological ageing is one of the principal risk factors for neurodegenerative diseases. It is becoming increasingly clear that acceleration of DNA methylation age, as measured by the epigenetic clock, is closely associated with many age-related diseases. METHODS We searched the PubMed and Web of Science databases to identify eligible studies reporting epigenetic clocks in several neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD). RESULTS Twenty-three studies (12 for AD, 4 for PD, 5 for ALS, and 2 for HD) were included. We systematically summarised the clinical utility of 11 epigenetic clocks (based on blood and brain tissues) in assessing the risk factors, age of onset, diagnosis, progression, prognosis and pathology of AD, PD, ALS and HD. We also critically described our current understandings to these evidences, and further discussed key challenges, potential mechanisms and future perspectives of epigenetic ageing in neurodegenerative diseases. CONCLUSIONS Epigenetic clocks hold great potential in neurodegenerative diseases. Further research is encouraged to evaluate the clinical utility and promote the application. PROSPERO REGISTRATION NUMBER CRD42022365233.
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Affiliation(s)
- Tianmi Yang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Yi Xiao
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Yangfan Cheng
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Jingxuan Huang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Qianqian Wei
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Chunyu Li
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Huifang Shang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
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37
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Mozhui K, Kim H, Villani F, Haghani A, Sen S, Horvath S. Pleiotropic influence of DNA methylation QTLs on physiological and ageing traits. Epigenetics 2023; 18:2252631. [PMID: 37691384 PMCID: PMC10496549 DOI: 10.1080/15592294.2023.2252631] [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: 05/01/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is influenced by genetic and non-genetic factors. Here, we chart quantitative trait loci (QTLs) that modulate levels of methylation at highly conserved CpGs using liver methylome data from mouse strains belonging to the BXD family. A regulatory hotspot on chromosome 5 had the highest density of trans-acting methylation QTLs (trans-meQTLs) associated with multiple distant CpGs. We refer to this locus as meQTL.5a. Trans-modulated CpGs showed age-dependent changes and were enriched in developmental genes, including several members of the MODY pathway (maturity onset diabetes of the young). The joint modulation by genotype and ageing resulted in a more 'aged methylome' for BXD strains that inherited the DBA/2J parental allele at meQTL.5a. Further, several gene expression traits, body weight, and lipid levels mapped to meQTL.5a, and there was a modest linkage with lifespan. DNA binding motif and protein-protein interaction enrichment analyses identified the hepatic nuclear factor, Hnf1a (MODY3 gene in humans), as a strong candidate. The pleiotropic effects of meQTL.5a could contribute to variations in body size and metabolic traits, and influence CpG methylation and epigenetic ageing that could have an impact on lifespan.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hyeonju Kim
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 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
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
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Qaria MA, Xu C, Hu R, Alsubki RA, Ali MY, Sivasamy S, Attia KA, Zhu D. Ectoine Globally Hypomethylates DNA in Skin Cells and Suppresses Cancer Proliferation. Mar Drugs 2023; 21:621. [PMID: 38132942 PMCID: PMC10744768 DOI: 10.3390/md21120621] [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: 09/18/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Epigenetic modifications, mainly aberrant DNA methylation, have been shown to silence the expression of genes involved in epigenetic diseases, including cancer suppression genes. Almost all conventional cancer therapeutic agents, such as the DNA hypomethylation drug 5-aza-2-deoxycytidine, have insurmountable side effects. To investigate the role of the well-known DNA protectant (ectoine) in skin cell DNA methylation and cancer cell proliferation, comprehensive methylome sequence analysis, 5-methyl cytosine (5mC) analysis, proliferation and tumorigenicity assays, and DNA epigenetic modifications-related gene analysis were performed. The results showed that extended ectoine treatment globally hypomethylated DNA in skin cells, especially in the CpG island (CGIs) element, and 5mC percentage was significantly reduced. Moreover, ectoine mildly inhibited skin cell proliferation and did not induce tumorigenicity in HaCaT cells injected into athymic nude mice. HaCaT cells treated with ectoine for 24 weeks modulated the mRNA expression levels of Dnmt1, Dnmt3a, Dnmt3b, Dnmt3l, Hdac1, Hdac2, Kdm3a, Mettl3, Mettl14, Snrpn, and Mest. Overall, ectoine mildly demethylates DNA in skin cells, modulates the expression of epigenetic modification-related genes, and reduces cell proliferation. This evidence suggests that ectoine is a potential anti-aging agent that prevents DNA hypermethylation and subsequently activates cancer-suppressing genes.
