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Ndhlovu LC, Bendall ML, Dwaraka V, Pang APS, Dopkins N, Carreras N, Smith R, Nixon DF, Corley MJ. Retro-age: A unique epigenetic biomarker of aging captured by DNA methylation states of retroelements. Aging Cell 2024:e14288. [PMID: 39092674 DOI: 10.1111/acel.14288] [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: 02/15/2024] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
Reactivation of retroelements in the human genome has been linked to aging. However, whether the epigenetic state of specific retroelements can predict chronological age remains unknown. We provide evidence that locus-specific retroelement DNA methylation can be used to create retroelement-based epigenetic clocks that accurately measure chronological age in the immune system, across human tissues, and pan-mammalian species. We also developed a highly accurate retroelement epigenetic clock compatible with EPICv.2.0 data that was constructed from CpGs that did not overlap with existing first- and second-generation epigenetic clocks, suggesting a unique signal for epigenetic clocks not previously captured. We found retroelement-based epigenetic clocks were reversed during transient epigenetic reprogramming, accelerated in people living with HIV-1, and responsive to antiretroviral therapy. Our findings highlight the utility of retroelement-based biomarkers of aging and support a renewed emphasis on the role of retroelements in geroscience.
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Affiliation(s)
- Lishomwa C Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
| | - Matthew L Bendall
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
| | | | - Alina P S Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
| | - Nicholas Dopkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
| | | | | | - Douglas F Nixon
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
| | - Michael J Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
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2
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Qian J, Fischer C, Burhan A, Mak M, Gerretsen P, Kolla N, Al-Chalabi N, Chaudhary Z, Qureshey A, Bani-Fatemi A, Graff A, Remington G, De Luca V. GWAS of biological aging to find longevity genes in schizophrenia. Eur Arch Psychiatry Clin Neurosci 2024; 274:1025-1036. [PMID: 37420032 DOI: 10.1007/s00406-023-01622-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 07/09/2023]
Abstract
Schizophrenia (SCZ) is a severe psychotic disorder associated with premature mortality and aging. Moreover, the symptoms and progression of psychiatric disorders in general are associated with decreased lifespan, biological aging, and poorer medical outcomes. In this study, we investigated the relationship between several epigenetic clocks and scanned the entire genome for association in a cohort of SCZ individuals (n = 107). Biological age was computed from blood DNA methylation (DNAm) and tested for association against common variants across the genome using general linear models. Genes affecting epigenetic age acceleration in our cohort were found mainly when using the telomeric length clock rather than the other biological clocks. These findings pair with existing evidence that there are some genes associated with longevity and suggest further investigations of putative biological mechanisms for morbidity and premature mortality, not only in patients with SCZ but also in the general population.
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Affiliation(s)
| | | | - Amer Burhan
- Ontario Shores Centre for Mental Health Sciences, Whitby, Canada
| | - Michael Mak
- CAMH, 250 College St, Toronto, M5T1R8, Canada
| | | | | | | | | | | | - Ali Bani-Fatemi
- Department of Occupational Science and Occupational Therapy, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Ariel Graff
- CAMH, 250 College St, Toronto, M5T1R8, Canada
| | | | - Vincenzo De Luca
- CAMH, 250 College St, Toronto, M5T1R8, Canada.
- St. Michael's Hospital, Toronto, Canada.
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3
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Xu P, Kong Y, Palmer ND, Ng MCY, Zhang B, Das SK. Integrated multi-omic analyses uncover the effects of aging on cell-type regulation in glucose-responsive tissues. Aging Cell 2024; 23:e14199. [PMID: 38932492 PMCID: PMC11320340 DOI: 10.1111/acel.14199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/27/2024] [Accepted: 05/01/2024] [Indexed: 06/28/2024] Open
Abstract
Aging significantly influences cellular activity and metabolism in glucose-responsive tissues, yet a comprehensive evaluation of the impacts of aging and associated cell-type responses has been lacking. This study integrates transcriptomic, methylomic, single-cell RNA sequencing, and metabolomic data to investigate aging-related regulations in adipose and muscle tissues. Through coexpression network analysis of the adipose tissue, we identified aging-associated network modules specific to certain cell types, including adipocytes and immune cells. Aging upregulates the metabolic functions of lysosomes and downregulates the branched-chain amino acids (BCAAs) degradation pathway. Additionally, aging-associated changes in cell proportions, methylation profiles, and single-cell expressions were observed in the adipose. In the muscle tissue, aging was found to repress the metabolic processes of glycolysis and oxidative phosphorylation, along with reduced gene activity of fast-twitch type II muscle fibers. Metabolomic profiling linked aging-related alterations in plasma metabolites to gene expression in glucose-responsive tissues, particularly in tRNA modifications, BCAA metabolism, and sex hormone signaling. Together, our multi-omic analyses provide a comprehensive understanding of the impacts of aging on glucose-responsive tissues and identify potential plasma biomarkers for these effects.
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Affiliation(s)
- Peng Xu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Advanced Institute for Life and HealthSoutheast UniversityNanjingChina
- Department of Genetics & Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn Genomics InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Pharmacological Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn Genomics InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Artificial Intelligence and Human Health, Mount Sinai Center for Transformative Disease Modeling, Icahn Genomics InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Yimeng Kong
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Advanced Institute for Life and HealthSoutheast UniversityNanjingChina
| | - Nicholette D. Palmer
- Department of BiochemistryWake Forest University School of MedicineWinston–SalemNorth CarolinaUSA
| | - Maggie C. Y. Ng
- Division of Genetic Medicine, Vanderbilt Genetics InstituteVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Bin Zhang
- Department of Genetics & Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn Genomics InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Pharmacological Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn Genomics InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Artificial Intelligence and Human Health, Mount Sinai Center for Transformative Disease Modeling, Icahn Genomics InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Swapan K. Das
- Department of Internal Medicine, Section on Endocrinology and MetabolismWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
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4
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Grootswagers P, Bach D, Biemans Y, Behrouzi P, Horvath S, Kramer CS, Liu S, Manson JE, Shadyab AH, Stewart JD, Whitsel E, Yang B, de Groot L. Discovering the direct relations between nutrients and epigenetic ageing. J Nutr Health Aging 2024; 28:100324. [PMID: 39067141 DOI: 10.1016/j.jnha.2024.100324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/12/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Along with the ageing of society, the absolute prevalence of age-related diseases is expected to rise, leading to a substantial burden on healthcare systems and society. Thus, there is an urgent need to promote healthy ageing. As opposed to chronological age, biological age was introduced to accurately represent the ageing process, as it considers physiological deterioration that is linked to morbidity and mortality risk. Furthermore, biological age responds to various factors, including nutritional factors, which have the potential to mitigate the risk of age-related diseases. As a result, a promising biomarker of biological age known as the epigenetic clock has emerged as a suitable measure to investigate the direct relations between nutritional factors and ageing, thereby identifying potential intervention targets to improve healthy ageing. METHODS In this study, we analysed data from 3,969 postmenopausal women from the Women's Health Initiative to identify nutrients that are associated with the rate of ageing by using an accurate measure of biological age called the PhenoAge epigenetic clock. We used Copula Graphical Models, a data-driven exploratory analysis tool, to identify direct relationships between nutrient intake and age-acceleration, while correcting for every variable in the dataset. RESULTS We revealed that increased dietary intakes of coumestrol, beta-carotene and arachidic acid were associated with decelerated epigenetic ageing. In contrast, increased intakes of added sugar, gondoic acid, behenic acid, arachidonic acid, vitamin A and ash were associated with accelerated epigenetic ageing in postmenopausal women. CONCLUSION Our study discovered direct relations between nutrients and epigenetic ageing, revealing promising areas for follow-up studies to determine the magnitude and causality of our estimated diet-epigenetic relationships.
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Affiliation(s)
- Pol Grootswagers
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, Netherlands.
| | - Daimy Bach
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, Netherlands
| | - Ynte Biemans
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, Netherlands
| | - Pariya Behrouzi
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, Wageningen, Netherlands
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA; Altos Labs, San Diego Institute of Science, San Diego, CA, USA; Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, USA
| | - Charlotte S Kramer
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, Netherlands
| | - Simin Liu
- Department of Epidemiology and Center for Global Cardiometabolic Health, School of Public Health, Departments of Medicine and Surgery, Alpert School of Medicine, Brown University, Providence, RI, USA
| | - JoAnn E Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | - James D Stewart
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eric Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Bo Yang
- Department of Epidemiology and Center for Global Cardiometabolic Health, School of Public Health, Brown University, Providence, RI, USA
| | - Lisette de Groot
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, Netherlands
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5
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Watowich MM, Costa CE, Chiou KL, Goldman EA, Petersen RM, Patterson S, Martínez MI, Sterner KN, Horvath JE, Montague MJ, Platt ML, Brent LJN, Higham JP, Lea AJ, Snyder-Mackler N. Immune gene regulation is associated with age and environmental adversity in a nonhuman primate. Mol Ecol 2024:e17445. [PMID: 39032090 DOI: 10.1111/mec.17445] [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: 12/12/2023] [Revised: 04/27/2024] [Accepted: 06/14/2024] [Indexed: 07/22/2024]
Abstract
Phenotypic aging is ubiquitous across mammalian species, suggesting shared underlying mechanisms of aging. Aging is linked to molecular changes to DNA methylation and gene expression, and environmental factors, such as severe external challenges or adversities, can moderate these age-related changes. Yet, it remains unclear whether environmental adversities affect gene regulation via the same molecular pathways as chronological, or 'primary', aging. Investigating molecular aging in naturalistic animal populations can fill this gap by providing insight into shared molecular mechanisms of aging and the effects of a greater diversity of environmental adversities - particularly those that can be challenging to study in humans or laboratory organisms. Here, we characterised molecular aging - specifically, CpG methylation - in a sample of free-ranging rhesus macaques living off the coast of Puerto Rico (n samples = 571, n individuals = 499), which endured a major hurricane during our study. Age was associated with methylation at 78,661 sites (31% of all sites tested). Age-associated hypermethylation occurred more frequently in areas of active gene regulation, while hypomethylation was enriched in regions that show less activity in immune cells, suggesting these regions may become de-repressed in older individuals. Age-associated hypomethylation also co-occurred with increased chromatin accessibility while hypermethylation showed the opposite trend, hinting at a coordinated, multi-level loss of epigenetic stability during aging. We detected 32,048 CpG sites significantly associated with exposure to a hurricane, and these sites overlapped age-associated sites, most strongly in regulatory regions and most weakly in quiescent regions. Together, our results suggest that environmental adversity may contribute to aging-related molecular phenotypes in regions of active gene transcription, but that primary aging has specific signatures in non-regulatory regions.
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Affiliation(s)
- Marina M Watowich
- Department of Biology, University of Washington, Seattle, Washington, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Christina E Costa
- Department of Anthropology, New York University, New York, New York, USA
- New York Consortium in Evolutionary Primatology, New York, New York, USA
| | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Elisabeth A Goldman
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Rachel M Petersen
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Sam Patterson
- Department of Anthropology, New York University, New York, New York, USA
| | - Melween I Martínez
- Caribbean Primate Research Center, Unit of Comparative Medicine, University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Kirstin N Sterner
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Julie E Horvath
- Research and Collections Section, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael L Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Marketing Department, Wharton School of Business, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - James P Higham
- Department of Anthropology, New York University, New York, New York, USA
- New York Consortium in Evolutionary Primatology, New York, New York, USA
| | - Amanda J Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Neurodegenerative Disease Research Center, Arizona State University, Tempe, Arizona, USA
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6
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Lukacsovich D, O’Shea D, Huang H, Zhang W, Young J, Chen XS, Dietrich ST, Kunkle B, Martin E, Wang L. MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer's disease. Database (Oxford) 2024; 2024:baae061. [PMID: 39028752 PMCID: PMC11259044 DOI: 10.1093/database/baae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 07/21/2024]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder with a significant impact on aging populations. DNA methylation (DNAm) alterations have been implicated in both the aging processes and the development of AD. Given that AD affects more women than men, it is also important to explore DNAm changes that occur specifically in each sex. We created MIAMI-AD, a comprehensive knowledgebase containing manually curated summary statistics from 98 published tables in 38 studies, all of which included at least 100 participants. MIAMI-AD enables easy browsing, querying, and downloading DNAm associations at multiple levels-at individual CpG, gene, genomic regions, or genome-wide, in one or multiple studies. Moreover, it also offers tools to perform integrative analyses, such as comparing DNAm associations across different phenotypes or tissues, as well as interactive visualizations. Using several use case examples, we demonstrated that MIAMI-AD facilitates our understanding of age-associated CpGs in AD and the sex-specific roles of DNAm in AD. This open-access resource is freely available to the research community, and all the underlying data can be downloaded. MIAMI-AD facilitates integrative explorations to better understand the interplay between DNAm across aging, sex, and AD. Database URL: https://miami-ad.org/.
