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Pruszkowska-Przybylska P, Noroozi R, Rudnicka J, Pisarek A, Wronka I, Kobus M, Wysocka B, Ossowski A, Spólnicka M, Wiktorska J, Iljin A, Pośpiech E, Branicki W, Sitek A. Potential Predictor of Epigenetic Age Acceleration in Men: 2D:4D Finger Pattern. Am J Hum Biol 2024:e24151. [PMID: 39243113 DOI: 10.1002/ajhb.24151] [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: 05/20/2024] [Revised: 08/23/2024] [Accepted: 08/24/2024] [Indexed: 09/09/2024] Open
Abstract
OBJECTIVES Second to fourth digit ratio is widely known indicator of prenatal sex hormones proportion. Higher prenatal androgenization results in longer fourth finger and lower 2D:4D index. The aim of this study was to determine whether the 2D:4D digit ratio is associated with DNA methylation (DNAm) age dependently on sex. MATERIAL AND METHODS The study included 182 adults (106 females and 76 males) with a mean age of 51.5 ± 13 years. The investigation consisted of three main parts: a survey, anthropometric dimensions measurements (fingers length) and methylome analysis using collected blood samples. Genome-wide methylation was analyzed using EPIC microarray technology. Epigenetic age and epigenetic age acceleration were calculated using several widely applied algorithms. RESULTS Males with the female left hand pattern had more accelerated epigenetic age than those with the male pattern as calculated with PhenoAge and DNAmTL clocks. CONCLUSIONS Finger female pattern 2D:4D above or equal to 1 in males is associated with epigenetic age acceleration, indicating that prenatal exposure to estrogens in males may be related to aging process in the later ontogenesis.
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Affiliation(s)
| | - Rezvan Noroozi
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Joanna Rudnicka
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Aleksandra Pisarek
- Laboratory of Anthropology, Institute of Zoology and Biomedical Research, Kraków, Poland
| | - Iwona Wronka
- Laboratory of Anthropology, Institute of Zoology and Biomedical Research, Kraków, Poland
| | - Magdalena Kobus
- Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszynski University in Warsaw, Warsaw, Poland
| | - Bożena Wysocka
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | | | | | - Aleksandra Iljin
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Lodz 90-153, Lodz, Poland
| | - Ewelina Pośpiech
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Wojciech Branicki
- Laboratory of Anthropology, Institute of Zoology and Biomedical Research, Kraków, Poland
| | - Aneta Sitek
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
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Zeng H, Wang B, Zhang R, Zhao L, Yang Y, Dong X, Gao Y, Gu C. Association of parent-child discrepancies in educational aspirations with physical fitness, quality of life and school adaptation among adolescents: a multiple mediation model. BMC Public Health 2024; 24:2135. [PMID: 39107725 PMCID: PMC11304611 DOI: 10.1186/s12889-024-19674-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND The global public health issue of diminishing physical fitness among adolescents has gained increasing attention. The impact of parents' negative emotions or pressure regarding adolescents' educational aspirations may have a passive impact on the quality of life and adaptation of adolescents in and out of school, and ultimately harm their physical health. This study aims to explore whether parent-child discrepancies in educational aspirations influence physical fitness in adolescents through school adaptation and quality of life. METHODS Participants consisted of 9,768 students, males 4,753(48.7%), females 5,015(51.3%), aged 11-19 years, males 14.3 ± 1.92, females 14.4 ± 1.93. The educational aspirations were gauged using a six-point scale for expectation scores. Physical fitness assessments were based on criteria from the National Student Physical Fitness and Health Survey. School adaptation was evaluated using the School Social Behaviors Scale-2. Quality of life for adolescents was measured using Chinese version of the Quality of Life Scale for Children and Adolescents. To analyze the multiple mediating effects, structural equation models were used, and 95% confidence intervals were determined through bootstrap methods. RESULTS The results illustrated that school adaptation and quality of life played a significant mediating role in the effect of parent-child discrepancies in educational aspirations and physical fitness. There were three intermediary paths were confirmed: (1) discrepancies in educational aspirations → school adaptation → physical fitness (β=-0.088 SE = 0.021; p<0.01; 95% CI: -0.135, -0.05); (2) discrepancies in educational aspirations → quality of life → physical fitness (β=-0.025; SE = 0.011; p = 0.010; 95% CI: -0.050, -0.006); (3) discrepancies in educational aspirations → school adaptation→ quality of life → physical fitness (β=-0.032; SE = 0.014; p = 0.011; 95% CI: -0.061, -0.007). CONCLUSION This study suggests that parents should reduce negative emotions and pressure regarding adolescents' academic aspirations may help their children get better physical fitness.
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Affiliation(s)
- Hui Zeng
- School of Physical Education, Shandong University, Jinan, 250061, China
| | - Bin Wang
- Shandong Provincial Institute of Education Science, Jinan, 250002, China
| | - Rui Zhang
- School of Physical Education, Shandong University, Jinan, 250061, China
- Jinan Licheng NO.2 High School, Jinan, 250109, China
| | - Liangyu Zhao
- School of Physical Education, Shandong University, Jinan, 250061, China
| | - Yuke Yang
- School of Physical Education, Shandong University, Jinan, 250061, China
| | - Xiaosheng Dong
- Centre for Health Management and Policy Research, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Yan Gao
- School of Physical Education, Shandong University, Jinan, 250061, China
| | - Chenguang Gu
- School of Education, Nanning University, Nanning, 530299, China.