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Affiliation(s)
- Majjid A. Qaria
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (M.A.Q.); (C.X.); (M.Y.A.); (S.S.)
| | - Chunyan Xu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (M.A.Q.); (C.X.); (M.Y.A.); (S.S.)
| | - Ran Hu
- School of Medicine, Jiangsu University, Zhenjiang 212013, China;
| | - Roua A. Alsubki
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Saud University, 2455, Riyadh 11451, Saudi Arabia;
| | - Mohamed Yassin Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (M.A.Q.); (C.X.); (M.Y.A.); (S.S.)
- Department of Biochemistry, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt
| | - Sethupathy Sivasamy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (M.A.Q.); (C.X.); (M.Y.A.); (S.S.)
| | - Kotb A. Attia
- Department of Biochemistry, College of Science, King Saud University, 2455, Riyadh 11451, Saudi Arabia
| | - Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (M.A.Q.); (C.X.); (M.Y.A.); (S.S.)
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Alvarez-Kuglen M, Rodriguez D, Qin H, Ninomiya K, Fiengo L, Farhy C, Hsu WM, Havas A, Feng GS, Roberts AJ, Anderson RM, Serrano M, Adams PD, Sharpee TO, Terskikh AV. Imaging-based chromatin and epigenetic age, ImAge, quantitates aging and rejuvenation. RESEARCH SQUARE 2023:rs.3.rs-3479973. [PMID: 37986947 PMCID: PMC10659560 DOI: 10.21203/rs.3.rs-3479973/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Biomarkers of biological age that predict the risk of disease and expected lifespan better than chronological age are key to efficient and cost-effective healthcare1-3. To advance a personalized approach to healthcare, such biomarkers must reliably and accurately capture individual biology, predict biological age, and provide scalable and cost-effective measurements. We developed a novel approach - image-based chromatin and epigenetic age (ImAge) that captures intrinsic progressions of biological age, which readily emerge as principal changes in the spatial organization of chromatin and epigenetic marks in single nuclei without regression on chronological age. ImAge captured the expected acceleration or deceleration of biological age in mice treated with chemotherapy or following a caloric restriction regimen, respectively. ImAge from chronologically identical mice inversely correlated with their locomotor activity (greater activity for younger ImAge), consistent with the widely accepted role of locomotion as an aging biomarker across species. Finally, we demonstrated that ImAge is reduced following transient expression of OSKM cassette in the liver and skeletal muscles and reveals heterogeneity of in vivo reprogramming. We propose that ImAge represents the first-in-class imaging-based biomarker of aging with single-cell resolution.
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Affiliation(s)
| | | | - Haodong Qin
- UCSD, Department of Physics, La Jolla, CA 92093, USA
| | | | | | - Chen Farhy
- Sanford Burnham Prebys, La Jolla CA 92037, USA
| | - Wei-Mien Hsu
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Aaron Havas
- Sanford Burnham Prebys, La Jolla CA 92037, USA
| | - Gen-Sheng Feng
- UCSD School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | | | | | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain
- Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Altos Labs, Cambridge Institute of Science, Granta Park CB21 6GP, UK
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40
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Adav SS, Ng KW. Recent omics advances in hair aging biology and hair biomarkers analysis. Ageing Res Rev 2023; 91:102041. [PMID: 37634889 DOI: 10.1016/j.arr.2023.102041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/27/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Aging is a complex natural process that leads to a decline in physiological functions, which is visible in signs such as hair graying, thinning, and loss. Although hair graying is characterized by a loss of pigment in the hair shaft, the underlying mechanism of age-associated hair graying is not fully understood. Hair graying and loss can have a significant impact on an individual's self-esteem and self-confidence, potentially leading to mental health problems such as depression and anxiety. Omics technologies, which have applications beyond clinical medicine, have led to the discovery of candidate hair biomarkers and may provide insight into the complex biology of hair aging and identify targets for effective therapies. This review provides an up-to-date overview of recent omics discoveries, including age-associated alterations of proteins and metabolites in the hair shaft and follicle, and highlights the significance of hair aging and graying biomarker discoveries. The decline in hair follicle stem cell activity with aging decreased the regeneration capacity of hair follicles. Cellular senescence, oxidative damage and altered extracellular matrix of hair follicle constituents characterized hair follicle and hair shaft aging and graying. The review attempts to correlate the impact of endogenous and exogenous factors on hair aging. We close by discussing the main challenges and limitations of the field, defining major open questions and offering an outlook for future research.