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Affiliation(s)
- David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
| | - Deirdre O’Shea
- Department of Neurology, Comprehensive Center for Brain Health, University of Miami, Miller School of Medicine, 7700 W Camino Real, Boca Raton, FL 33433, USA
| | - Hanchen Huang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
| | - Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
| | - Juan Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - X Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, 1475 NW 12th Ave, Miami, FL 33136, USA
| | - Sven-Thorsten Dietrich
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - Eden Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, 1475 NW 12th Ave, Miami, FL 33136, USA
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7
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Yusipov I, Kalyakulina A, Trukhanov A, Franceschi C, Ivanchenko M. Map of epigenetic age acceleration: A worldwide analysis. Ageing Res Rev 2024; 100:102418. [PMID: 39002646 DOI: 10.1016/j.arr.2024.102418] [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: 04/17/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
We present a systematic analysis of epigenetic age acceleration based on by far the largest collection of publicly available DNA methylation data for healthy samples (93 datasets, 23 K samples), focusing on the geographic (25 countries) and ethnic (31 ethnicities) aspects around the world. We employed the most popular epigenetic tools for assessing age acceleration and examined their quality metrics and ability to extrapolate to epigenetic data from different tissue types and age ranges different from the training data of these models. In most cases, the models proved to be inconsistent with each other and showed different signs of age acceleration, with the PhenoAge model tending to systematically underestimate and different versions of the GrimAge model tending to systematically overestimate the age prediction of healthy subjects. Referring to data availability and consistency, most countries and populations are still not represented in GEO, moreover, different datasets use different criteria for determining healthy controls. Because of this, it is difficult to fully isolate the contribution of "geography/environment", "ethnicity" and "healthiness" to epigenetic age acceleration. Among the explored metrics, only the DunedinPACE, which measures aging rate, appears to adequately reflect the standard of living and socioeconomic indicators in countries, although it has a limited application to blood methylation data only. Invariably, by epigenetic age acceleration, males age faster than females in most of the studied countries and populations.
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Affiliation(s)
- Igor Yusipov
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Alena Kalyakulina
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Arseniy Trukhanov
- Mriya Life Institute, National Academy of Active Longevity, Moscow 124489, Russia.
| | - Claudio Franceschi
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Mikhail Ivanchenko
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
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8
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Postberg J, Schubert MT, Nin V, Wagner L, Piefke M. A perspective on epigenomic aging processes in the human brain and their plasticity in patients with mental disorders - a systematic review. Neurogenetics 2024:10.1007/s10048-024-00771-x. [PMID: 38967831 DOI: 10.1007/s10048-024-00771-x] [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: 03/15/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
The debate surrounding nature versus nurture remains a central question in neuroscience, psychology, and in psychiatry, holding implications for both aging processes and the etiology of mental illness. Epigenetics can serve as a bridge between genetic predisposition and environmental influences, thus offering a potential avenue for addressing these questions. Epigenetic clocks, in particular, offer a theoretical framework for measuring biological age based on DNA methylation signatures, enabling the identification of disparities between biological and chronological age. This structured review seeks to consolidate current knowledge regarding the relationship between mental disorders and epigenetic age within the brain. Through a comprehensive literature search encompassing databases such as EBSCO, PubMed, and ClinicalTrials.gov, relevant studies were identified and analyzed. Studies that met inclusion criteria were scrutinized, focusing on those with large sample sizes, analyses of both brain tissue and blood samples, investigation of frontal cortex markers, and a specific emphasis on schizophrenia and depressive disorders. Our review revealed a paucity of significant findings, yet notable insights emerged from studies meeting specific criteria. Studies characterized by extensive sample sizes, analysis of brain tissue and blood samples, assessment of frontal cortex markers, and a focus on schizophrenia and depressive disorders yielded particularly noteworthy results. Despite the limited number of significant findings, these studies shed light on the complex interplay between epigenetic aging and mental illness. While the current body of literature on epigenetic aging in mental disorders presents limited significant findings, it underscores the importance of further research in this area. Future studies should prioritize large sample sizes, comprehensive analyses of brain tissue and blood samples, exploration of specific brain regions such as the frontal cortex, and a focus on key mental disorders. Such endeavors will contribute to a deeper understanding of the relationship between epigenetic aging and mental illness, potentially informing novel diagnostic and therapeutic approaches.
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Affiliation(s)
- Jan Postberg
- Clinical Molecular Genetics and Epigenetics, Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany.
- Centre for Biomedical Education & Research (ZBAF), Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany.
| | - Michèle Tina Schubert
- Neurobiology and Genetics of Behavior, Department of Psychology and Psychotherapy, Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany
| | - Vincent Nin
- Neurobiology and Genetics of Behavior, Department of Psychology and Psychotherapy, Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany
| | - Lukas Wagner
- Neurobiology and Genetics of Behavior, Department of Psychology and Psychotherapy, Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany
| | - Martina Piefke
- Centre for Biomedical Education & Research (ZBAF), Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany
- Neurobiology and Genetics of Behavior, Department of Psychology and Psychotherapy, Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany
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9
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Corveleyn L, Sen P, Adams P, Sidoli S. Linking Aging to Cancer: The Role of Chromatin Biology. J Gerontol A Biol Sci Med Sci 2024; 79:glae133. [PMID: 38761362 PMCID: PMC11170291 DOI: 10.1093/gerona/glae133] [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: 02/20/2024] [Indexed: 05/20/2024] Open
Abstract
Epigenetic changes have been established to be a hallmark of aging, which implies that aging science requires collaborating with the field of chromatin biology. DNA methylation patterns, changes in relative abundance of histone post-translational modifications, and chromatin remodeling are the central players in modifying chromatin structure. Aging is commonly associated with an overall increase in chromatin instability, loss of homeostasis, and decondensation. However, numerous publications have highlighted that the link between aging and chromatin changes is not nearly as linear as previously expected. This complex interplay of these epigenetic elements during the lifetime of an organism likely contributes to cellular senescence, genomic instability, and disease susceptibility. Yet, the causal links between these phenomena still need to be fully unraveled. In this perspective article, we discuss potential future directions of aging chromatin biology.
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Affiliation(s)
- Laura Corveleyn
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, Maryland, USA
| | - Peter Adams
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, California, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, USA
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10
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Yuen ZWS, Shanmuganandam S, Stanley M, Jiang S, Hein N, Daniel R, McNevin D, Jack C, Eyras E. Profiling age and body fluid DNA methylation markers using nanopore adaptive sampling. Forensic Sci Int Genet 2024; 71:103048. [PMID: 38640705 DOI: 10.1016/j.fsigen.2024.103048] [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: 12/11/2023] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/21/2024]
Abstract
DNA methylation plays essential roles in regulating physiological processes, from tissue and organ development to gene expression and aging processes and has emerged as a widely used biomarker for the identification of body fluids and age prediction. Currently, methylation markers are targeted independently at specific CpG sites as part of a multiplexed assay rather than through a unified assay. Methylation detection is also dependent on divergent methodologies, ranging from enzyme digestion and affinity enrichment to bisulfite treatment, alongside various technologies for high-throughput profiling, including microarray and sequencing. In this pilot study, we test the simultaneous identification of age-associated and body fluid-specific methylation markers using a single technology, nanopore adaptive sampling. This innovative approach enables the profiling of multiple CpG marker sites across entire gene regions from a single sample without the need for specialized DNA preparation or additional biochemical treatments. Our study demonstrates that adaptive sampling achieves sufficient coverage in regions of interest to accurately determine the methylation status, shows a robust consistency with whole-genome bisulfite sequencing data, and corroborates known CpG markers of age and body fluids. Our work also resulted in the identification of new sites strongly correlated with age, suggesting new possible age methylation markers. This study lays the groundwork for the systematic development of nanopore-based methodologies in both age prediction and body fluid identification, highlighting the feasibility and potential of nanopore adaptive sampling while acknowledging the need for further validation and expansion in future research.
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Affiliation(s)
- Zaka Wing-Sze Yuen
- EMBL Australia Partner Laboratory Network, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; The Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; The Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Somasundhari Shanmuganandam
- Department of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra, ACT 2601, Australia
| | - Maurice Stanley
- Department of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra, ACT 2601, Australia
| | - Simon Jiang
- Department of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra, ACT 2601, Australia; Department of Renal Medicine, The Canberra Hospital, Canberra, ACT 2605, Australia
| | - Nadine Hein
- ACRF Department of Cancer Biology and Therapeutics and Division of Genome Sciences and Cancer, John Curtin School of Medical Research, Australian National University, Acton, Canberra, Australia
| | - Runa Daniel
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
| | - Dennis McNevin
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, Australia
| | - Cameron Jack
- ANU Bioinformatics Consultancy, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Eduardo Eyras
- EMBL Australia Partner Laboratory Network, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; The Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; The Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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11
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Griñán-Ferré C, Bellver-Sanchis A, Guerrero A, Pallàs M. Advancing personalized medicine in neurodegenerative diseases: The role of epigenetics and pharmacoepigenomics in pharmacotherapy. Pharmacol Res 2024; 205:107247. [PMID: 38834164 DOI: 10.1016/j.phrs.2024.107247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/23/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
About 80 % of brain disorders have a genetic basis. The pathogenesis of most neurodegenerative diseases is associated with a myriad of genetic defects, epigenetic alterations (DNA methylation, histone/chromatin remodeling, miRNA dysregulation), and environmental factors. The emergence of new sequencing technologies and tools to study the epigenome has led to identifying predictive biomarkers for earlier diagnosis, opening up the possibility of prophylactical interventions. As a result, advances in pharmacogenetics and pharmacoepigenomics now allow for personalized treatments based on the profile of each patient and the specific genetic and epigenetic mechanisms involved. This Review highlights the complexity of neurodegenerative diseases and the variability in patient responses to pharmacotherapy, emphasizing the influence of genetic polymorphisms on the pharmacokinetics and pharmacodynamics of drugs used to treat those conditions. We specifically discuss the potential modulatory effect of several genetic polymorphisms associated with an increased risk of developing different neurodegenerative diseases. We explore genetic and genomic technologies and the potential of analyzing individual-specific drug metabolism to predict and influence drug response and associated clinical outcomes. We also provide insights into the mechanism of action of the drugs under investigation and their potential impact on disease-modifying pathways. Finally, the Review underscores the great potential of this field to enhance the effectiveness and safety of drug treatments through personalized medicine.