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Gomez-Pinilla F, Thapak P. Exercise epigenetics is fueled by cell bioenergetics: Supporting role on brain plasticity and cognition. Free Radic Biol Med 2024; 220:43-55. [PMID: 38677488 PMCID: PMC11144461 DOI: 10.1016/j.freeradbiomed.2024.04.237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/04/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Exercise has the unique aptitude to benefit overall health of body and brain. Evidence indicates that the effects of exercise can be saved in the epigenome for considerable time to elevate the threshold for various diseases. The action of exercise on epigenetic regulation seems central to building an "epigenetic memory" to influence long-term brain function and behavior. As an intrinsic bioenergetic process, exercise engages the function of the mitochondria and redox pathways to impinge upon molecular mechanisms that regulate synaptic plasticity and learning and memory. We discuss how the action of exercise uses mechanisms of bioenergetics to support a "epigenetic memory" with long-term implications for neural and behavioral plasticity. This information is crucial for directing the power of exercise to reduce the burden of neurological and psychiatric disorders.
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Affiliation(s)
- Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Department of Neurosurgery, UCLA Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Pavan Thapak
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Chen GY, Liu C, Xia Y, Wang PX, Zhao ZY, Li AY, Zhou CQ, Xiang C, Zhang JL, Zeng Y, Gu P, Li H. Effects of walking on epigenetic age acceleration: a Mendelian randomization study. Clin Epigenetics 2024; 16:94. [PMID: 39026267 PMCID: PMC11256679 DOI: 10.1186/s13148-024-01707-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: 03/12/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
INTRODUCTION Walking stands as the most prevalent physical activity in the daily lives of individuals and is closely associated with physical functioning and the aging process. Nonetheless, the precise cause-and-effect connection between walking and aging remains unexplored. The epigenetic clock emerges as the most promising biological indicator of aging, capable of mirroring the biological age of the human body and facilitating an investigation into the association between walking and aging. Our primary objective is to investigate the causal impact of walking with epigenetic age acceleration (EAA). METHODS We conducted a two-sample two-way Mendelian randomization (MR) study to investigate the causal relationship between walking and EAA. Walking and Leisure sedentary behavior data were sourced from UK Biobank, while EAA data were gathered from a total of 28 cohorts. The MR analysis was carried out using several methods, including the inverse variance weighted (IVW), weighted median, MR-Egger, and robust adjusted profile score (RAPS). To ensure the robustness of our findings, we conducted sensitivity analyses, which involved the MR-Egger intercept test, Cochran's Q test, and MR-PRESSO, to account for and mitigate potential pleiotropy. RESULTS The IVW MR results indicate a significant impact of usual walking pace on GrimAge (BETA = - 1.84, 95% CI (- 2.94, - 0.75)), PhenoAge (BETA = - 1.57, 95% CI (- 3.05, - 0.08)), Horvath (BETA = - 1.09 (- 2.14, - 0.04)), and Hannum (BETA = - 1.63, 95% CI (- 2.70, - 0.56)). Usual walking pace is significantly associated with a delay in epigenetic aging acceleration (EAA) (P < 0.05). Moreover, the direction of effect predicted by the gene remained consistent across RAPS outcomes and sensitivity MR analyses. There is a lack of robust causal relationships between other walking conditions, such as walking duration and walking frequency, on EAA (P > 0.05). CONCLUSION Our evidence demonstrates that a higher usual walking pace is associated with a deceleration of the acceleration of all four classical epigenetic clocks acceleration.
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Affiliation(s)
- Guan-Yi Chen
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Chao Liu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Yu Xia
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Ping-Xiao Wang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Zi-Yue Zhao
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Ao-Yu Li
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Chu-Qiao Zhou
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Cheng Xiang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Jia-Lin Zhang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Yi Zeng
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Peng Gu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China
| | - Hui Li
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China.
- Hunan Engineering Laboratory for Orthopedic Biomaterials, Changsha, China.
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Martínez-Magaña JJ, Hurtado-Soriano J, Rivero-Segura NA, Montalvo-Ortiz JL, Garcia-delaTorre P, Becerril-Rojas K, Gomez-Verjan JC. Towards a Novel Frontier in the Use of Epigenetic Clocks in Epidemiology. Arch Med Res 2024; 55:103033. [PMID: 38955096 DOI: 10.1016/j.arcmed.2024.103033] [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: 01/10/2024] [Revised: 05/10/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
Health problems associated with aging are a major public health concern for the future. Aging is a complex process with wide intervariability among individuals. Therefore, there is a need for innovative public health strategies that target factors associated with aging and the development of tools to assess the effectiveness of these strategies accurately. Novel approaches to measure biological age, such as epigenetic clocks, have become relevant. These clocks use non-sequential variable information from the genome and employ mathematical algorithms to estimate biological age based on DNA methylation levels. Therefore, in the present study, we comprehensively review the current status of the epigenetic clocks and their associations across the human phenome. We emphasize the potential utility of these tools in an epidemiological context, particularly in evaluating the impact of public health interventions focused on promoting healthy aging. Our review describes associations between epigenetic clocks and multiple traits across the life and health span. Additionally, we highlighted the evolution of studies beyond mere associations to establish causal mechanisms between epigenetic age and disease. We explored the application of epigenetic clocks to measure the efficacy of interventions focusing on rejuvenation.