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Affiliation(s)
- Sunil S Adav
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Kee Woei Ng
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, 637141, Singapore.
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Hicken MT, Dou J, Kershaw KN, Liu Y, Hajat A, Bakulski KM. Racial and Ethnic Residential Segregation and Monocyte DNA Methylation Age Acceleration. JAMA Netw Open 2023; 6:e2344722. [PMID: 38019517 PMCID: PMC10687663 DOI: 10.1001/jamanetworkopen.2023.44722] [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: 06/09/2023] [Accepted: 10/12/2023] [Indexed: 11/30/2023] Open
Abstract
Importance Neighborhood segregation and poverty may be important drivers of health inequities. Epigenomic factors, including DNA methylation clocks that may mark underlying biological aging, have been implicated in the link between social factors and health. Objective To examine the associations of neighborhood segregation and poverty with 4 DNA methylation clocks trained to capture either chronological age or physiological dysregulation. Design, Setting, and Participants This cohort study uses data from the Multi-Ethnic Study of Atherosclerosis (MESA), a longitudinal study that started in 2000 to 2002, with follow-up in 2002 to 2004, 2004 to 2005, 2005 to 2007, and 2010 to 2012. In 2000 to 2002, adults who identified as White or Black race or Hispanic or Chinese ethnicity in 6 US sites (Baltimore, Maryland; Chicago, Illinois; Forsyth County, North Carolina; Los Angeles County, California; Northern Manhattan, New York; and St. Paul, Minnesota) were sampled for recruitment. A random subsample of 4 sites (Maryland, North Carolina, New York, and Minnesota) were selected for inclusion in the MESA epigenomics ancillary study at examination 5 (2010-2012). Participants who identified as White or Black race or Hispanic ethnicity, were aged 45 to 84 years, and did not have clinical cardiovascular disease were included in this analysis. Data were analyzed from May 2021 to October 2023. Exposure Information on 2000 census tract poverty and Getis-Ord G statistic segregation of Hispanic residents, non-Hispanic Black residents, or non-Hispanic White residents were linked to participant addresses at examination 1 (2000-2002). Main Outcomes and Measures At examination 5, DNA methylation was measured in purified monocytes. DNA methylation age acceleration was calculated using 4 clocks trained on either chronological age or physiological dysregulation. Linear regressions were used to test associations. Results A total of 1102 participants (mean [SD] age, 69.7 [9.4] years; 562 [51%] women) were included, with 348 Hispanic participants, 222 non-Hispanic Black participants, and 533 non-Hispanic White participants. For non-Hispanic Black participants, living in tracts with greater segregation of Black residents was associated with GrimAge DNA methylation age acceleration, a clock designed to capture physiological dysregulation. A 1-SD increase in segregation was associated with 0.42 (95% CI, 0.20-0.64) years age acceleration (P < .001); this association was not observed with other clocks. This association was particularly pronounced for participants living in high poverty tracts (interaction term, 0.24; 95% CI, 0.07-0.42; P = .006). In the overall sample, census tract poverty level was associated with GrimAge DNA methylation age acceleration (β = 0.45; 95% CI, 0.20-0.71; adjusted P = .005). Conclusions and Relevance These findings suggest that epigenomic mechanisms may play a role in the associations of segregated and poor neighborhoods with chronic conditions.