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Affiliation(s)
- Christian Griñán-Ferré
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain; Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
| | - Aina Bellver-Sanchis
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain
| | - Ana Guerrero
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain
| | - Mercè Pallàs
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain; Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
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12
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Czajka N, Northrup JM, Jones MJ, Shafer ABA. Epigenetic clocks, sex markers and age-class diagnostics in three harvested large mammals. Mol Ecol Resour 2024; 24:e13956. [PMID: 38553977 DOI: 10.1111/1755-0998.13956] [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: 11/23/2023] [Revised: 02/05/2024] [Accepted: 03/14/2024] [Indexed: 06/04/2024]
Abstract
The development of epigenetic clocks, or the DNA methylation-based inference of age, is an emerging tool for ageing in free ranging populations. In this study, we developed epigenetic clocks for three species of large mammals that are the focus of extensive management throughout their range in North America: white-tailed deer, black bear and mountain goat. We quantified differential DNA methylation patterns at over 30,000 cytosine-guanine sites (CpGs) from tissue samples of all three species (black bear n = 49; white-tailed deer n = 47; mountain goat n = 45). We used a penalized regression model (elastic net) to build explanatory (black bear r = .95; white-tailed deer r = .99; mountain goat r = .97) and robust (black bear Median Absolute Error or MAE = 1.33; white-tailed deer MAE = 0.29; mountain goat MAE = 0.61) models of age or clocks. We also characterized individual CpG sites within each species that demonstrated clear differences in methylation levels between age classes and sex, which can be used to develop a suite of accessible diagnostic markers. This tool has the potential to contribute to wildlife monitoring by providing easily obtainable representations of age structure in managed populations.
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Affiliation(s)
- Natalie Czajka
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Joseph M Northrup
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Meaghan J Jones
- Department of Biochemistry and Medical Genetics, Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Aaron B A Shafer
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
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13
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Holmes HE, Valentin RE, Jernerén F, de Jager Loots CA, Refsum H, Smith AD, Guarente L, Dellinger RW, Sampson D. Elevated homocysteine is associated with increased rates of epigenetic aging in a population with mild cognitive impairment. Aging Cell 2024:e14255. [PMID: 38937999 DOI: 10.1111/acel.14255] [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: 01/25/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
Elevated plasma total homocysteine (tHcy) is associated with the development of Alzheimer's disease and other forms of dementia. In this study, we report the relationship between tHcy and epigenetic age in older adults with mild cognitive impairment from the VITACOG study. Epigenetic age and rate of aging (ROA) were assessed using various epigenetic clocks, including those developed by Horvath and Hannum, DNAmPhenoAge, and with a focus on Index, a new principal component-based epigenetic clock that, like DNAmPhenoAge, is trained to predict an individual's "PhenoAge." We identified significant associations between tHcy levels and ROA, suggesting that hyperhomocysteinemic individuals were aging at a faster rate. Moreover, Index revealed a normalization of accelerated epigenetic aging in these individuals following treatment with tHcy-lowering B-vitamins. Our results indicate that elevated tHcy is a risk factor for accelerated epigenetic aging, and this can be ameliorated with B-vitamins. These findings have broad relevance for the sizable proportion of the worldwide population with elevated tHcy.
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Affiliation(s)
| | | | - Fredrik Jernerén
- From the Oxford Project to Investigate Memory and Ageing (OPTIMA), Department of Pharmacology, University of Oxford, Oxford, UK
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Celeste A de Jager Loots
- From the Oxford Project to Investigate Memory and Ageing (OPTIMA), Department of Pharmacology, University of Oxford, Oxford, UK
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, UK
| | - Helga Refsum
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - A David Smith
- From the Oxford Project to Investigate Memory and Ageing (OPTIMA), Department of Pharmacology, University of Oxford, Oxford, UK
| | - Leonard Guarente
- Elysium Health, New York, New York, USA
- Department of Biology, MIT, Cambridge, Massachusetts, USA
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14
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Schuurmans IK, Mulder RH, Baltramonaityte V, Lahtinen A, Qiuyu F, Rothmann LM, Staginnus M, Tuulari J, Burt SA, Buss C, Craig JM, Donald KA, Felix JF, Freeman TP, Grassi-Oliveira R, Huels A, Hyde LW, Jones SA, Karlsson H, Karlsson L, Koen N, Lawn W, Mitchell C, Monk CS, Mooney MA, Muetzel R, Nigg JT, Belangero SIN, Notterman D, O'Connor T, O'Donnell KJ, Pan PM, Paunio T, Ryabinin P, Saffery R, Salum GA, Seal M, Silk TJ, Stein DJ, Zar H, Walton E, Cecil CAM. Consortium Profile: The Methylation, Imaging and NeuroDevelopment (MIND) Consortium. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.23.24309353. [PMID: 38978656 PMCID: PMC11230303 DOI: 10.1101/2024.06.23.24309353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Epigenetic processes, such as DNA methylation, show potential as biological markers and mechanisms underlying gene-environment interplay in the prediction of mental health and other brain-based phenotypes. However, little is known about how peripheral epigenetic patterns relate to individual differences in the brain itself. An increasingly popular approach to address this is by combining epigenetic and neuroimaging data; yet, research in this area is almost entirely comprised of cross-sectional studies in adults. To bridge this gap, we established the Methylation, Imaging and NeuroDevelopment (MIND) Consortium, which aims to bring a developmental focus to the emerging field of Neuroimaging Epigenetics by (i) promoting collaborative, adequately powered developmental research via multi-cohort analyses; (ii) increasing scientific rigor through the establishment of shared pipelines and open science practices; and (iii) advancing our understanding of DNA methylation-brain dynamics at different developmental periods (from birth to emerging adulthood), by leveraging data from prospective, longitudinal pediatric studies. MIND currently integrates 15 cohorts worldwide, comprising (repeated) measures of DNA methylation in peripheral tissues (blood, buccal cells, and saliva) and neuroimaging by magnetic resonance imaging across up to five time points over a period of up to 21 years (Npooled DNAm = 11,299; Npooled neuroimaging = 10,133; Npooled combined = 4,914). By triangulating associations across multiple developmental time points and study types, we hope to generate new insights into the dynamic relationships between peripheral DNA methylation and the brain, and how these ultimately relate to neurodevelopmental and psychiatric phenotypes.
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15
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Shiau S, Zumpano F, Wang Z, Shah J, Tien PC, Ross RD, Sharma A, Yin MT. Epigenetic Aging and Musculoskeletal Outcomes in a Cohort of Women Living With HIV. J Infect Dis 2024; 229:1803-1811. [PMID: 38366369 PMCID: PMC11175700 DOI: 10.1093/infdis/jiae016] [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: 09/07/2023] [Accepted: 01/19/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND The relationship between accelerated epigenetic aging and musculoskeletal outcomes in women with HIV (WWH) has not been studied. METHODS We measured DNA methylation age using the Infinium MethylationEPIC BeadChip in a cohort from the Women's Interagency HIV Study (n = 190) with measures of bone mineral density (BMD) and physical function. We estimated 6 biomarkers of epigenetic aging-epigenetic age acceleration (EAA), extrinsic EAA, intrinsic EAA, GrimAge, PhenoAge, and DNA methylation-estimated telomere length-and evaluated associations of epigenetic aging measures with BMD and physical function. We also performed epigenome-wide association studies to examine associations of DNA methylation signatures with BMD and physical function. RESULTS This study included 118 WWH (mean age, 49.7 years; 69% Black) and 72 without HIV (mean age, 48.9 years; 69% Black). WWH had higher EAA (mean ± SD, 1.44 ± 5.36 vs -1.88 ± 5.07; P < .001) and lower DNA methylation-estimated telomere length (7.13 ± 0.31 vs 7.34 ± 0.23, P < .001) than women without HIV. There were no significant associations between accelerated epigenetic aging and BMD. Rather, measures of accelerated epigenetic aging were associated with lower physical function. CONCLUSIONS Accelerated epigenetic aging was observed in WWH as compared with women without HIV and was associated with lower physical function in both groups.
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Affiliation(s)
- Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey
| | - Francesca Zumpano
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey
| | - Ziyi Wang
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey
| | - Jayesh Shah
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Phyllis C Tien
- Department of Medicine, Veterans Affairs Medical Center
- Department of Medicine, University of California San Francisco
| | - Ryan D Ross
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Michael T Yin
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
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16
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Jeong H, Mendizabal I, Yi SV. Human Brain Aging is Associated with Dysregulation of Cell-Type Epigenetic Identity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596981. [PMID: 38895434 PMCID: PMC11185522 DOI: 10.1101/2024.06.01.596981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Significant links between aging and DNA methylation are emerging from recent studies. On the one hand, DNA methylation undergoes changes with age, a process termed as epigenetic drift. On the other hand, DNA methylation serves as a readily accessible and accurate biomarker for aging. A key missing piece of information, however, is the molecular mechanisms underlying these processes, and how they are related, if any. Addressing the limitations of previous research due to the limited number of investigated CpGs and the heterogeneous nature of tissue samples, here we have examined DNA methylation of over 20 million CpGs across a broad age span in neurons and non-neuronal cells, primarily oligodendrocytes. We show that aging is a primary predictor of DNA methylation variation, surpassing the influence of factors such as sex and schizophrenia diagnosis, among others. On the genome-wide scale, epigenetic drift manifests as significant yet subtle trends that are influenced by the methylation level of individual CpGs. We reveal that CpGs that are highly differentiated between cell types are especially prone to age-associated DNA methylation alterations, leading to the divergence of epigenetic cell type identities as individuals age. On the other hand, CpGs that are included in commonly used epigenetic clocks tend to be those sites that are not highly cell type differentiated. Therefore, dysregulation of epigenetic cell-type identities and current DNA epigenetic clocks represent distinct features of age-associated DNA methylation alterations.
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Affiliation(s)
- Hyeonsoo Jeong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Current Address: Altos Labs, San Diego, CA, USA
| | - Isabel Mendizabal
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Translational prostate cancer Research lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Derio, Spain
| | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Ecology, Evolution, and Marine Biology, Department of Molecular, Cellular, and Cell Biology, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, USA
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17
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da Silva Rodrigues G, Noma IHY, Noronha NY, Watanabe LM, da Silva Sobrinho AC, de Lima JGR, Sae-Lee C, Benjamim CJR, Nonino CB, Bueno CR. Eight Weeks of Physical Training Decreases 2 Years of DNA Methylation Age of Sedentary Women. RESEARCH QUARTERLY FOR EXERCISE AND SPORT 2024; 95:405-415. [PMID: 37466924 DOI: 10.1080/02701367.2023.2228388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/06/2023] [Indexed: 07/20/2023]
Abstract
Purpose: The acceleration of epigenetic age is a predictor of mortality and contributes to the increase in chronic diseases. Adherence to a healthy lifestyle is a strategy to reduce epigenetic age. The present study aimed to determine whether eight weeks of combined (aerobic and strength) training (CT) can influence the epigenetic age of women between 50 and 70 years old and the differences in sites and methylated regions. Methods: Eighteen women (AARLow: lower age acceleration residual, n = 10; AARHigh: higher age acceleration residual, n = 8) participated in a combined exercise training program (60 minutes, 3× a week) for eight weeks. DNA was extracted from whole blood using the salting out technique. DNA methylation was performed using the array technique (Illumina's Infinium Methylation BeadChip 850k). We used the DNA Methylation Age Calculator platform to calculate the biological epigenetic age. Two-way ANOVA followed by FISHER LSD posthoc was Applied, adopting p < .05. Results: After eight weeks of CT, there were no changes to the epigenetic age acceleration for the AARLow group (PRE: -2.3 ± 3.2 to POST: -2.3 ± 3.6). However, the AARHigh group significantly decreased the age acceleration (PRE: 3.6 ± 2.6 to POST: 2.2 ± 2.7) (group effect, p = .01; time effect, p = .31; group vs. time effect, p = .005). Conclusion: CT for eight weeks benefits the epigenetic clock of women with the most accelerated age.
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18
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Zhong Y, Zhou X, Pan Z, Zhang J, Pan J. Role of epigenetic regulatory mechanisms in age-related bone homeostasis imbalance. FASEB J 2024; 38:e23642. [PMID: 38690719 DOI: 10.1096/fj.202302665r] [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: 12/24/2023] [Revised: 03/05/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
Alterations to the human organism that are brought about by aging are comprehensive and detrimental. Of these, an imbalance in bone homeostasis is a major outward manifestation of aging. In older adults, the decreased osteogenic activity of bone marrow mesenchymal stem cells and the inhibition of bone marrow mesenchymal stem cell differentiation lead to decreased bone mass, increased risk of fracture, and impaired bone injury healing. In the past decades, numerous studies have reported the epigenetic alterations that occur during aging, such as decreased core histones, altered DNA methylation patterns, and abnormalities in noncoding RNAs, which ultimately lead to genomic abnormalities and affect the expression of downstream signaling osteoporosis treatment and promoter of fracture healing in older adults. The current review summarizes the impact of epigenetic regulation mechanisms on age-related bone homeostasis imbalance.