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Affiliation(s)
- José Jaime Martínez-Magaña
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; U.S. Department of Veterans Affairs National Center for Post-Traumatic Stress Disorder, Clinical Neuroscience Division, West Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | | | | | - Janitza L Montalvo-Ortiz
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; U.S. Department of Veterans Affairs National Center for Post-Traumatic Stress Disorder, Clinical Neuroscience Division, West Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | - Paola Garcia-delaTorre
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Área de Envejecimiento, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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Koncevičius K, Nair A, Šveikauskaitė A, Šeštokaitė A, Kazlauskaitė A, Dulskas A, Petronis A. Epigenetic age oscillates during the day. Aging Cell 2024; 23:e14170. [PMID: 38638005 PMCID: PMC11258449 DOI: 10.1111/acel.14170] [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: 11/30/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024] Open
Abstract
Since their introduction, epigenetic clocks have been extensively used in aging, human disease, and rejuvenation studies. In this article, we report an intriguing pattern: epigenetic age predictions display a 24-h periodicity. We tested a circadian blood sample collection using 17 epigenetic clocks addressing different aspects of aging. Thirteen clocks exhibited significant oscillations with the youngest and oldest age estimates around midnight and noon, respectively. In addition, daily oscillations were consistent with the changes of epigenetic age across different times of day observed in an independant populational dataset. While these oscillations can in part be attributed to variations in white blood cell type composition, cell count correction methods might not fully resolve the issue. Furthermore, some epigenetic clocks exhibited 24-h periodicity even in the purified fraction of neutrophils pointing at plausible contributions of intracellular epigenomic oscillations. Evidence for circadian variation in epigenetic clocks emphasizes the importance of the time-of-day for obtaining accurate estimates of epigenetic age.
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Affiliation(s)
- Karolis Koncevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
| | - Akhil Nair
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental HealthTorontoOntarioCanada
| | - Aušrinė Šveikauskaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
| | - Agnė Šeštokaitė
- Laboratory for Genetic DiagnosticsNational Cancer InstituteVilniusLithuania
| | - Auksė Kazlauskaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
| | - Audrius Dulskas
- Department of Abdominal and General Surgery and OncologyNational Cancer InstituteVilniusLithuania
- Faculty of MedicineVilnius UniversityVilniusLithuania
| | - Artūras Petronis
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental HealthTorontoOntarioCanada
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Phyo AZZ, Espinoza SE, Murray AM, Fransquet PD, Wrigglesworth J, Woods RL, Ryan J. Epigenetic age acceleration and the risk of frailty, and persistent activities of daily living (ADL) disability. Age Ageing 2024; 53:afae127. [PMID: 38941117 PMCID: PMC11212488 DOI: 10.1093/ageing/afae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Epigenetic ageing is among the most promising ageing biomarkers and may be a useful marker of physical function decline, beyond chronological age. This study investigated whether epigenetic age acceleration (AA) is associated with the change in frailty scores over 7 years and the 7-year risk of incident frailty and persistent Activities of Daily Living (ADL) disability among 560 Australians (50.7% females) aged ≥70 years. METHODS Seven AA indices, including GrimAge, GrimAge2, FitAge and DunedinPACE, were estimated from baseline peripheral-blood DNA-methylation. Frailty was assessed using both the 67-item deficit-accumulation frailty index (FI) and Fried phenotype (Fried). Persistent ADL disability was defined as loss of ability to perform one or more basic ADLs for at least 6 months. Linear mixed models and Cox proportional-hazard regression models were used as appropriate. RESULTS Accelerated GrimAge, GrimAge2, FitAge and DunedinPACE at baseline were associated with increasing FI scores per year (adjusted-Beta ranged from 0.0015 to 0.0021, P < 0.05), and accelerated GrimAge and GrimAge2 were associated with an increased risk of incident FI-defined frailty (adjusted-HRs 1.43 and 1.39, respectively, P < 0.05). The association between DunedinPACE and the change in FI scores was stronger in females (adjusted-Beta 0.0029, P 0.001 than in males (adjusted-Beta 0.0002, P 0.81). DunedinPACE, but not the other AA measures, was also associated with worsening Fried scores (adjusted-Beta 0.0175, P 0.04). No associations were observed with persistent ADL disability. CONCLUSION Epigenetic AA in later life is associated with increasing frailty scores per year and the risk of incident FI-defined frailty.
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Affiliation(s)
- Aung Zaw Zaw Phyo
- Biological Neuropsychiatry & Dementia Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Sara E Espinoza
- Center for Translational Geroscience, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anne M Murray
- Berman Center for Outcomes and Clinical Research, Hennepin HealthCare Research Institute, Minneapolis, MN, USA
- Division of Geriatrics, Department of Medicine, Hennepin HealthCare and University of Minnesota, Minneapolis, MN, USA
| | - Peter D Fransquet
- Biological Neuropsychiatry & Dementia Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
- School of Psychology, Deakin University, Burwood, Melbourne, VIC 3125, Australia
| | - Jo Wrigglesworth
- Biological Neuropsychiatry & Dementia Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Robyn L Woods
- ASPREE Research Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Joanne Ryan
- Biological Neuropsychiatry & Dementia Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
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Kawamura T, Higuchi M, Ito T, Kawakami R, Usui C, McGreevy KM, Horvath S, Zsolt R, Torii S, Suzuki K, Ishii K, Sakamoto S, Oka K, Muraoka I, Tanisawa K. Healthy Japanese dietary pattern is associated with slower biological aging in older men: WASEDA'S health study. Front Nutr 2024; 11:1373806. [PMID: 38854166 PMCID: PMC11157009 DOI: 10.3389/fnut.2024.1373806] [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: 01/20/2024] [Accepted: 05/14/2024] [Indexed: 06/11/2024] Open
Abstract
Aging is the greatest risk factor for numerous diseases and mortality, and establishing geroprotective interventions targeting aging is required. Previous studies have suggested that healthy dietary patterns, such as the Mediterranean diet, are associated with delayed biological aging; however, these associations depend on nationality and sex. Therefore, this study aimed to investigate the relationship between dietary patterns identified through principal component analysis and biological aging in older men of Japan, one of the countries with the longest life expectancies. Principal component analysis identified two dietary patterns: a healthy Japanese dietary pattern and a Western-style dietary pattern. Eight epigenetic clocks, some of the most accurate aging biomarkers, were identified using DNA methylation data from whole-blood samples. Correlation analyses revealed that healthy Japanese dietary patterns were significantly negatively or positively correlated with multiple epigenetic age accelerations (AgeAccel), including AgeAccelGrim, FitAgeAccel, and age-adjusted DNAm-based telomere length (DNAmTLAdjAge). Conversely, the Western-style dietary pattern was observed not to correlate significantly with any of the examined AgeAccels or age-adjusted values. After adjusting for covariates, the healthy Japanese dietary pattern remained significantly positively correlated with DNAmTLAdjAge. Regression analysis showed that healthy Japanese dietary pattern contributed less to epigenetic age acceleration than smoking status. These findings suggest that a Western-style dietary pattern may not be associated with biological aging, whereas a healthy Japanese dietary pattern is associated with delayed biological aging in older Japanese men. Our findings provide evidence that healthy dietary patterns may have mild beneficial effects on delayed biological aging in older Japanese men.