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Affiliation(s)
| | - John Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor
| | - Kiarri N. Kershaw
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Yongmei Liu
- Department of Medicine, Duke University, Durham, North Carolina
| | - Anjum Hajat
- Department of Epidemiology, University of Washington, Seattle
| | - Kelly M. Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor
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Dickey BL, Putney RM, Suneja G, Kresovich JK, Spivak AM, Patel AB, Teng M, Extermann M, Giuliano AR, Gillis N, Berglund A, Coghill AE. Differences in epigenetic age by HIV status among patients with a non-AIDS defining cancer. AIDS 2023; 37:2049-2057. [PMID: 37467055 PMCID: PMC10538418 DOI: 10.1097/qad.0000000000003661] [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: 07/21/2023]
Abstract
OBJECTIVE People with HIV (PWH) are living longer and experiencing higher numbers of non-AIDS-defining cancers (NADC). Epigenetic aging biomarkers have been linked to cancer risk, and cancer is now a leading cause of death in PWH, but these biomarkers have not been investigated in PWH and cancer. DESIGN In order to compare epigenetic age by HIV status, HIV-uninfected participants were matched to PWH by reported age, tumor site, tumor sequence number, and cancer treatment status. METHODS DNA from blood was assayed using Illumina MethylationEPIC BeadChip, and we estimated immune cell composition and aging from three epigenetic clocks: Horvath, GrimAge, and epiTOC2. Age acceleration by clock was computed as the residual from the expected value, calculated using linear regression, for each study participant. Comparisons across HIV status used the Wilcoxon rank sum test. Hazard ratios and 95% confidence intervals for the association between age acceleration and survival in PWH were estimated with Cox regression. RESULTS Among 65 NADC participants with HIV and 64 without, biological age from epiTOC2 ( P < 0.0001) and GrimAge ( P = 0.017) was significantly higher in PWH. Biological age acceleration was significantly higher in PWH using epiTOC2 ( P < 0.01) and GrimAge ( P < 0.0001), with the difference in GrimAge remaining statistically significant after adjustment for immune cell composition. Among PWH, GrimAge acceleration was significantly associated with increased risk of death (hazard ratio 1.11; 95% confidence interval (CI) 1.04-1.18). CONCLUSION We observed a higher epigenetic age in PWH with a NADC diagnosis compared with their HIV-uninfected counterparts, as well as a significant association between this accelerated biological aging and survival for patients diagnosed with a NADC.
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Affiliation(s)
| | - Ryan M Putney
- Biostatistics/Bioinformatics Division, Moffitt Cancer Center
| | - Gita Suneja
- Department of Radiation Oncology, University of Utah
| | - Jacob K Kresovich
- Department of Cancer Epidemiology
- Department of Breast Oncology, Moffitt Cancer Center
| | - Adam M Spivak
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine
| | - Ami B Patel
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, Utah
| | - Mingxiang Teng
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute
| | | | - Anna R Giuliano
- Department of Cancer Epidemiology
- Center for Immunization and Infection Research in Cancer
| | | | - Anders Berglund
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute
| | - Anna E Coghill
- Department of Cancer Epidemiology
- Center for Immunization and Infection Research in Cancer
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, Florida, USA
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Felt JM, Yusupov N, Harrington KD, Fietz J, Zhang Z“Z, Sliwinski MJ, Ram N, O'Donnell KJ, Meaney MJ, Putnam FW, Noll JG, Binder EB, Shenk CE. Epigenetic age acceleration as a biomarker for impaired cognitive abilities in adulthood following early life adversity and psychiatric disorders. Neurobiol Stress 2023; 27:100577. [PMID: 37885906 PMCID: PMC10597797 DOI: 10.1016/j.ynstr.2023.100577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/28/2023] Open
Abstract
Background Early life adversity and psychiatric disorders are associated with earlier declines in neurocognitive abilities during adulthood. These declines may be preceded by changes in biological aging, specifically epigenetic age acceleration, providing an opportunity to uncover genome-wide biomarkers that identify individuals most likely to benefit from early screening and prevention. Methods Five unique epigenetic age acceleration clocks derived from peripheral blood were examined in relation to latent variables of general and speeded cognitive abilities across two independent cohorts: 1) the Female Growth and Development Study (FGDS; n = 86), a 30-year prospective cohort study of substantiated child sexual abuse and non-abused controls, and 2) the Biological Classification of Mental Disorders study (BeCOME; n = 313), an adult community cohort established based on psychiatric disorders. Results A faster pace of biological aging (DunedinPoAm) was associated with lower general cognitive abilities in both cohorts and slower speeded abilities in the BeCOME cohort. Acceleration in the Horvath clock was significantly associated with slower speeded abilities in the BeCOME cohort but not the FGDS. Acceleration in the Hannum clock and the GrimAge clock were not significantly associated with either cognitive ability. Accelerated PhenoAge was associated with slower speeded abilities in the FGDS but not the BeCOME cohort. Conclusions The present results suggest that epigenetic age acceleration has the potential to serve as a biomarker for neurocognitive decline in adults with a history of early life adversity or psychiatric disorders. Estimates of epigenetic aging may identify adults at risk of cognitive decline that could benefit from early neurocognitive screening.