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Affiliation(s)
- Yunyu Zhong
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xueer Zhou
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zijian Pan
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jiankang Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jian Pan
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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19
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Filoglu G, Sımsek SZ, Ersoy G, Can K, Bulbul O. Epigenetic-based age prediction in blood samples: Model development. J Forensic Sci 2024; 69:869-879. [PMID: 38308398 DOI: 10.1111/1556-4029.15478] [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: 09/11/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
Aging is a complex process influenced by genetic, epigenetic, and environmental factors that lead to tissue deterioration and frailty. Epigenetic mechanisms, such as DNA methylation, play a significant role in gene expression regulation and aging. This study presents a new age estimation model developed for the Turkish population using blood samples. Eight CpG sites in loci TOM1L1, ELOVL2, ASPA, FHL2, C1orf132, CCDC102B, cg07082267, and RASSF5 were selected based on their correlation with age. Methylation patterns of these sites were analyzed in blood samples from 100 volunteers, grouped into age categories (20-35, 36-55, and ≥56). Sensitivity analysis indicated a reliable performance with DNA inputs ≥1 ng. Statistical modeling, utilizing Multiple Linear Regression, underscores the reliability of the primary 6-CpG model, excluding cg07082267 and TOM1L1. This model demonstrates strong correlations with chronological age (r = 0.941) and explains 88% of the age variance with low error rates (MAE = 4.07, RMSE = 5.73 years). Validation procedures, including a training-test split and fivefold cross-validation, consistently confirm the model's accuracy and consistency. The study indicates minimal variation in error scores across age cohorts and no significant gender differences. The developed model showed strong predictive accuracy, with the ability to estimate age within certain prediction intervals. This study contributes to the age prediction by using DNA methylation patterns, which can have disparate applications, including forensic and clinical assessments.
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Affiliation(s)
- Gonul Filoglu
- Department of Science, Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Sumeyye Zulal Sımsek
- Department of Science, Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Gokhan Ersoy
- Department of Forensic Medicine, Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Kadriye Can
- Department of Science, Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ozlem Bulbul
- Department of Science, Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
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20
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Malyutina S, Chervova O, Maximov V, Nikitenko T, Ryabikov A, Voevoda M. Blood-Based Epigenetic Age Acceleration and Incident Colorectal Cancer Risk: Findings from a Population-Based Case-Control Study. Int J Mol Sci 2024; 25:4850. [PMID: 38732069 PMCID: PMC11084311 DOI: 10.3390/ijms25094850] [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: 04/03/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
This study investigates the association between epigenetic age acceleration (EAA) derived from DNA methylation and the risk of incident colorectal cancer (CRC). We utilized data from a random population sample of 9,360 individuals (men and women, aged 45-69) from the HAPIEE Study who had been followed up for 16 years. A nested case-control design yielded 35 incident CRC cases and 354 matched controls. Six baseline epigenetic age (EA) measures (Horvath, Hannum, PhenoAge, Skin and Blood (SB), BLUP, and Elastic Net (EN)) were calculated along with their respective EAAs. After adjustment, the odds ratios (ORs) for CRC risk per decile increase in EAA ranged from 1.20 (95% CI: 1.04-1.39) to 1.44 (95% CI: 1.21-1.76) for the Horvath, Hannum, PhenoAge, and BLUP measures. Conversely, the SB and EN EAA measures showed borderline inverse associations with ORs of 0.86-0.87 (95% CI: 0.76-0.99). Tertile analysis reinforced a positive association between CRC risk and four EAA measures (Horvath, Hannum, PhenoAge, and BLUP) and a modest inverse relationship with EN EAA. Our findings from a prospective population-based-case-control study indicate a direct association between incident CRC and four markers of accelerated baseline epigenetic age. In contrast, two markers showed a negative association or no association. These results warrant further exploration in larger cohorts and may have implications for CRC risk assessment and prevention.
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Affiliation(s)
- Sofia Malyutina
- Research Institute of Internal and Preventive Medicine-Branch of Institute of Cytology and Genetics SB RAS, Novosibirsk 630089, Russia; (V.M.); (T.N.); (A.R.); (M.V.)
| | | | - Vladimir Maximov
- Research Institute of Internal and Preventive Medicine-Branch of Institute of Cytology and Genetics SB RAS, Novosibirsk 630089, Russia; (V.M.); (T.N.); (A.R.); (M.V.)
| | - Tatiana Nikitenko
- Research Institute of Internal and Preventive Medicine-Branch of Institute of Cytology and Genetics SB RAS, Novosibirsk 630089, Russia; (V.M.); (T.N.); (A.R.); (M.V.)
| | - Andrew Ryabikov
- Research Institute of Internal and Preventive Medicine-Branch of Institute of Cytology and Genetics SB RAS, Novosibirsk 630089, Russia; (V.M.); (T.N.); (A.R.); (M.V.)
| | - Mikhail Voevoda
- Research Institute of Internal and Preventive Medicine-Branch of Institute of Cytology and Genetics SB RAS, Novosibirsk 630089, Russia; (V.M.); (T.N.); (A.R.); (M.V.)
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Wang K, Sartor MA, Colacino JA, Dolinoy DC, Svoboda LK. Sex-Specific Deflection of Age-Related DNA Methylation and Gene Expression in Mouse Heart by Perinatal Toxicant Exposures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591125. [PMID: 38712146 PMCID: PMC11071472 DOI: 10.1101/2024.04.25.591125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Background Global and site-specific changes in DNA methylation and gene expression are associated with cardiovascular aging and disease, but how toxicant exposures during early development influence the normal trajectory of these age-related molecular changes, and whether there are sex differences, has not yet been investigated. Objectives We used an established mouse model of developmental exposures to investigate the effects of perinatal exposure to either lead (Pb) or diethylhexyl phthalate (DEHP), two ubiquitous environmental contaminants strongly associated with CVD, on age-related cardiac DNA methylation and gene expression. Methods Dams were randomly assigned to receive human physiologically relevant levels of Pb (32 ppm in water), DEHP (25 mg/kg chow), or control water and chow. Exposures started two weeks prior to mating and continued until weaning at postnatal day 21 (3 weeks of age). Approximately one male and one female offspring per litter were followed to 3 weeks, 5 months, or 10 months of age, at which time whole hearts were collected (n ≥ 5 per sex per exposure). Enhanced reduced representation bisulfite sequencing (ERRBS) was used to assess the cardiac DNA methylome at 3 weeks and 10 months, and RNA-seq was conducted at all 3 time points. MethylSig and edgeR were used to identify age-related differentially methylated regions (DMRs) and differentially expressed genes (DEGs), respectively, within each sex and exposure group. Cell type deconvolution of bulk RNA-seq data was conducted using the MuSiC algorithm and publicly available single cell RNA-seq data. Results Thousands of DMRs and hundreds of DEGs were identified in control, DEHP, and Pb-exposed hearts across time between 3 weeks and 10 months of age. A closer look at the genes and pathways showing differential DNA methylation revealed that the majority were unique to each sex and exposure group. Overall, pathways governing development and differentiation were most frequently altered with age in all conditions. A small number of genes in each group showed significant changes in DNA methylation and gene expression with age, including several that were altered by both toxicants but were unchanged in control. We also observed subtle, but significant changes in the proportion of several cell types due to age, sex, and developmental exposure. Discussion Together these data show that perinatal Pb or DEHP exposures deflect normal age-related gene expression, DNA methylation programs, and cellular composition across the life course, long after cessation of exposure, and highlight potential biomarkers of developmental toxicant exposures. Further studies are needed to investigate how these epigenetic and transcriptional changes impact cardiovascular health across the life course.
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Fernández-Pérez I, Jiménez-Balado J, Macias-Gómez A, Suárez-Pérez A, Vallverdú-Prats M, Pérez-Giraldo A, Viles-García M, Peris-Subiza J, Vidal-Notari S, Giralt-Steinhauer E, Guisado-Alonso D, Esteller M, Rodriguez-Campello A, Jiménez-Conde J, Ois A, Cuadrado-Godia E. Blood DNA Methylation Analysis Reveals a Distinctive Epigenetic Signature of Vasospasm in Aneurysmal Subarachnoid Hemorrhage. Transl Stroke Res 2024:10.1007/s12975-024-01252-x. [PMID: 38649590 DOI: 10.1007/s12975-024-01252-x] [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: 02/27/2024] [Revised: 03/28/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024]
Abstract
Vasospasm is a potentially preventable cause of poor prognosis in patients with aneurysmal subarachnoid hemorrhage (aSAH). Epigenetics might provide insight on its molecular mechanisms. We aimed to analyze the association between differential DNA methylation (DNAm) and development of vasospasm. We conducted an epigenome-wide association study in 282 patients with aSAH admitted to our hospital. DNAm was assessed with the EPIC Illumina chip (> 850 K CpG sites) in whole-blood samples collected at hospital admission. We identified differentially methylated positions (DMPs) at the CpG level using Cox regression models adjusted for potential confounders, and then we used the DMP results to find differentially methylated regions (DMRs) and enriched biological pathways. A total of 145 patients (51%) experienced vasospasm. In the DMP analysis, we identified 31 CpGs associated with vasospasm at p-value < 10-5. One of them (cg26189827) was significant at the genome-wide level (p-value < 10-8), being hypermethylated in patients with vasospasm and annotated to SUGCT gene, mainly expressed in arteries. Region analysis revealed 13 DMRs, some of them annotated to interesting genes such as POU5F1, HLA-DPA1, RUFY1, and CYP1A1. Functional enrichment analysis showed the involvement of biological processes related to immunity, inflammatory response, oxidative stress, endothelial nitric oxide, and apoptosis. Our findings show, for the first time, a distinctive epigenetic signature of vasospasm in aSAH, establishing novel links with essential biological pathways, including inflammation, immune responses, and oxidative stress. Although further validation is required, our results provide a foundation for future research into the complex pathophysiology of vasospasm.
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Affiliation(s)
- Isabel Fernández-Pérez
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Joan Jiménez-Balado
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain.
| | - Adrià Macias-Gómez
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Antoni Suárez-Pérez
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Marta Vallverdú-Prats
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | | | - Marc Viles-García
- Neuroradiology Department, Hospital del Mar, Barcelona, Catalunya, Spain
| | | | | | - Eva Giralt-Steinhauer
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Daniel Guisado-Alonso
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Research Institute Against Leukemia Josep Carreras, Badalona, Catalunya, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalunya, Spain
| | - Ana Rodriguez-Campello
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Jordi Jiménez-Conde
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Angel Ois
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Elisa Cuadrado-Godia
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
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Ge T, Brickner JH. Inheritance of epigenetic transcriptional memory. Curr Opin Genet Dev 2024; 85:102174. [PMID: 38430840 PMCID: PMC10947848 DOI: 10.1016/j.gde.2024.102174] [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: 11/09/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Epigenetic memory allows organisms to stably alter their transcriptional program in response to developmental or environmental stimuli. Such transcriptional programs are mediated by heritable regulation of the function of enhancers and promoters. Memory involves read-write systems that enable self-propagation and mitotic inheritance of cis-acting epigenetic marks to induce stable changes in transcription. Also, in response to environmental cues, cells can induce epigenetic transcriptional memory to poise inducible genes for faster induction in the future. Here, we discuss modes of epigenetic inheritance and the molecular basis of epigenetic transcriptional memory.