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Affiliation(s)
- Takuji Kawamura
- Waseda Institute for Sport Sciences, Waseda University, Saitama, Japan
- Research Center for Molecular Exercise Science, Hungarian University of Sports Science, Budapest, Hungary
| | - Mitsuru Higuchi
- Faculty of Sport Sciences, Waseda University, Saitama, Japan
| | - Tomoko Ito
- Waseda Institute for Sport Sciences, Waseda University, Saitama, Japan
- Department of Food and Nutrition, Tokyo Kasei University, Tokyo, Japan
| | - Ryoko Kawakami
- Waseda Institute for Sport Sciences, Waseda University, Saitama, Japan
- Physical Fitness Research Institute, Meiji Yasuda Life Foundation of Health and Welfare, Tokyo, Japan
| | - Chiyoko Usui
- Waseda Institute for Sport Sciences, Waseda University, Saitama, Japan
- Center for Liberal Education and Learning, Sophia University, Tokyo, Japan
| | - Kristen M. McGreevy
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, United States
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Altos Labs, San Diego Institute of Science, San Diego, CA, United States
| | - Radak Zsolt
- Research Center for Molecular Exercise Science, Hungarian University of Sports Science, Budapest, Hungary
- Faculty of Sport Sciences, Waseda University, Saitama, Japan
| | - Suguru Torii
- Faculty of Sport Sciences, Waseda University, Saitama, Japan
| | | | - Kaori Ishii
- Faculty of Sport Sciences, Waseda University, Saitama, Japan
| | - Shizuo Sakamoto
- Faculty of Sport Sciences, Waseda University, Saitama, Japan
- Faculty of Sport Science, Surugadai University, Saitama, Japan
| | - Koichiro Oka
- Faculty of Sport Sciences, Waseda University, Saitama, Japan
| | - Isao Muraoka
- Faculty of Sport Sciences, Waseda University, Saitama, Japan
| | - Kumpei Tanisawa
- Faculty of Sport Sciences, Waseda University, Saitama, Japan
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9
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Xu Z, Niu L, Kresovich JK, Taylor JA. methscore: a comprehensive R function for DNA methylation-based health predictors. Bioinformatics 2024; 40:btae302. [PMID: 38702768 PMCID: PMC11105949 DOI: 10.1093/bioinformatics/btae302] [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: 11/10/2023] [Revised: 04/10/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024] Open
Abstract
MOTIVATION DNA methylation-based predictors of various biological metrics have been widely published and are becoming valuable tools in epidemiologic studies of epigenetics and personalized medicine. However, generating these predictors from original source software and web servers is complex and time consuming. Furthermore, different predictors were often derived based on data from different types of arrays, where array differences and batch effects can make predictors difficult to compare across studies. RESULTS We integrate these published methods into a single R function to produce 158 previously published predictors for chronological age, biological age, exposures, lifestyle traits and serum protein levels using both classical and principal component-based methods. To mitigate batch and array differences, we also provide a modified RCP method (ref-RCP) that normalize input DNA methylation data to reference data prior to estimation. Evaluations in real datasets show that this approach improves estimate precision and comparability across studies. AVAILABILITY AND IMPLEMENTATION The function was included in software package ENmix, and is freely available from Bioconductor website (https://www.bioconductor.org/packages/release/bioc/html/ENmix.html).
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Affiliation(s)
- Zongli Xu
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, United States
| | - Liang Niu
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, United States
| | - Jacob K Kresovich
- Departments of Cancer Epidemiology & Breast Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, United States
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, United States
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10
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Bierhoff H. [Genetics, epigenetics, and environmental factors in life expectancy-What role does nature-versus-nurture play in aging?]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2024; 67:521-527. [PMID: 38637469 PMCID: PMC11093831 DOI: 10.1007/s00103-024-03873-x] [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: 11/01/2023] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
In Germany and worldwide, the average age of the population is continuously rising. With this general increase in chronological age, the focus on biological age, meaning the actual health and fitness status, is becoming more and more important. The key question is to what extent the age-related decline in fitness is genetically predetermined or malleable by environmental factors and lifestyle.Many epigenetic studies in aging research have provided interesting insights in this nature-versus-nurture debate. In most model organisms, aging is associated with specific epigenetic changes, which can be countered by certain interventions like moderate caloric restriction or increased physical activity. Since these interventions also have positive effects on lifespan and health, epigenetics appears to be the interface between environmental factors and the aging process. This notion is supported by the fact that an epigenetic drift occurs through the life course of identical twins, which is related to the different manifestations of aging symptoms. Furthermore, biological age can be determined with high precision based on DNA methylation patterns, further emphasizing the importance of epigenetics in aging.This article provides an overview of the importance of genetic and epigenetic parameters for life expectancy. A major focus will be on the possibilities of maintaining a young epigenome through lifestyle and environmental factors, thereby slowing down biological aging.