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Affiliation(s)
- John M. Felt
- Center for Healthy Aging, The Pennsylvania State University, United States
| | - Natan Yusupov
- Department Genes and Environment, Max Planck Institute of Psychiatry - Munich, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Germany
| | | | - Julia Fietz
- Department Genes and Environment, Max Planck Institute of Psychiatry - Munich, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Germany
| | | | - Martin J. Sliwinski
- Center for Healthy Aging, The Pennsylvania State University, United States
- Department of Human Development and Family Studies, The Pennsylvania State University, United States
| | - Nilam Ram
- Department of Communications, Stanford University, United States
- Department of Psychology, Stanford University, United States
| | - Kieran J. O'Donnell
- Child Study Center, Yale University, United States
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University, United States
- The Douglas Hospital Research Centre, Department of Psychiatry, McGill University, Canada
- Child and Brain Development Program, Canadian Institute for Advanced Research, Canada
| | - BeCOME Working Group
- Department Genes and Environment, Max Planck Institute of Psychiatry - Munich, Germany
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Michael J. Meaney
- The Douglas Hospital Research Centre, Department of Psychiatry, McGill University, Canada
- Child and Brain Development Program, Canadian Institute for Advanced Research, Canada
- Singapore Institute of Clinical Sciences, Singapore
| | - Frank W. Putnam
- Department of Psychiatry, University of North Carolina School of Medicine, United States
| | - Jennie G. Noll
- Department of Human Development and Family Studies, The Pennsylvania State University, United States
| | - Elisabeth B. Binder
- Department Genes and Environment, Max Planck Institute of Psychiatry - Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, United States
| | - Chad E. Shenk
- Department of Human Development and Family Studies, The Pennsylvania State University, United States
- Department of Pediatrics, The Pennsylvania State University College of Medicine, United States
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Hong T, Li J, Guo L, Cavalier M, Wang T, Dou Y, DeLaFuente A, Fang S, Guzman A, Wohlan K, Kapadia C, Rosas C, Yang Y, Yin CC, Li S, You MJ, Cheng X, Goodell MA, Zhou Y, Huang Y. TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells. NATURE AGING 2023; 3:1387-1400. [PMID: 37884767 DOI: 10.1038/s43587-023-00505-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
DNA methylation deregulation at partially methylated domains (PMDs) represents an epigenetic signature of aging and cancer, yet the underlying molecular basis and resulting biological consequences remain unresolved. We report herein a mechanistic link between disrupted DNA methylation at PMDs and the spatial relocalization of H3K9me3-marked heterochromatin in aged hematopoietic stem and progenitor cells (HSPCs) or those with impaired DNA methylation. We uncover that TET2 modulates the spatial redistribution of H3K9me3-marked heterochromatin to mediate the upregulation of endogenous retroviruses (ERVs) and interferon-stimulated genes (ISGs), hence contributing to functional decline of aged HSPCs. TET2-deficient HSPCs retain perinuclear distribution of heterochromatin and exhibit age-related clonal expansion. Reverse transcriptase inhibitors suppress ERVs and ISGs expression, thereby restoring age-related defects in aged HSPCs. Collectively, our findings deepen the understanding of the functional interplay between DNA methylation and histone modifications, which is vital for maintaining heterochromatin function and safeguarding genome stability in stem cells.
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Affiliation(s)
- Tingting Hong
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Jia Li
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Lei Guo
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Maryn Cavalier
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Tianlu Wang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yaling Dou
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Aaron DeLaFuente
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Shaohai Fang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Anna Guzman
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Katherina Wohlan
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Chiraag Kapadia
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Carina Rosas
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Yaling Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C Cameron Yin
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoying Li
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M James You
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Yubin Zhou
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA.
| | - Yun Huang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA.