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Affiliation(s)
- Tiffany Ge
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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24
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Harris KM, Levitt B, Gaydosh L, Martin C, Meyer JM, Mishra AA, Kelly AL, Aiello AE. The Sociodemographic and Lifestyle Correlates of Epigenetic Aging in a Nationally Representative U.S. Study of Younger Adults. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585983. [PMID: 38585956 PMCID: PMC10996523 DOI: 10.1101/2024.03.21.585983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Importance Epigenetic clocks represent molecular evidence of disease risk and aging processes and have been used to identify how social and lifestyle characteristics are associated with accelerated biological aging. However, most of this research is based on older adult samples who already have measurable chronic disease. Objective To investigate whether and how sociodemographic and lifestyle characteristics are related to biological aging in a younger adult sample across a wide array of epigenetic clock measures. Design Nationally representative prospective cohort study. Setting United States (U.S.). Participants Data come from the National Longitudinal Study of Adolescent to Adult Health, a national cohort of adolescents in grades 7-12 in U.S. in 1994 followed for 25 years over five interview waves. Our analytic sample includes participants followed-up through Wave V in 2016-18 who provided blood samples for DNA methylation (DNAm) testing (n=4237) at Wave V. Exposure Sociodemographic (sex, race/ethnicity, immigrant status, socioeconomic status, geographic location) and lifestyle (obesity status, exercise, tobacco, and alcohol use) characteristics. Main Outcome Biological aging assessed from blood DNAm using 16 epigenetic clocks when the cohort was aged 33-44 in Wave V. Results While there is considerable variation in the mean and distribution of epigenetic clock estimates and in the correlations among the clocks, we found sociodemographic and lifestyle factors are more often associated with biological aging in clocks trained to predict current or dynamic phenotypes (e.g., PhenoAge, GrimAge and DunedinPACE) as opposed to clocks trained to predict chronological age alone (e.g., Horvath). Consistent and strong associations of faster biological aging were found for those with lower levels of education and income, and those with severe obesity, no weekly exercise, and tobacco use. Conclusions and Relevance Our study found important social and lifestyle factors associated with biological aging in a nationally representative cohort of younger-aged adults. These findings indicate that molecular processes underlying disease risk can be identified in adults entering midlife before disease is manifest and represent useful targets for interventions to reduce social inequalities in heathy aging and longevity. Key Points Question: Are epigenetic clocks, measures of biological aging developed mainly on older-adult samples, meaningful for younger adults and associated with sociodemographic and lifestyle characteristics in expected patterns found in prior aging research?Findings: Sociodemographic and lifestyle factors were associated with biological aging in clocks trained to predict morbidity and mortality showing accelerated aging among those with lower levels of education and income, and those with severe obesity, no weekly exercise, and tobacco use.Meaning: Age-related molecular processes can be identified in younger-aged adults before disease manifests and represent potential interventions to reduce social inequalities in heathy aging and longevity.
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Jones EF, Haldar A, Oza VH, Lasseigne BN. Quantifying transcriptome diversity: a review. Brief Funct Genomics 2024; 23:83-94. [PMID: 37225889 DOI: 10.1093/bfgp/elad019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/14/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
Following the central dogma of molecular biology, gene expression heterogeneity can aid in predicting and explaining the wide variety of protein products, functions and, ultimately, heterogeneity in phenotypes. There is currently overlapping terminology used to describe the types of diversity in gene expression profiles, and overlooking these nuances can misrepresent important biological information. Here, we describe transcriptome diversity as a measure of the heterogeneity in (1) the expression of all genes within a sample or a single gene across samples in a population (gene-level diversity) or (2) the isoform-specific expression of a given gene (isoform-level diversity). We first overview modulators and quantification of transcriptome diversity at the gene level. Then, we discuss the role alternative splicing plays in driving transcript isoform-level diversity and how it can be quantified. Additionally, we overview computational resources for calculating gene-level and isoform-level diversity for high-throughput sequencing data. Finally, we discuss future applications of transcriptome diversity. This review provides a comprehensive overview of how gene expression diversity arises, and how measuring it determines a more complete picture of heterogeneity across proteins, cells, tissues, organisms and species.
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Affiliation(s)
- Emma F Jones
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anisha Haldar
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishal H Oza
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brittany N Lasseigne
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
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Park S, Laskow TC, Chen J, Guha P, Dawn B, Kim D. Microphysiological systems for human aging research. Aging Cell 2024; 23:e14070. [PMID: 38180277 PMCID: PMC10928588 DOI: 10.1111/acel.14070] [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: 06/30/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Recent advances in microphysiological systems (MPS), also known as organs-on-a-chip (OoC), enable the recapitulation of more complex organ and tissue functions on a smaller scale in vitro. MPS therefore provide the potential to better understand human diseases and physiology. To date, numerous MPS platforms have been developed for various tissues and organs, including the heart, liver, kidney, blood vessels, muscle, and adipose tissue. However, only a few studies have explored using MPS platforms to unravel the effects of aging on human physiology and the pathogenesis of age-related diseases. Age is one of the risk factors for many diseases, and enormous interest has been devoted to aging research. As such, a human MPS aging model could provide a more predictive tool to understand the molecular and cellular mechanisms underlying human aging and age-related diseases. These models can also be used to evaluate preclinical drugs for age-related diseases and translate them into clinical settings. Here, we provide a review on the application of MPS in aging research. First, we offer an overview of the molecular, cellular, and physiological changes with age in several tissues or organs. Next, we discuss previous aging models and the current state of MPS for studying human aging and age-related conditions. Lastly, we address the limitations of current MPS and present future directions on the potential of MPS platforms for human aging research.
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Affiliation(s)
- Seungman Park
- Department of Mechanical EngineeringUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Thomas C. Laskow
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jingchun Chen
- Nevada Institute of Personalized MedicineUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Prasun Guha
- Nevada Institute of Personalized MedicineUniversity of Nevada, Las VegasLas VegasNevadaUSA
- School of Life SciencesUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Buddhadeb Dawn
- Department of Internal Medicine, Kirk Kerkorian School of MedicineUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Deok‐Ho Kim
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
- Center for Microphysiological SystemsJohns Hopkins UniversityBaltimoreMarylandUSA
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27
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Ali M, Wani SUD, Dey T, Sridhar SB, Qadrie ZL. A common molecular and cellular pathway in developing Alzheimer and cancer. Biochem Biophys Rep 2024; 37:101625. [PMID: 38225990 PMCID: PMC10788207 DOI: 10.1016/j.bbrep.2023.101625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/17/2024] Open
Abstract
Globally cancer and Alzheimer's disease (AD) are two major diseases and still, there is no clearly defined molecular mechanism. There is an opposite relation between cancer and AD which are the proportion of emerging cancer was importantly slower in AD patients, whereas slow emerging AD in patients with cancer. In cancer, regulation of cell mechanisms is interrupted by an increase in cell survival and proliferation, while on the contrary, AD is related to augmented neuronal death, that may be either produced by or associated with amyloid-β (Aβ) and tau deposition. Stated that the probability that disruption of mechanisms takes part in the regulation of cell survival/death and might be implicated in both diseases. The mechanism of actions such as DNA-methylation, genetic polymorphisms, or another mechanism of actions that induce alteration in the action of drugs with significant roles in resolving the finding to repair and live or die might take part in the pathogenesis of these two ailments. The functions of miRNA, p53, Pin1, the Wnt signaling pathway, PI3 KINASE/Akt/mTOR signaling pathway GRK2 signaling pathway, and the pathophysiological role of oxidative stress are presented in this review as potential candidates which hypothetically describe inverse relations between cancer and AD. Innovative materials almost mutual mechanisms in the aetiology of cancer and AD advocates novel treatment approaches. Among these treatment strategies, the most promising use treatment such as tyrosine kinase inhibitor, nilotinib, protein kinase C, and bexarotene.
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Affiliation(s)
- Mohammad Ali
- Department of Pharmacology, Sri Adichunchanagiri College of Pharmacy, Adichunchanagiri University, B.G Nagar, Nagamagala, Bellur, Karnataka, 571418, India
- Department of Pharmacy Practice, East Point College of Pharmacy, Bangalore, 560049, India
| | - Shahid Ud Din Wani
- Division of Pharmaceutics, Department of Pharmaceutical Sciences, School of Applied Sciences and Technology, University of Kashmir, Srinagar, 190006, India
| | - Tathagata Dey
- Department of Pharmaceutical Chemistry, East Point College of Pharmacy, Bangalore, 560049, India
| | - Sathvik B. Sridhar
- Department of Clinical Pharmacy and Pharmacology, RAK College of Pharmacy, RAK Medical and Health Sciences University, Ras Al Khaimah, PO Box 11172, United Arab Emirates
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28
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Yamagishi T, Sakurai W, Watanabe K, Toyomane K, Akutsu T. Development and comparison of forensic interval age prediction models by statistical and machine learning methods based on the methylation rates of ELOVL2 in blood DNA. Forensic Sci Int Genet 2024; 69:103004. [PMID: 38160598 DOI: 10.1016/j.fsigen.2023.103004] [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: 10/05/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Age estimation can be useful information for narrowing down candidates of unidentified donors in criminal investigations. Various age estimation models based on DNA methylation biomarkers have been developed for forensic usage in the past decade. However, many of these models using ordinary least squares regression cannot generate an appropriate estimation due to the deterioration in prediction accuracy caused by an increased prediction error in older age groups. In the present study, to address this problem, we developed age estimation models that set an appropriate prediction interval for all age groups by two approaches: a statistical method using quantile regression (QR) and a machine learning method using an artificial neural network (ANN). Methylation datasets (n = 1280, age 0-91 years) of the promoter for the gene encoding ELOVL fatty acid elongase 2 were used to develop the QR and ANN models. By validation using several test datasets, both models were shown to enlarge prediction intervals in accordance with aging and have a high level of correct prediction (>90 %) for older age groups. The QR and ANN models also generated a point age prediction with high accuracy. The ANN model enabled a prediction with a mean absolute error (MAE) of 5.3 years and root mean square error (RMSE) of 7.3 years for the test dataset (n = 549), which were comparable to those of the QR model (MAE = 5.6 years, RMSE = 7.8 years). Their applicability to casework was also confirmed using bloodstain samples stored for various periods of time (1-14 years), indicating the stability of the models for aged bloodstain samples. From these results, it was considered that the proposed models can provide more useful and effective age estimation in forensic settings.
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Affiliation(s)
- Takayuki Yamagishi
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Wataru Sakurai
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Ken Watanabe
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kochi Toyomane
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tomoko Akutsu
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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29
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Gupta N, El-Gawaad NSA, Mallasiy LO, Gupta H, Yadav VK, Alghamdi S, Qusty NF. Microbial dysbiosis and the aging process: a review on the potential age-deceleration role of Lactiplantibacillus plantarum. Front Microbiol 2024; 15:1260793. [PMID: 38440135 PMCID: PMC10909992 DOI: 10.3389/fmicb.2024.1260793] [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: 07/18/2023] [Accepted: 02/01/2024] [Indexed: 03/06/2024] Open
Abstract
Gut microbiota dysbiosis has been a serious risk factor for several gastric and systemic diseases. Recently, gut microbiota's role in aging was discussed. Available preclinical evidence suggests that the probiotic bacteria Lactiplantibacillus plantarums (LP) may influence the aging process via modulation of the gut microbiota. The present review summarized compelling evidence of LP's potential effect on aging hallmarks such as oxidative stress, inflammation, DNA methylation, and mitochondrial dysfunction. LP gavage modulates gut microbiota and improves overall endurance in aging animal models. LP cell constituents exert considerable antioxidant potential which may reduce ROS levels directly. In addition, restored gut microbiota facilitate a healthy intestinal milieu and accelerate multi-channel communication via signaling factors such as SCFA and GABA. Signaling factors further activate specific transcription factor Nrf2 in order to reduce oxidative damage. Nrf2 regulates cellular defense systems involving anti-inflammatory cytokines, MMPs, and protective enzymes against MAPKs. We concluded that LP supplementation may be an effective approach to managing aging and associated health risks.