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Affiliation(s)
- Holger Bierhoff
- Institut für Biochemie und Biophysik, Friedrich-Schiller-Universität Jena, Hans-Knöll-Straße 2, 07745, Jena, Deutschland.
- Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut (FLI), Jena, Deutschland.
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11
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Kuo CL, Chen Z, Liu P, Pilling LC, Atkins JL, Fortinsky RH, Kuchel GA, Diniz BS. Proteomic aging clock (PAC) predicts age-related outcomes in middle-aged and older adults. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.12.19.23300228. [PMID: 38196645 PMCID: PMC10775323 DOI: 10.1101/2023.12.19.23300228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Beyond mere prognostication, optimal biomarkers of aging provide insights into qualitative and quantitative features of biological aging and might, therefore, offer useful information for the testing and, ultimately, clinical use of gerotherapeutics. We aimed to develop a proteomic aging clock (PAC) for all-cause mortality risk as a proxy of biological age. Data were from the UK Biobank Pharma Proteomics Project, including 53,021 participants aged between 39 and 70 years and 2,923 plasma proteins assessed using the Olink Explore 3072 assay®. The Spearman correlation between PAC proteomic age and chronological age was 0.77. A total of 10.9% of the participants died during a mean follow-up of 13.3 years, with the mean age at death 70.1 years. We developed a proteomic aging clock (PAC) for all-cause mortality risk as a surrogate of BA using a combination of least absolute shrinkage and selection operator (LASSO) penalized Cox regression and Gompertz proportional hazards models. PAC showed robust age-adjusted associations and predictions for all-cause mortality and the onset of various diseases in general and disease-free participants. The proteins associated with PAC were enriched in several processes related to the hallmarks of biological aging. Our results expand previous findings by showing that age acceleration, based on PAC, strongly predicts all-cause mortality and several incident disease outcomes. Particularly, it facilitates the evaluation of risk for multiple conditions in a disease-free population, thereby, contributing to the prevention of initial diseases, which vary among individuals and may subsequently lead to additional comorbidities.
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Affiliation(s)
- Chia-Ling Kuo
- Department of Public Health Sciences, University of Connecticut Health Center, Farmington CT, USA
- The Cato T. Laurencin Institute for Regenerative Engineering, University of Connecticut Health Center, Farmington, CT, USA
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
| | - Zhiduo Chen
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
| | - Peiran Liu
- The Cato T. Laurencin Institute for Regenerative Engineering, University of Connecticut Health Center, Farmington, CT, USA
| | - Luke C Pilling
- Epidemiology and Public Health Group, Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - Janice L Atkins
- Epidemiology and Public Health Group, Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - Richard H Fortinsky
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
| | - George A Kuchel
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
| | - Breno S Diniz
- Department of Public Health Sciences, University of Connecticut Health Center, Farmington CT, USA
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
- Department of Psychiatry, University of Connecticut Health Center, Farmington CT, USA
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12
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Noroozi R, Rudnicka J, Pisarek A, Wysocka B, Masny A, Boroń M, Migacz-Gruszka K, Pruszkowska-Przybylska P, Kobus M, Lisman D, Zielińska G, Iljin A, Wiktorska JA, Michalczyk M, Kaczka P, Krzysztofik M, Sitek A, Ossowski A, Spólnicka M, Branicki W, Pośpiech E. Analysis of epigenetic clocks links yoga, sleep, education, reduced meat intake, coffee, and a SOCS2 gene variant to slower epigenetic aging. GeroScience 2024; 46:2583-2604. [PMID: 38103096 PMCID: PMC10828238 DOI: 10.1007/s11357-023-01029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
DNA methylation (DNAm) clocks hold promise for measuring biological age, useful for guiding clinical interventions and forensic identification. This study compared the commonly used DNAm clocks, using DNA methylation and SNP data generated from nearly 1000 human blood or buccal swab samples. We evaluated different preprocessing methods for age estimation, investigated the association of epigenetic age acceleration (EAA) with various lifestyle and sociodemographic factors, and undertook a series of novel genome-wide association analyses for different EAA measures to find associated genetic variants. Our results highlighted the Skin&Blood clock with ssNoob normalization as the most accurate predictor of chronological age. We provided novel evidence for an association between the practice of yoga and a reduction in the pace of aging (DunedinPACE). Increased sleep and physical activity were associated with lower mortality risk score (MRS) in our dataset. University degree, vegetable consumption, and coffee intake were associated with reduced levels of epigenetic aging, whereas smoking, higher BMI, meat consumption, and manual occupation correlated well with faster epigenetic aging, with FitAge, GrimAge, and DunedinPACE clocks showing the most robust associations. In addition, we found a novel association signal for SOCS2 rs73218878 (p = 2.87 × 10-8) and accelerated GrimAge. Our study emphasizes the importance of an optimized DNAm analysis workflow for accurate estimation of epigenetic age, which may influence downstream analyses. The results support the influence of genetic background on EAA. The associated SOCS2 is a member of the suppressor of cytokine signaling family known for its role in human longevity. The reported association between various risk factors and EAA has practical implications for the development of health programs to improve quality of life and reduce premature mortality associated with age-related diseases.
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Affiliation(s)
- Rezvan Noroozi
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joanna Rudnicka
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aleksandra Pisarek
- Institute of Zoology and Biomedical Research of the Jagiellonian University, Krakow, Poland
| | - Bożena Wysocka
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | | | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | | | | | - Magdalena Kobus
- Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszynski University in Warsaw, Warsaw, Poland
| | - Dagmara Lisman
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Grażyna Zielińska
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Aleksandra Iljin
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Lodz, Lodz, Poland
| | | | - Małgorzata Michalczyk
- Department of Sport Nutrition, The Jerzy Kukuczka Academy of Physical Education in Katowice, Katowice, Poland
| | - Piotr Kaczka
- Department of Sport Nutrition, The Jerzy Kukuczka Academy of Physical Education in Katowice, Katowice, Poland
| | - Michał Krzysztofik
- Department of Sport Nutrition, The Jerzy Kukuczka Academy of Physical Education in Katowice, Katowice, Poland
| | - Aneta Sitek
- Department of Anthropology, University of Lodz, Lodz, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | | | - Wojciech Branicki
- Institute of Zoology and Biomedical Research of the Jagiellonian University, Krakow, Poland
- Institute of Forensic Research, Krakow, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.