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McDade TW, Ryan CP, Adair LS, Lee NR, Carba DB, MacIsaac JL, Dever K, Atashzay P, Kobor M, Kuzawa CW. Association between infectious exposures in infancy and epigenetic age acceleration in young adulthood in metropolitan Cebu, Philippines. Am J Hum Biol 2023; 35:e23948. [PMID: 37338007 PMCID: PMC10730771 DOI: 10.1002/ajhb.23948] [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: 12/21/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023] Open
Abstract
OBJECTIVES The drivers of human life expectancy gains over the past 200 years are not well-established, with a potential role for historical reductions in infectious disease. We investigate whether infectious exposures in infancy predict biological aging using DNA methylation-based markers that forecast patterns of morbidity and mortality later in life. METHODS N = 1450 participants from the Cebu Longitudinal Health and Nutrition Survey-a prospective birth cohort initiated in 1983-provided complete data for the analyses. Mean chronological age was 20.9 years when venous whole blood samples were drawn for DNA extraction and methylation analysis, with subsequent calculation of three epigenetic age markers: Horvath, GrimAge, and DunedinPACE. Unadjusted and adjusted least squares regression models were evaluated to test the hypothesis that infectious exposures in infancy are associated with epigenetic age. RESULTS Birth in the dry season, a proxy measure for increased infectious exposure in the first year of life, as well as the number of symptomatic infections in the first year of infancy, predicted lower epigenetic age. Infectious exposures were associated with the distribution of white blood cells in adulthood, which were also associated with measures of epigenetic age. CONCLUSIONS We document negative associations between measures of infectious exposure in infancy and DNA methylation-based measures of aging. Additional research, across a wider range of epidemiological settings, is needed to clarify the role of infectious disease in shaping immunophenotypes and trajectories of biological aging and human life expectancy.
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Affiliation(s)
- Thomas W. McDade
- Department of Anthropology, Northwestern University,
Evanston, IL 60208
- Institute for Policy Research, Northwestern University,
Evanston, IL 60208
| | - Calen P. Ryan
- Robert N. Butler Columbia Aging Center, Department of
Epidemiology, Columbia University Mailman School of Public Health
| | - Linda S. Adair
- Department of Nutrition, Gillings School of Global Public
Health, Carolina Population Center, CB #8120, University of North Carolina at Chapel
Hill
| | - Nanette R. Lee
- Office of Population Studies Foundation, University of San
Carlos, Talamban, Cebu City Philippines
| | - Delia B. Carba
- Office of Population Studies Foundation, University of San
Carlos, Talamban, Cebu City Philippines
| | - Julia L. MacIsaac
- Department of Medical Genetics, Faculty of Medicine,
University of British Columbia, Vancouver, Canada
- Edwin S.H. Leong Healthy Aging Program, University of
British Columbia, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver,
British Columbia, Vancouver, Canada
| | - Kristy Dever
- Department of Medical Genetics, Faculty of Medicine,
University of British Columbia, Vancouver, Canada
- Edwin S.H. Leong Healthy Aging Program, University of
British Columbia, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver,
British Columbia, Vancouver, Canada
| | - Parmida Atashzay
- Department of Medical Genetics, Faculty of Medicine,
University of British Columbia, Vancouver, Canada
- Edwin S.H. Leong Healthy Aging Program, University of
British Columbia, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver,
British Columbia, Vancouver, Canada
| | - Mike Kobor
- Department of Medical Genetics, Faculty of Medicine,
University of British Columbia, Vancouver, Canada
- Edwin S.H. Leong Healthy Aging Program, University of
British Columbia, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver,
British Columbia, Vancouver, Canada
| | - Christopher W. Kuzawa
- Department of Anthropology, Northwestern University,
Evanston, IL 60208
- Institute for Policy Research, Northwestern University,
Evanston, IL 60208
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Nguyen VTC, Nguyen TH, Doan NNT, Pham TMQ, Nguyen GTH, Nguyen TD, Tran TTT, Vo DL, Phan TH, Jasmine TX, Nguyen VC, Nguyen HT, Nguyen TV, Nguyen THH, Huynh LAK, Tran TH, Dang QT, Doan TN, Tran AM, Nguyen VH, Nguyen VTA, Ho LMQ, Tran QD, Pham TTT, Ho TD, Nguyen BT, Nguyen TNV, Nguyen TD, Phu DTB, Phan BHH, Vo TL, Nai THT, Tran TT, Truong MH, Tran NC, Le TK, Tran THT, Duong ML, Bach HPT, Kim VV, Pham TA, Tran DH, Le TNA, Pham TVN, Le MT, Vo DH, Tran TMT, Nguyen MN, Van TTV, Nguyen AN, Tran TT, Tran VU, Le MP, Do TT, Phan TV, Nguyen HDL, Nguyen DS, Cao VT, Do TTT, Truong DK, Tang HS, Giang H, Nguyen HN, Phan MD, Tran LS. Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization. eLife 2023; 12:RP89083. [PMID: 37819044 PMCID: PMC10567114 DOI: 10.7554/elife.89083] [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: 10/13/2023] Open
Abstract
Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (screening for the presence of tumor by methylation and size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (~0.55×) of cell-free DNA. We applied SPOT-MAS to 738 non-metastatic patients with breast, colorectal, gastric, lung, and liver cancer, and 1550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 73.9% and 62.3% for stages I and II, respectively, increasing to 88.3% for non-metastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening.