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Affiliation(s)
- Nishant Gupta
- Medical Research and Development, River Engineering, Noida, India
| | - N. S. Abd El-Gawaad
- Department of Physics, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - L. O. Mallasiy
- Department of Home Economics, Faculty of Science and Arts in Tihama, King Khalid University, Muhayil, Saudi Arabia
| | | | | | - Saad Alghamdi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, University of Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naeem F. Qusty
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, University of Umm Al-Qura University, Makkah, Saudi Arabia
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30
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Luan Y, Zhu X, Jiao Y, Liu H, Huang Z, Pei J, Xu Y, Yang Y, Ren K. Cardiac cell senescence: molecular mechanisms, key proteins and therapeutic targets. Cell Death Discov 2024; 10:78. [PMID: 38355681 PMCID: PMC10866973 DOI: 10.1038/s41420-023-01792-5] [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: 09/04/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 02/16/2024] Open
Abstract
Cardiac aging, particularly cardiac cell senescence, is a natural process that occurs as we age. Heart function gradually declines in old age, leading to continuous heart failure, even in people without a prior history of heart disease. To address this issue and improve cardiac cell function, it is crucial to investigate the molecular mechanisms underlying cardiac senescence. This review summarizes the main mechanisms and key proteins involved in cardiac cell senescence. This review further discusses the molecular modulators of cellular senescence in aging hearts. Furthermore, the discussion will encompass comprehensive descriptions of the key drugs, modes of action and potential targets for intervention in cardiac senescence. By offering a fresh perspective and comprehensive insights into the molecular mechanisms of cardiac senescence, this review seeks to provide a fresh perspective and important theoretical foundations for the development of drugs targeting this condition.
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Affiliation(s)
- Yi Luan
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Xiaofan Zhu
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Yuxue Jiao
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Hui Liu
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Zhen Huang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Jinyan Pei
- Quality Management Department, Henan No.3 Provincial People's Hospital, Zhengzhou, 450052, P. R. China
| | - Yawei Xu
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
| | - Yang Yang
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
| | - Kaidi Ren
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, P. R. China.
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31
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Chaudhary V, Bhattacharjee D, Devi NK, Saraswathy KN. Global DNA Methylation Levels Viz-a-Viz Genetic and Biochemical Variations in One Carbon Metabolic Pathway: An Exploratory Study from North India. Biochem Genet 2024:10.1007/s10528-023-10659-4. [PMID: 38356009 DOI: 10.1007/s10528-023-10659-4] [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: 09/06/2023] [Accepted: 12/29/2023] [Indexed: 02/16/2024]
Abstract
Despite the importance of one carbon metabolic pathway (OCMP) in modulating the DNA methylation process, only a few population-based studies have explored their relationship among healthy individuals. This study aimed to understand the variations in global DNA methylation levels with respect to selected genetic (CBS 844ins68, MTRR A66G, MTR A2756G, and MTHFR C677T polymorphisms) and biochemical (folate, vitamin B12, and homocysteine) markers associated with OCMP among healthy North Indian adults. The study has been conducted among 1095 individuals of either sex (69.5% females), aged 30-75 years. A sample of 5 mL of blood was collected from each participant. Homocysteine, folate, and vitamin B12 levels were determined using the chemiluminescence technique. Restriction digestion was performed for genotyping MTRR A66G, MTR A2756G, and MTHFR C677T polymorphisms and allele-specific PCR amplification for CBS 844ins68 polymorphism. Global DNA methylation levels were analyzed using ELISA-based colorimetric technique. Of the selected genetic and biochemical markers, the mutant MTRR A66G allele was positively associated with global DNA methylation levels. Further, advanced age was inversely associated with methylation levels. MTRR 66GG genotype group was hypermethylated than other genotypes in folate replete and vitamin B12 deficient group (a condition prevalent among vegetarians), suggesting that the G allele may be more efficient than the wild-type allele in such conditions. Global DNA methylation levels appeared to be more influenced by genetic than biochemical factors. MTRR 66G allele may have a selective advantage in vitamin B12 deficient conditions. Further research should be undertaken to understand how genetics affects epigenetic processes.
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Affiliation(s)
- Vineet Chaudhary
- Department of Anthropology, University of Delhi, Delhi, 110007, India
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Ramirez P, Sun W, Kazempour Dehkordi S, Zare H, Fongang B, Bieniek KF, Frost B. Nanopore-based DNA long-read sequencing analysis of the aged human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578450. [PMID: 38370753 PMCID: PMC10871260 DOI: 10.1101/2024.02.01.578450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Aging disrupts cellular processes such as DNA repair and epigenetic control, leading to a gradual buildup of genomic alterations that can have detrimental effects in post-mitotic cells. Genomic alterations in regions of the genome that are rich in repetitive sequences, often termed "dark loci," are difficult to resolve using traditional sequencing approaches. New long-read technologies offer promising avenues for exploration of previously inaccessible regions of the genome. Using nanopore-based long-read whole-genome sequencing of DNA extracted from aged 18 human brains, we identify previously unreported structural variants and methylation patterns within repetitive DNA, focusing on transposable elements ("jumping genes") as crucial sources of variation, particularly in dark loci. Our analyses reveal potential somatic insertion variants and provides DNA methylation frequencies for many retrotransposon families. We further demonstrate the utility of this technology for the study of these challenging genomic regions in brains affected by Alzheimer's disease and identify significant differences in DNA methylation in pathologically normal brains versus those affected by Alzheimer's disease. Highlighting the power of this approach, we discover specific polymorphic retrotransposons with altered DNA methylation patterns. These retrotransposon loci have the potential to contribute to pathology, warranting further investigation in Alzheimer's disease research. Taken together, our study provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, structural variants, and DNA methylation in the aging brain affected with Alzheimer's disease neuropathology.
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Affiliation(s)
- Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Wenyan Sun
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
- School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri
| | - Shiva Kazempour Dehkordi
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Kevin F. Bieniek
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Pathology, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
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Wang Y, Grant OA, Zhai X, Mcdonald-Maier KD, Schalkwyk LC. Insights into ageing rates comparison across tissues from recalibrating cerebellum DNA methylation clock. GeroScience 2024; 46:39-56. [PMID: 37597113 PMCID: PMC10828477 DOI: 10.1007/s11357-023-00871-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/07/2023] [Indexed: 08/21/2023] Open
Abstract
DNA methylation (DNAm)-based age clocks have been studied extensively as a biomarker of human ageing and a risk factor for age-related diseases. Despite different tissues having vastly different rates of proliferation, it is still largely unknown whether they age at different rates. It was previously reported that the cerebellum ages slowly; however, this claim was drawn from a single clock using a relatively small sample size and so warrants further investigation. We collected the largest cerebellum DNAm dataset (N = 752) to date. We found the respective epigenetic ages are all severely underestimated by six representative DNAm age clocks, with the underestimation effects more pronounced in the four clocks whose training datasets do not include brain-related tissues. We identified 613 age-associated CpGs in the cerebellum, which accounts for only 14.5% of the number found in the middle temporal gyrus from the same population (N = 404). From the 613 cerebellum age-associated CpGs, we built a highly accurate age prediction model for the cerebellum named CerebellumClockspecific (Pearson correlation=0.941, MAD=3.18 years). Ageing rate comparisons based on the two tissue-specific clocks constructed on the 201 overlapping age-associated CpGs support the cerebellum has younger DNAm age. Nevertheless, we built BrainCortexClock to prove a single DNAm clock is able to unbiasedly estimate DNAm ages of both cerebellum and cerebral cortex, when they are adequately and equally represented in the training dataset. Comparing ageing rates across tissues using DNA methylation multi-tissue clocks is flawed. The large underestimation of age prediction for cerebellums by previous clocks mainly reflects the improper usage of these age clocks. There exist strong and consistent ageing effects on the cerebellar methylome, and we suggest the smaller number of age-associated CpG sites in cerebellum is largely attributed to its extremely low average cell replication rates.
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Affiliation(s)
- Yucheng Wang
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ, UK
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Olivia A Grant
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- Institute of Social and Economic Research, University of Essex, Colchester, CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Xiaojun Zhai
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ, UK.
| | - Klaus D Mcdonald-Maier
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ, UK
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Lindroth Y, Pedersen L, Alssamaray J, Berglund T, Sundqvist A, Borgfeldt C, Forslund O. Cervix cytology samples revealed increased methylation of the human markers FAM19A4/miR124-2 up to 8 years before adenocarcinoma. Acta Obstet Gynecol Scand 2024; 103:378-386. [PMID: 37964497 PMCID: PMC10823397 DOI: 10.1111/aogs.14707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/13/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023]
Abstract
INTRODUCTION Methylation analysis of the promoter region of tumor-suppressor genes has previously shown high sensitivity for detection of high-grade cervical intraepithelial neoplasia (CIN) and cancer. HPV-testing has a high sensitivity to identify women at risk to develop cancer, and has been implemented in cervical screening programs in several countries. But in most HPV-positive women the infection will clear and they will not develop cancer. Testing for methylation could help to identify women who have potentially progressive cervical disease and need closer follow-up. The goal of the present study was to investigate the potential use of methylation as a triage test of HPV-positive women in the screening program. MATERIAL AND METHODS A collection of liquid-based cytology (LBC) samples from 106 women, collected between 4 months and 8 years before histologically confirmed cervical cancer or CIN3, was analyzed for hypermethylation of the human genes FAM19A4 and miR124-2. RESULTS Methylation was detected in 45% (33/73) of normal LBC samples from women who later developed CIN3+, compared with 10% (3/31) of normal LBC samples from women without subsequent dysplasia (P = 0.0006). Overall, methylation was detected in 39% (14/36), 51% (19/37), 61% (14/23) and 70% (7/10) of LBC samples from women who later developed CIN3, adenocarcinoma in situ (AIS), squamous cell carcinoma (SCC) and adenocarcinoma (ADC), respectively. Positive methylation analysis was not significantly more frequent than abnormal cytology of atypical squamous cells of unclear significance or worse (ASCUS+) in LBC samples collected 4 months to 8 years before SCC or AIS; however, prior to the development of ADC, methylation was observed in 7/10 LBC samples, despite normal cytology. Overall, LBC samples collected before invasive cancer (ADC and SCC) were more frequently positive in the methylation analysis than in cytological analysis of ASCUS+ (P = 0.048). For LBC samples collected more than 2 years before the development of AIS, SCC or ADC, methylation analysis showed a higher positivity rate than cytology did. CONCLUSIONS Testing for methylation of FAM19A4/miR124-2 as a triage for HPV-positive women would be useful to identify women at risk of cancer development, especially adenocarcinoma. Further studies are needed to estimate the cost-effectiveness before introducing methylation testing in the screening program.
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Affiliation(s)
- Ylva Lindroth
- Department of Laboratory MedicineLund UniversityLundSweden
- Clinical Microbiology, Infection Prevention and Control, Office for Medical ServicesLundSweden
| | - Louise Pedersen
- Clinical Microbiology, Infection Prevention and Control, Office for Medical ServicesLundSweden
| | - Jacob Alssamaray
- Clinical Microbiology, Infection Prevention and Control, Office for Medical ServicesLundSweden
| | - Tim Berglund
- Clinical Microbiology, Infection Prevention and Control, Office for Medical ServicesLundSweden
| | - Avalon Sundqvist
- Department of Obstetrics and GynecologySkåne University Hospital, Lund UniversityLundSweden
| | - Christer Borgfeldt
- Department of Obstetrics and GynecologySkåne University Hospital, Lund UniversityLundSweden
| | - Ola Forslund
- Department of Laboratory MedicineLund UniversityLundSweden
- Clinical Microbiology, Infection Prevention and Control, Office for Medical ServicesLundSweden
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Ma X, Zhao LL, Yu YC, Cheng Y. Engrailed: Pathological and physiological effects of a multifunctional developmental gene. Genesis 2024; 62:e23557. [PMID: 37830136 DOI: 10.1002/dvg.23557] [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: 06/23/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Engrailed-1 (EN1) is a developmental gene that encodes En1, a highly conserved transcription factor involved in regionalization during early embryogenesis and in the later maintenance of normal neurons. After birth, EN1 still plays a role in the development and physiology of the body; for example, it exerts a protective effect on midbrain dopaminergic (mDA) neurons, and loss of EN1 causes mDA neurons in the ventral midbrain to gradually die approximately 6 weeks after birth, resulting in motor and nonmotor symptoms similar to those observed in Parkinson's disease. Notably, EN1 has been identified as a possible susceptibility gene for idiopathic Parkinson's disease in humans. EN1 is involved in the processes of wound-healing scar production and tissue and organ fibrosis. Additionally, EN1 can lead to tumorigenesis and thus provides a target for the treatment of some tumors. In this review, we summarize the effects of EN1 on embryonic organ development, describe the consequences of the deletion or overexpression of the EN1 gene, and discuss the pathways in which EN1 is involved. We hope to clarify the role of EN1 as a developmental gene and present potential therapeutic targets for diseases involving the EN1 gene.