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13
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Torma F, Kerepesi C, Jókai M, Babszki G, Koltai E, Ligeti B, Kalcsevszki R, McGreevy KM, Horvath S, Radák Z. Alterations of the gut microbiome are associated with epigenetic age acceleration and physical fitness. Aging Cell 2024; 23:e14101. [PMID: 38414315 PMCID: PMC11019127 DOI: 10.1111/acel.14101] [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: 10/23/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Epigenetic clocks can measure aging and predict the incidence of diseases and mortality. Higher levels of physical fitness are associated with a slower aging process and a healthier lifespan. Microbiome alterations occur in various diseases and during the aging process, yet their relation to epigenetic clocks is not explored. To fill this gap, we collected metagenomic (from stool), epigenetic (from blood), and exercise-related data from physically active individuals and, by applying epigenetic clocks, we examined the relationship between gut flora, blood-based epigenetic age acceleration, and physical fitness. We revealed that an increased entropy in the gut microbiome of physically active middle-aged/old individuals is associated with accelerated epigenetic aging, decreased fitness, or impaired health status. We also observed that a slower epigenetic aging and higher fitness level can be linked to altered abundance of some bacterial species often linked to anti-inflammatory effects. Overall our data suggest that alterations in the microbiome can be associated with epigenetic age acceleration and physical fitness.
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Affiliation(s)
- Ferenc Torma
- Research Institute of Sport ScienceHungarian University of Sport ScienceBudapestHungary
- Sports Neuroscience Division, Advanced Research Initiative for Human High Performance (ARIHHP), Faculty of Health and Sport SciencesUniversity of TsukubaTsukubaIbarakiJapan
- Laboratory of Exercise Biochemistry and Neuroendocrinology, Faculty of Health and Sport SciencesUniversity of TsukubaTsukubaIbarakiJapan
| | - Csaba Kerepesi
- Institute for Computer Science and Control (SZTAKI)Hungarian Research Network (HUN‐REN)BudapestHungary
| | - Mátyás Jókai
- Research Institute of Sport ScienceHungarian University of Sport ScienceBudapestHungary
| | - Gergely Babszki
- Research Institute of Sport ScienceHungarian University of Sport ScienceBudapestHungary
| | - Erika Koltai
- Research Institute of Sport ScienceHungarian University of Sport ScienceBudapestHungary
| | - Balázs Ligeti
- Faculty of Information Technology and BionicsPázmány Péter Catholic UniversityBudapestHungary
| | - Regina Kalcsevszki
- Faculty of Information Technology and BionicsPázmány Péter Catholic UniversityBudapestHungary
| | - Kristen M. McGreevy
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Altos Labs, Cambridge Institute of ScienceCambridgeUK
| | - Zsolt Radák
- Research Institute of Sport ScienceHungarian University of Sport ScienceBudapestHungary
- Waseda UniversityTokorozawaJapan
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14
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de Lima Camillo LP. pyaging: a Python-based compendium of GPU-optimized aging clocks. Bioinformatics 2024; 40:btae200. [PMID: 38603598 PMCID: PMC11058068 DOI: 10.1093/bioinformatics/btae200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/28/2024] [Accepted: 04/09/2024] [Indexed: 04/13/2024] Open
Abstract
MOTIVATION Aging is intricately linked to diseases and mortality. It is reflected in molecular changes across various tissues which can be leveraged for the development of biomarkers of aging using machine learning models, known as aging clocks. Despite advancements in the field, a significant challenge remains: the lack of robust, Python-based software tools for integrating and comparing these diverse models. This gap highlights the need for comprehensive solutions that can handle the complexity and variety of data in aging research. RESULTS To address this gap, I introduce pyaging, a comprehensive open-source Python package designed to facilitate aging research. pyaging harmonizes dozens of aging clocks, covering a range of molecular data types such as DNA methylation, transcriptomics, histone mark ChIP-Seq, and ATAC-Seq. The package is not limited to traditional model types; it features a diverse array, from linear and principal component models to neural networks and automatic relevance determination models. Thanks to a PyTorch-based backend that enables GPU acceleration, pyaging is capable of rapid inference, even when dealing with large datasets and complex models. In addition, the package's support for multi-species analysis extends its utility across various organisms, including humans, various mammals, and Caenorhabditis elegans. AVAILABILITY AND IMPLEMENTATION pyaging is accessible on GitHub, at https://github.com/rsinghlab/pyaging, and the distribution is available on PyPi, at https://pypi.org/project/pyaging/. The software is also archived on Zenodo, at https://zenodo.org/doi/10.5281/zenodo.10335011.