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Hughes BK, Wallis R, Bishop CL. Yearning for machine learning: applications for the classification and characterisation of senescence. Cell Tissue Res 2023; 394:1-16. [PMID: 37016180 PMCID: PMC10558380 DOI: 10.1007/s00441-023-03768-4] [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: 11/15/2022] [Accepted: 03/05/2023] [Indexed: 04/06/2023]
Abstract
Senescence is a widely appreciated tumour suppressive mechanism, which acts as a barrier to cancer development by arresting cell cycle progression in response to harmful stimuli. However, senescent cell accumulation becomes deleterious in aging and contributes to a wide range of age-related pathologies. Furthermore, senescence has beneficial roles and is associated with a growing list of normal physiological processes including wound healing and embryonic development. Therefore, the biological role of senescent cells has become increasingly nuanced and complex. The emergence of sophisticated, next-generation profiling technologies, such as single-cell RNA sequencing, has accelerated our understanding of the heterogeneity of senescence, with distinct final cell states emerging within models as well as between cell types and tissues. In order to explore data sets of increasing size and complexity, the senescence field has begun to employ machine learning (ML) methodologies to probe these intricacies. Most notably, ML has been used to aid the classification of cells as senescent, as well as to characterise the final senescence phenotypes. Here, we provide a background to the principles of ML tasks, as well as some of the most commonly used methodologies from both traditional and deep ML. We focus on the application of these within the context of senescence research, by addressing the utility of ML for the analysis of data from different laboratory technologies (microscopy, transcriptomics, proteomics, methylomics), as well as the potential within senolytic drug discovery. Together, we aim to highlight both the progress and potential for the application of ML within senescence research.
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Affiliation(s)
- Bethany K Hughes
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Ryan Wallis
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Cleo L Bishop
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
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Naue J. Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications. Genes Genomics 2023; 45:1239-1261. [PMID: 37253906 PMCID: PMC10504122 DOI: 10.1007/s13258-023-01392-8] [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: 02/28/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals. OBJECTIVE This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application. METHODS The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics. CONCLUSION The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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Ni X, Zhao H, Li R, Su H, Jiao J, Yang Z, Lv Y, Pang G, Sun M, Hu C, Yuan H. Development of a model for the prediction of biological age. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 240:107686. [PMID: 37421874 DOI: 10.1016/j.cmpb.2023.107686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/04/2023] [Accepted: 06/20/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND AND OBJECTIVE Rates of aging vary markedly among individuals, and biological age serves as a more reliable predictor of current health status than does chronological age. As such, the ability to predict biological age can support appropriate and timely active interventions aimed at improving coping with the aging process. However, the aging process is highly complex and multifactorial. Therefore, it is more scientific to construct a prediction model for biological age from multiple dimensions systematically. METHODS Physiological and biochemical parameters were evaluated to gage individual health status. Then, age-related indices were screened for inclusion in a model capable of predicting biological age. For subsequent modeling analyses, samples were divided into training and validation sets for subsequent deep learning model-based analyses (e.g. linear regression, lasso model, ridge regression, bayesian ridge regression, elasticity network, k-nearest neighbor, linear support vector machine, support vector machine, and decision tree models, and so on), with the model exhibiting the best ability to predict biological age thereby being identified. RESULTS First, we defined the individual biological age according to the individual health status. Then, after 22 candidate indices (DNA methylation, leukocyte telomere length, and specific physiological and biochemical indicators) were screened for inclusion in a model capable of predicting biological age, 14 age-related indices and gender were used to construct a model via the Bagged Trees method, which was found to be the most reliable qualitative prediction model for biological age (accuracy=75.6%, AUC=0.84) by comparing 30 different classification algorithm models. The most reliable quantitative predictive model for biological age was found to be the model developed using the Rational Quadratic method (R2=0.85, RMSE=8.731 years) by comparing 24 regression algorithm models. CONCLUSIONS Both qualitative model and quantitative model of biological age were successfully constructed from a multi-dimensional and systematic perspective. The predictive performance of our models was similar in both smaller and larger datasets, making it well-suited to predicting a given individual's biological age.