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Affiliation(s)
- Xiang Ma
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Liang-Liang Zhao
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Yi-Chun Yu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Yan Cheng
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
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Linders AN, Dias IB, López Fernández T, Tocchetti CG, Bomer N, Van der Meer P. A review of the pathophysiological mechanisms of doxorubicin-induced cardiotoxicity and aging. NPJ AGING 2024; 10:9. [PMID: 38263284 PMCID: PMC10806194 DOI: 10.1038/s41514-024-00135-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
The population of cancer survivors is rapidly increasing due to improving healthcare. However, cancer therapies often have long-term side effects. One example is cancer therapy-related cardiac dysfunction (CTRCD) caused by doxorubicin: up to 9% of the cancer patients treated with this drug develop heart failure at a later stage. In recent years, doxorubicin-induced cardiotoxicity has been associated with an accelerated aging phenotype and cellular senescence in the heart. In this review we explain the evidence of an accelerated aging phenotype in the doxorubicin-treated heart by comparing it to healthy aged hearts, and shed light on treatment strategies that are proposed in pre-clinical settings. We will discuss the accelerated aging phenotype and the impact it could have in the clinic and future research.
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Affiliation(s)
- Annet Nicole Linders
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30.001, Groningen, The Netherlands
| | - Itamar Braga Dias
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30.001, Groningen, The Netherlands
| | - Teresa López Fernández
- Division of Cardiology, Cardiac Imaging and Cardio-Oncology Unit, La Paz University Hospital, IdiPAZ Research Institute, Madrid, Spain
| | - Carlo Gabriele Tocchetti
- Department of Translational Medical Sciences (DISMET), Federico II University, Naples, Italy
- Centre for Basic and Clinical Immunology Research (CISI), Federico II University, Naples, Italy
- Interdepartmental Centre of Clinical and Translational Sciences (CIRCET), Federico II University, Naples, Italy
- Interdepartmental Hypertension Research Centre (CIRIAPA), Federico II University, Naples, Italy
| | - Nils Bomer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30.001, Groningen, The Netherlands
| | - Peter Van der Meer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30.001, Groningen, The Netherlands.
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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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Huang K, Liu X, Zhang Z, Wang T, Xu H, Li Q, Jia Y, Huang L, Kim P, Zhou X. AgeAnnoMO: a knowledgebase of multi-omics annotation for animal aging. Nucleic Acids Res 2024; 52:D822-D834. [PMID: 37850649 PMCID: PMC10767957 DOI: 10.1093/nar/gkad884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/16/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023] Open
Abstract
Aging entails gradual functional decline influenced by interconnected factors. Multiple hallmarks proposed as common and conserved underlying denominators of aging on the molecular, cellular and systemic levels across multiple species. Thus, understanding the function of aging hallmarks and their relationships across species can facilitate the translation of anti-aging drug development from model organisms to humans. Here, we built AgeAnnoMO (https://relab.xidian.edu.cn/AgeAnnoMO/#/), a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8596 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes multiple aging regulators across species via multi-omics data, comprehensively annotating aging-related genes, proteins, metabolites, mitochondrial genes, microbiotas and age-specific TCR and BCR sequences tied to aging hallmarks for these species and tissues. AgeAnnoMO not only facilitates a deeper and more generalizable understanding of aging mechanisms, but also provides potential insights of the specificity across tissues and species in aging process, which is important to develop the effective anti-aging interventions for diverse populations. We anticipate that AgeAnnoMO will provide a valuable resource for comprehending and integrating the conserved driving hallmarks in aging biology and identifying the targetable biomarkers for aging research.
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Affiliation(s)
- Kexin Huang
- The Center of Gerontology and Geriatrics and West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Xi Liu
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Zhaocan Zhang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Tiangang Wang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Haixia Xu
- The Center of Gerontology and Geriatrics and West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Qingxuan Li
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Yuhao Jia
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Li H, Wu S, Li J, Xiong Z, Yang K, Ye W, Ren J, Wang Q, Xiong M, Zheng Z, Zhang S, Han Z, Yang P, Jiang B, Ping J, Zuo Y, Lu X, Zhai Q, Yan H, Wang S, Ma S, Zhang B, Ye J, Qu J, Yang YG, Zhang F, Liu GH, Bao Y, Zhang W. HALL: a comprehensive database for human aging and longevity studies. Nucleic Acids Res 2024; 52:D909-D918. [PMID: 37870433 PMCID: PMC10767887 DOI: 10.1093/nar/gkad880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/15/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
Diverse individuals age at different rates and display variable susceptibilities to tissue aging, functional decline and aging-related diseases. Centenarians, exemplifying extreme longevity, serve as models for healthy aging. The field of human aging and longevity research is rapidly advancing, garnering significant attention and accumulating substantial data in recent years. Omics technologies, encompassing phenomics, genomics, transcriptomics, proteomics, metabolomics and microbiomics, have provided multidimensional insights and revolutionized cohort-based investigations into human aging and longevity. Accumulated data, covering diverse cells, tissues and cohorts across the lifespan necessitates the establishment of an open and integrated database. Addressing this, we established the Human Aging and Longevity Landscape (HALL), a comprehensive multi-omics repository encompassing a diverse spectrum of human cohorts, spanning from young adults to centenarians. The core objective of HALL is to foster healthy aging by offering an extensive repository of information on biomarkers that gauge the trajectory of human aging. Moreover, the database facilitates the development of diagnostic tools for aging-related conditions and empowers targeted interventions to enhance longevity. HALL is publicly available at https://ngdc.cncb.ac.cn/hall/index.
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Affiliation(s)
- Hao Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuang Xiong
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou 350002, China
| | - Kuan Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Weidong Ye
- Department of Vascular Surgery, Quzhou Affiliated Hospital of Wenzhou Medical University, Beijing 100101, China
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, 324000, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muzhao Xiong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zikai Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuo Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zichu Han
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Beier Jiang
- Department of Vascular Surgery, Quzhou Affiliated Hospital of Wenzhou Medical University, Beijing 100101, China
| | - Jiale Ping
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuesheng Zuo
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyong Lu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaocheng Zhai
- Department of Vascular Surgery, Quzhou Affiliated Hospital of Wenzhou Medical University, Beijing 100101, China
| | - Haoteng Yan
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Bing Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Jinlin Ye
- Department of Vascular Surgery, Quzhou Affiliated Hospital of Wenzhou Medical University, Beijing 100101, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Feng Zhang
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, 324000, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Yiming Bao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
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40
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Heo SJ, Jee YS. Intensity-effects of strengthening exercise on thigh muscle volume, pro- or anti-inflammatory cytokines, and immunocytes in the older adults: A randomized controlled trial. Arch Gerontol Geriatr 2024; 116:105136. [PMID: 37541052 DOI: 10.1016/j.archger.2023.105136] [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: 06/12/2023] [Revised: 07/05/2023] [Accepted: 07/21/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND This study investigated the intensity-effects of strength training on thigh muscle mass, cytokines, and immunocytes in the older adults. MATERIALS AND METHODS A total of 81 participated in this study. Participants were assigned randomly to four groups: control group (CON), low- (LSE), moderate- (MSE), and high-intensity strength exercise (HSE) groups. Three exercise groups worked out for 50 min/day, 3 days/week for 12 weeks. RESULTS In the thigh volume analyzed by computed tomography, the exercise groups showed a significant increase in the muscle mass, with a clear pattern of change observed in the groups who exercised with moderate to high intensity. The lowest levels of interleukin (IL)-6 in the MSE group (-20.94%) and tumor necrosis factor-α in the HSE group (-28.75%) were observed. Notably, IL-10 showed a significant increase (35.72%) only in the MSE group. In the CON group, natural killer (NK) cells showed a decrease, while in the exercise groups, their levels increased. The highest levels of NK cells were observed in the HSE group. Similar patterns of change were observed in CD4 T cells and CD19 B cells. CD3 and CD8 T cells exhibited significant increases in the MSE and HSE groups. CONCLUSIONS This study presents evidence that engaging in moderate to high-intensity exercise may have a positive impact on cytokines and immunocytes by increasing muscle mass in older adults who may have sarcopenia. SIMPLE SUMMARY Engaging in strength training exercises is considered crucial for maintaining the health of older individuals who are susceptible to sarcopenia. When resistance exercises are performed at a moderate to strenuous intensity, it is anticipated that positive changes can occur in cytokines and immunocytes. These changes can be observed through improvements in thigh muscle volumes as measured by computed tomography.
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Affiliation(s)
- Seung-Jae Heo
- Department of Physical Education, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Korea
| | - Yong-Seok Jee
- Research Institute of Sports and Industry Science, Hanseo University, #1 Hanseo-ro, Haemi-myeon, Seosan, 31962, Korea.
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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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42
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Zeng Y, Mao Y, Chen Y, Wang Y, Xu S. DNA methylation induces subtle mechanical alteration but significant chiral selectivity. Chem Commun (Camb) 2023; 59:14855-14858. [PMID: 38015496 PMCID: PMC10794036 DOI: 10.1039/d3cc05211g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
DNA methylation is a major epigenetic modification that is closely related to human health. Many experimental techniques as well as theoretical methods have been used to detect the modified nucleotides and identify their effects on molecular binding. It remains challenging to resolve the effect of few methylations of nucleic acids. Using super-resolution force spectroscopy, we firstly revealed that single cytosine methylation increases the mechanical stability of the DNA duplex by 1.9 ± 0.3 pN. Methylation also induces significant chiral selectivity towards drug molecules such as d,l-tetrahydropalmatine. Our results precisely quantify the mechanical effect of methylation and suggest that drug design should take methylation into consideration for enhanced selectivity.
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Affiliation(s)
- Yi Zeng
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
| | - Yujia Mao
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
| | - Yanjun Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, TX 77204, USA.
| | - Shoujun Xu
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
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Arai K, Qi H, Inoue-Murayama M. Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM). PLoS One 2023; 18:e0294994. [PMID: 38079426 PMCID: PMC10712859 DOI: 10.1371/journal.pone.0294994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Age is an important parameter for bettering the understanding of biodemographic trends-development, survival, reproduction and environmental effects-critical for conservation. However, current age estimation methods are challenging to apply to many species, and no standardised technique has been adopted yet. This study examined the potential use of methylation-sensitive high-resolution melting (MS-HRM), a labour-, time-, and cost-effective method to estimate chronological age from DNA methylation in Asian elephants (Elephas maximus). The objective of this study was to investigate the accuracy and validation of MS-HRM use for age determination in long-lived species, such as Asian elephants. The average lifespan of Asian elephants is between 50-70 years but some have been known to survive for more than 80 years. DNA was extracted from 53 blood samples of captive Asian elephants across 11 zoos in Japan, with known ages ranging from a few months to 65 years. Methylation rates of two candidate age-related epigenetic genes, RALYL and TET2, were significantly correlated with chronological age. Finally, we established a linear, unisex age estimation model with a mean absolute error (MAE) of 7.36 years. This exploratory study suggests an avenue to further explore MS-HRM as an alternative method to estimate the chronological age of Asian elephants.