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15
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Ungvari Z, Tabák AG, Adany R, Purebl G, Kaposvári C, Fazekas-Pongor V, Csípő T, Szarvas Z, Horváth K, Mukli P, Balog P, Bodizs R, Ujma P, Stauder A, Belsky DW, Kovács I, Yabluchanskiy A, Maier AB, Moizs M, Östlin P, Yon Y, Varga P, Vokó Z, Papp M, Takács I, Vásárhelyi B, Torzsa P, Ferdinandy P, Csiszar A, Benyó Z, Szabó AJ, Dörnyei G, Kivimäki M, Kellermayer M, Merkely B. The Semmelweis Study: a longitudinal occupational cohort study within the framework of the Semmelweis Caring University Model Program for supporting healthy aging. GeroScience 2024; 46:191-218. [PMID: 38060158 PMCID: PMC10828351 DOI: 10.1007/s11357-023-01018-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/11/2023] [Indexed: 12/08/2023] Open
Abstract
The Semmelweis Study is a prospective occupational cohort study that seeks to enroll all employees of Semmelweis University (Budapest, Hungary) aged 25 years and older, with a population of 8866 people, 70.5% of whom are women. The study builds on the successful experiences of the Whitehall II study and aims to investigate the complex relationships between lifestyle, environmental, and occupational risk factors, and the development and progression of chronic age-associated diseases. An important goal of the Semmelweis Study is to identify groups of people who are aging unsuccessfully and therefore have an increased risk of developing age-associated diseases. To achieve this, the study takes a multidisciplinary approach, collecting economic, social, psychological, cognitive, health, and biological data. The Semmelweis Study comprises a baseline data collection with open healthcare data linkage, followed by repeated data collection waves every 5 years. Data are collected through computer-assisted self-completed questionnaires, followed by a physical health examination, physiological measurements, and the assessment of biomarkers. This article provides a comprehensive overview of the Semmelweis Study, including its origin, context, objectives, design, relevance, and expected contributions.
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Affiliation(s)
- Zoltan Ungvari
- International Training Program in Geroscience/Healthy Aging Program, Doctoral School of Basic and Translational Medicine/Department of Public Health, Semmelweis University, Budapest, Hungary.
- Vascular Cognitive Impairment, Neurodegeneration and Healthy Brain Aging Program, Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Health Promotion Sciences, The Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Adam G Tabák
- International Training Program in Geroscience/Healthy Aging Program, Doctoral School of Basic and Translational Medicine/Department of Public Health, Semmelweis University, Budapest, Hungary
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- UCL Brain Sciences, University College London, London, UK
- Department of Internal Medicine and Oncology, Semmelweis University, Faculty of Medicine, Budapest, Hungary
| | - Roza Adany
- International Training Program in Geroscience/Healthy Aging Program, Doctoral School of Basic and Translational Medicine/Department of Public Health, Semmelweis University, Budapest, Hungary
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- HUN-REN-UD Public Health Research Group, Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - György Purebl
- Institute of Behavioral Sciences, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Csilla Kaposvári
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Vince Fazekas-Pongor
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Tamás Csípő
- International Training Program in Geroscience/Healthy Aging Program, Doctoral School of Basic and Translational Medicine/Department of Public Health, Semmelweis University, Budapest, Hungary
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Zsófia Szarvas
- International Training Program in Geroscience/Healthy Aging Program, Doctoral School of Basic and Translational Medicine/Department of Public Health, Semmelweis University, Budapest, Hungary
- Vascular Cognitive Impairment, Neurodegeneration and Healthy Brain Aging Program, Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Health Promotion Sciences, The Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Krisztián Horváth
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Peter Mukli
- International Training Program in Geroscience/Healthy Aging Program, Doctoral School of Basic and Translational Medicine/Department of Public Health, Semmelweis University, Budapest, Hungary
- Vascular Cognitive Impairment, Neurodegeneration and Healthy Brain Aging Program, Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Piroska Balog
- Institute of Behavioral Sciences, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Robert Bodizs
- Institute of Behavioral Sciences, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Peter Ujma
- Institute of Behavioral Sciences, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Adrienne Stauder
- Institute of Behavioral Sciences, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Daniel W Belsky
- Robert N. Butler Columbia Aging Center, Columbia University, New York, NY, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Illés Kovács
- Department of Ophthalmology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Department of Ophthalmology, Weill Cornell Medical College, New York City, NY, USA
- Department of Clinical Ophthalmology, Faculty of Health Sciences, Semmelweis University, Budapest, Hungary
| | - Andriy Yabluchanskiy
- Vascular Cognitive Impairment, Neurodegeneration and Healthy Brain Aging Program, Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Health Promotion Sciences, The Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Andrea B Maier
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Centre for Healthy Longevity, National University Health System, Singapore, Singapore
- Department of Human Movement Sciences, @AgeAmsterdam, Vrije Universiteit, Amsterdam Movement Sciences, Amsterdam, The Netherlands
| | - Mariann Moizs
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Ministry of Interior of Hungary, Budapest, Hungary
| | | | - Yongjie Yon
- WHO Regional Office for Europe, Copenhagen, Denmark
| | - Péter Varga
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Clinical Center, Semmelweis University, Budapest, Hungary
| | - Zoltán Vokó
- Center for Health Technology Assessment, Semmelweis University, Budapest, Hungary
| | - Magor Papp
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - István Takács
- UCL Brain Sciences, University College London, London, UK
| | - Barna Vásárhelyi
- Department of Laboratory Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Torzsa
- Department of Family Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Anna Csiszar
- Vascular Cognitive Impairment, Neurodegeneration and Healthy Brain Aging Program, Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Health Promotion Sciences, The Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Zoltán Benyó