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Affiliation(s)
- Xiaolin Ni
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China
| | - Hanqing Zhao
- College of Traditional Chinese Medicine, Hebei University, Baoding, 071000, PR China
| | - Rongqiao Li
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, Nanning, 530021, PR China
| | - Huabin Su
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, Nanning, 530021, PR China
| | - Juan Jiao
- Clinical Lab, The Seventh Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100700, China
| | - Ze Yang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China
| | - Yuan Lv
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, Nanning, 530021, PR China
| | - Guofang Pang
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, Nanning, 530021, PR China
| | - Meiqi Sun
- College of Traditional Chinese Medicine, Hebei University, Baoding, 071000, PR China
| | - Caiyou Hu
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, Nanning, 530021, PR China.
| | - Huiping Yuan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China.
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Zhang B, Yuan Q, Luan Y, Xia J. Effect of women's fertility and sexual development on epigenetic clock: Mendelian randomization study. Clin Epigenetics 2023; 15:154. [PMID: 37770973 PMCID: PMC10540426 DOI: 10.1186/s13148-023-01572-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: 05/12/2023] [Accepted: 09/25/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND AND OBJECTIVES In observational studies, women's fertility and sexual development traits may have implications for DNA methylation patterns, and pregnancy-related risk factors can also affect maternal DNA methylation patterns. The aim of our study is to disentangle any potential causal associations between women's fertility and sexual development traits and epigenetic clocks, as well as to search for probable mediators by using the Mendelian randomization (MR) method. METHODS Instrumental variables for exposures, mediators, and outcomes were adopted from genome-wide association studies data of European ancestry individuals. The potential causal relationship between women's fertility and sexual development traits and four epigenetic clocks were evaluated by inverse variance weighted method and verified by other two methods. Furthermore, we employed multivariable MR (MVMR) adjusting for hypertension, hyperglycemia, BMI changes, and insomnia. Then, combining the MVMR results and previous research, we performed two-step MR to explore the mediating effects of BMI, AFS, and AFB. Multiple sensitivity analyses were further performed to verify the robustness of our findings. RESULTS Leveraging two-sample MR analysis, we observed statistically significant associations between earlier age at first birth (AFB) with a higher HannumAge, PhenoAge and GrimAge acceleration(β = - 0.429, 95% CI [- 0.781 to - 0.077], p = 0.017 for HannumAge; β = - 0.571, 95% CI [- 1.006 to - 0.136], p = 0.010 for PhenoAge, and β = - 1.136, 95% CI [- 1.508 to - 0.765], p = 2.03E-09 for GrimAge respectively) and age at first sexual intercourse (AFS) with a higher HannumAge and GrimAge acceleration(β = - 0.175, 95% CI [- 0.336 to - 0.014], p = 0.033 for HannumAge; β = - 0.210, 95% CI [- 0.350 to - 0.070], p = 0.003 for GrimAge, respectively). Further analyses indicated that BMI, AFB and AFS played mediator roles in the path from women's fertility and sexual development traits to epigenetic aging. CONCLUSIONS Our study suggested that AFS and AFB are associated with epigenetic aging. These findings may prove valuable in informing the development of prevention strategies and interventions targeted towards women's fertility and sexual development experiences and their relationship with epigenetic aging-related diseases.
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Affiliation(s)
- Boxin Zhang
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Road of Kaifu District, Changsha, 410008, China
- Hunan Clinical Research Center for Cerebrovascular Disease, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qizhi Yuan
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Road of Kaifu District, Changsha, 410008, China
- Hunan Clinical Research Center for Cerebrovascular Disease, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yining Luan
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Road of Kaifu District, Changsha, 410008, China
- Hunan Clinical Research Center for Cerebrovascular Disease, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jian Xia
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Road of Kaifu District, Changsha, 410008, China.
- Hunan Clinical Research Center for Cerebrovascular Disease, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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