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Affiliation(s)
- Kana Arai
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
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44
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Ndhlovu LC, Bendall ML, Dwaraka V, Pang APS, Dopkins N, Carreras N, Smith R, Nixon DF, Corley MJ. Retroelement-Age Clocks: Epigenetic Age Captured by Human Endogenous Retrovirus and LINE-1 DNA methylation states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570422. [PMID: 38106164 PMCID: PMC10723416 DOI: 10.1101/2023.12.06.570422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human endogenous retroviruses (HERVs), the remnants of ancient viral infections embedded within the human genome, and long interspersed nuclear elements 1 (LINE-1), a class of autonomous retrotransposons, are silenced by host epigenetic mechanisms including DNA methylation. The resurrection of particular retroelements has been linked to biological aging. Whether the DNA methylation states of locus specific HERVs and LINEs can be used as a biomarker of chronological age in humans remains unclear. We show that highly predictive epigenetic clocks of chronological age can be constructed from retroelement DNA methylation states in the immune system, across human tissues, and pan-mammalian species. We found retroelement epigenetic clocks were reversed during transient epigenetic reprogramming, accelerated in people living with HIV-1, responsive to antiretroviral therapy, and accurate in estimating long-term culture ages of human brain organoids. Our findings support the hypothesis of epigenetic dysregulation of retroelements as a potential contributor to the biological hallmarks of aging.
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Affiliation(s)
- Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Matthew L. Bendall
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | - Alina PS Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Nicholas Dopkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | | | - Douglas F. Nixon
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
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Lukacsovich D, O’Shea D, Huang H, Zhang W, Young JI, Steven Chen X, Dietrich ST, Kunkle B, Martin ER, Wang L. MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.04.23299412. [PMID: 38105943 PMCID: PMC10723513 DOI: 10.1101/2023.12.04.23299412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder with a significant impact on aging populations. DNA methylation (DNAm) alterations have been implicated in both the aging processes and the development of AD. Given that AD affects more women than men, it is also important to explore DNAm changes that occur specifically in each sex. We created MIAMI-AD, a comprehensive knowledge base containing manually curated summary statistics from 97 published tables in 37 studies, all of which included at least 100 participants. MIAMI-AD enables easy browsing, querying, and downloading DNAm associations at multiple levels - at individual CpG, gene, genomic regions, or genome-wide, in one or multiple studies. Moreover, it also offers tools to perform integrative analyses, such as comparing DNAm associations across different phenotypes or tissues, as well as interactive visualizations. Using several use case examples, we demonstrated that MIAMI-AD facilitates our understanding of age-associated CpGs in AD and the sex-specific roles of DNAm in AD. This open-access resource is freely available to the research community, and all the underlying data can be downloaded. MIAMI-AD (https://miami-ad.org/) facilitates integrative explorations to better understand the interplay between DNAm across aging, sex, and AD.
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Affiliation(s)
- David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Deirdre O’Shea
- Department of Neurology, Comprehensive Center for Brain Health, University of Miami Miller School of Medicine, Boca Raton, FL, 33433
| | - Hanchen Huang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Sven-Thorsten Dietrich
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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46
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Le Clercq LS, Kotzé A, Grobler JP, Dalton DL. Biological clocks as age estimation markers in animals: a systematic review and meta-analysis. Biol Rev Camb Philos Soc 2023; 98:1972-2011. [PMID: 37356823 DOI: 10.1111/brv.12992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023]
Abstract
Various biological attributes associated with individual fitness in animals change predictably over the lifespan of an organism. Therefore, the study of animal ecology and the work of conservationists frequently relies upon the ability to assign animals to functionally relevant age classes to model population fitness. Several approaches have been applied to determining individual age and, while these methods have proved useful, they are not without limitations and often lack standardisation or are only applicable to specific species. For these reasons, scientists have explored the potential use of biological clocks towards creating a universal age-determination method. Two biological clocks, tooth layer annulation and otolith layering have found universal appeal. Both methods are highly invasive and most appropriate for post-mortem age-at-death estimation. More recently, attributes of cellular ageing previously explored in humans have been adapted to studying ageing in animals for the use of less-invasive molecular methods for determining age. Here, we review two such methods, assessment of methylation and telomere length, describing (i) what they are, (ii) how they change with age, and providing (iii) a summary and meta-analysis of studies that have explored their utility in animal age determination. We found that both attributes have been studied across multiple vertebrate classes, however, telomere studies were used before methylation studies and telomere length has been modelled in nearly twice as many studies. Telomere length studies included in the review often related changes to stress responses and illustrated that telomere length is sensitive to environmental and social stressors and, in the absence of repair mechanisms such as telomerase or alternative lengthening modes, lacks the ability to recover. Methylation studies, however, while also detecting sensitivity to stressors and toxins, illustrated the ability to recover from such stresses after a period of accelerated ageing, likely due to constitutive expression or reactivation of repair enzymes such as DNA methyl transferases. We also found that both studied attributes have parentally heritable features, but the mode of inheritance differs among taxa and may relate to heterogamy. Our meta-analysis included more than 40 species in common for methylation and telomere length, although both analyses included at least 60 age-estimation models. We found that methylation outperforms telomere length in terms of predictive power evidenced from effect sizes (more than double that observed for telomeres) and smaller prediction intervals. Both methods produced age correlation models using similar sample sizes and were able to classify individuals into young, middle, or old age classes with high accuracy. Our review and meta-analysis illustrate that both methods are well suited to studying age in animals and do not suffer significantly from variation due to differences in the lifespan of the species, genome size, karyotype, or tissue type but rather that quantitative method, patterns of inheritance, and environmental factors should be the main considerations. Thus, provided that complex factors affecting the measured trait can be accounted for, both methylation and telomere length are promising targets to develop as biomarkers for age determination in animals.
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Affiliation(s)
- Louis-Stéphane Le Clercq
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Desiré Lee Dalton
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BA, UK
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47
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Singh M, Spendlove SJ, Wei A, Bondhus LM, Nava AA, de L Vitorino FN, Amano S, Lee J, Echeverria G, Gomez D, Garcia BA, Arboleda VA. KAT6A mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior HOXC cluster. Hum Genet 2023; 142:1705-1720. [PMID: 37861717 PMCID: PMC10676314 DOI: 10.1007/s00439-023-02608-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features, including intellectual disability, developmental and speech delay, and hypotonia, and affects multiple organ systems. KAT6A is the enzymatic core of a histone-acetylation protein complex; however, the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n = 8) and control (n = 14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23% (14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, and HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.
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Affiliation(s)
- Meghna Singh
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sarah J Spendlove
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA
| | - Angela Wei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA
| | - Leroy M Bondhus
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Aileen A Nava
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Francisca N de L Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Seth Amano
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jacob Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gesenia Echeverria
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Dianne Gomez
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Valerie A Arboleda
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA.
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48
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Protti G, Rubbi L, Gören T, Sabirli R, Civlan S, Kurt Ö, Türkçüer İ, Köseler A, Pellegrini M. The methylome of buccal epithelial cells is influenced by age, sex, and physiological properties. Physiol Genomics 2023; 55:618-633. [PMID: 37781740 DOI: 10.1152/physiolgenomics.00063.2023] [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: 06/22/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023] Open
Abstract
Epigenetic modifications, particularly DNA methylation, have emerged as regulators of gene expression and are implicated in various biological processes and disease states. Understanding the factors influencing the epigenome is essential for unraveling its complexity. In this study, we aimed to identify how the methylome of buccal epithelial cells, a noninvasive and easily accessible tissue, is associated with demographic and health-related variables commonly used in clinical settings, such as age, sex, blood immune composition, hemoglobin levels, and others. We developed a model to assess the association of multiple factors with the human methylome and identify the genomic loci significantly impacted by each trait. We demonstrated that DNA methylation variation is accurately modeled by several factors. We confirmed the well-known impact of age and sex and unveiled novel clinical factors associated with DNA methylation, such as blood neutrophils, hemoglobin, red blood cell distribution width, high-density lipoprotein cholesterol, and urea. Genomic regions significantly associated with these traits were enriched in relevant transcription factors, drugs, and diseases. Among our findings, we showed that neutrophil-impacted loci were involved in neutrophil functionality and maturation. Similarly, hemoglobin-influenced sites were associated with several diseases, including aplastic anemia, and the genomic loci affected by urea were related to congenital anomalies of the kidney and urinary tract. Our findings contribute to a better understanding of the human methylome plasticity and provide insights into novel factors shaping DNA methylation patterns, highlighting their potential clinical implications as biomarkers and the importance of considering these physiological traits in future medical epigenomic investigations.NEW & NOTEWORTHY We have developed a quantitative model to assess how the human methylome is associated with several factors and to identify the genomic loci significantly impacted by each trait. We reported novel health-related factors driving DNA methylation patterns and new site-specific regulations that further elucidate methylome dynamics. Our study contributes to a better understanding of the plasticity of the human methylome and unveils novel physiological traits with a potential role in future medical epigenomic investigations.
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Affiliation(s)
- Giulia Protti
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
| | - Tarik Gören
- Emergency Department, Pamukkale University Medical Faculty, Denizli, Turkey
| | - Ramazan Sabirli
- Emergency Department, Bakircay University Faculty of Medicine Cigli Training and Research Hospital, Izmir, Turkey
| | - Serkan Civlan
- Department of Neurosurgery, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Özgür Kurt
- Department of Microbiology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - İbrahim Türkçüer
- Emergency Department, Pamukkale University Medical Faculty, Denizli, Turkey
| | - Aylin Köseler
- Department of Biophysics, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
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Quinn EB, Hsiao CJ, Maisha FM, Mulligan CJ. Prenatal maternal stress is associated with site-specific and age acceleration changes in maternal and newborn DNA methylation. Epigenetics 2023; 18:2222473. [PMID: 37300821 PMCID: PMC10259347 DOI: 10.1080/15592294.2023.2222473] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/10/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
Prenatal maternal stress has a negative impact on child health but the mechanisms through which maternal stress affects child health are unclear. Epigenetic variation, such as DNA methylation, is a likely mechanistic candidate as DNA methylation is sensitive to environmental insults and can regulate long-term changes in gene expression. We recruited 155 mother-newborn dyads in the Democratic Republic of Congo to investigate the effects of maternal stress on DNA methylation in mothers and newborns. We used four measures of maternal stress to capture a range of stressful experiences: general trauma, sexual trauma, war trauma, and chronic stress. We identified differentially methylated positions (DMPs) associated with general trauma, sexual trauma, and war trauma in both mothers and newborns. No DMPs were associated with chronic stress. Sexual trauma was positively associated with epigenetic age acceleration across several epigenetic clocks in mothers. General trauma and war trauma were positively associated with newborn epigenetic age acceleration using the extrinsic epigenetic age clock. We tested the top DMPs for enrichment of DNase I hypersensitive sites (DHS) and found no enrichment in mothers. In newborns, top DMPs associated with war trauma were enriched for DHS in embryonic and foetal cell types. Finally, one of the top DMPs associated with war trauma in newborns also predicted birthweight, completing the cycle from maternal stress to DNA methylation to newborn health outcome. Our results indicate that maternal stress is associated with site-specific changes in DNAm and epigenetic age acceleration in both mothers and newborns.
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Affiliation(s)
- Edward B. Quinn
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Chu J. Hsiao
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- College of Medicine, University of Florida, Gainesville, FL, USA
| | - Felicien M. Maisha
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Democratic Republic of Congo, HEAL Africa Hospital, Goma, USA
- Democratic Republic of Congo, Maisha Institute, Goma, USA
| | - Connie J. Mulligan
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
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Ashokan M, Jayanthi KV, Elango K, Sneha K, Ramesha KP, Reshma RS, Saravanan KA, Naveen KGS. Biological methylation: redefining the link between genotype and phenotype. Anim Biotechnol 2023; 34:3174-3186. [PMID: 35468300 DOI: 10.1080/10495398.2022.2065999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.
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Affiliation(s)
- M Ashokan
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K V Jayanthi
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K Elango
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Kadimetla Sneha
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K P Ramesha
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Raj S Reshma
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kumar G S Naveen
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
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