- Department of Translational Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- HUN-REN-SU Cerebrovascular and Neurocognitive Diseases Research Group, Budapest, Hungary
| | - Attila J Szabó
- First Department of Pediatrics, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- HUN-REN-SU Pediatrics and Nephrology Research Group, Semmelweis University, Budapest, Hungary
| | - Gabriella Dörnyei
- Department of Morphology and Physiology, Faculty of Health Sciences, Semmelweis University, Budapest, Hungary
| | - Mika Kivimäki
- UCL Brain Sciences, University College London, London, UK
| | - Miklos Kellermayer
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Bela Merkely
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary
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16
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Kawamura T, Radak Z, Tabata H, Akiyama H, Nakamura N, Kawakami R, Ito T, Usui C, Jokai M, Torma F, Kim H, Miyachi M, Torii S, Suzuki K, Ishii K, Sakamoto S, Oka K, Higuchi M, Muraoka I, McGreevy KM, Horvath S, Tanisawa K. Associations between cardiorespiratory fitness and lifestyle-related factors with DNA methylation-based ageing clocks in older men: WASEDA'S Health Study. Aging Cell 2024; 23:e13960. [PMID: 37584423 PMCID: PMC10776125 DOI: 10.1111/acel.13960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/17/2023] Open
Abstract
DNA methylation-based age estimators (DNAm ageing clocks) are currently one of the most promising biomarkers for predicting biological age. However, the relationships between cardiorespiratory fitness (CRF), measured directly by expiratory gas analysis, and DNAm ageing clocks are largely unknown. We investigated the relationships between CRF and the age-adjusted value from the residuals of the regression of DNAm ageing clock to chronological age (DNAmAgeAcceleration: DNAmAgeAccel) and attempted to determine the relative contribution of CRF to DNAmAgeAccel in the presence of other lifestyle factors. DNA samples from 144 Japanese men aged 65-72 years were used to appraise first- (i.e., DNAmHorvath and DNAmHannum) and second- (i.e., DNAmPhenoAge, DNAmGrimAge, and DNAmFitAge) generation DNAm ageing clocks. Various surveys and measurements were conducted, including physical fitness, body composition, blood biochemical parameters, nutrient intake, smoking, alcohol consumption, disease status, sleep status, and chronotype. Both oxygen uptake at ventilatory threshold (VO2 /kg at VT) and peak oxygen uptake (VO2 /kg at Peak) showed a significant negative correlation with GrimAgeAccel, even after adjustments for chronological age and smoking and drinking status. Notably, VO2 /kg at VT and VO2 /kg at Peak above the reference value were also associated with delayed GrimAgeAccel. Multiple regression analysis showed that calf circumference, serum triglyceride, carbohydrate intake, and smoking status, rather than CRF, contributed more to GrimAgeAccel and FitAgeAccel. In conclusion, although the contribution of CRF to GrimAgeAccel and FitAgeAccel is relatively low compared to lifestyle-related factors such as smoking, the results suggest that the maintenance of CRF is associated with delayed biological ageing in older men.
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Affiliation(s)
- Takuji Kawamura
- Waseda Institute for Sport Sciences, Waseda UniversitySaitamaJapan
- Research Centre for Molecular Exercise ScienceHungarian University of Sports ScienceBudapestHungary
| | - Zsolt Radak
- Research Centre for Molecular Exercise ScienceHungarian University of Sports ScienceBudapestHungary
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | - Hiroki Tabata
- Waseda Institute for Sport Sciences, Waseda UniversitySaitamaJapan
- Sportology CentreJuntendo University Graduate School of MedicineTokyoJapan
| | - Hiroshi Akiyama
- Graduate School of Sport SciencesWaseda UniversitySaitamaJapan
| | | | - Ryoko Kawakami
- Waseda Institute for Sport Sciences, Waseda UniversitySaitamaJapan
- Physical Fitness Research Institute, Meiji Yasuda Life Foundation of Health and WelfareTokyoJapan
| | - Tomoko Ito
- Waseda Institute for Sport Sciences, Waseda UniversitySaitamaJapan
- Department of Food and NutritionTokyo Kasei UniversityTokyoJapan
| | - Chiyoko Usui
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | - Matyas Jokai
- Research Centre for Molecular Exercise ScienceHungarian University of Sports ScienceBudapestHungary
| | - Ferenc Torma
- Faculty of Health and Sport SciencesUniversity of TsukubaIbarakiJapan
| | - Hyeon‐Ki Kim
- Research Centre for Molecular Exercise ScienceHungarian University of Sports ScienceBudapestHungary
| | | | - Suguru Torii
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | | | - Kaori Ishii
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | - Shizuo Sakamoto
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
- Faculty of Sport ScienceSurugadai UniversitySaitamaJapan
| | - Koichiro Oka
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | | | - Isao Muraoka
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | - Kristen M. McGreevy
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Department of Human Genetics, David Geffen School of MedicineUniversity of California Los AngelesLos AngelesCaliforniaUSA
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17
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Radak Z, Pan L, Zhou L, Mozaffaritabar S, Gu Y, A Pinho R, Zheng X, Ba X, Boldogh I. Epigenetic and "redoxogenetic" adaptation to physical exercise. Free Radic Biol Med 2024; 210:65-74. [PMID: 37977212 DOI: 10.1016/j.freeradbiomed.2023.11.005] [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: 10/04/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Exercise-induced adaptation is achieved by altering the epigenetic landscape of the entire genome leading to the expression of genes involved in various processes including regulatory, metabolic, adaptive, immune, and myogenic functions. Clinical and experimental data suggest that the methylation pattern/levels of promoter/enhancer is not linearly correlated with gene expression and proteome levels during physical activity implying a level of complexity and interplay with other regulatory modulators. It has been shown that a higher level of physical fitness is associated with a slower DNA methylation-based aging clock. There is strong evidence supporting exercise-induced ROS being a key regulatory mediator through overlapping events, both as signaling entities and through oxidative modifications to various protein mediators and DNA molecules. ROS generated by physical activity shapes epigenome both directly and indirectly, a complexity we are beginning to unravel within the epigenetic arrangement. Oxidative modification of guanine to 8-oxoguanine is a non-genotoxic alteration, does not distort DNA helix and serves as an epigenetic-like mark. The reader and eraser of oxidized guanine is the 8-oxoguanine DNA glycosylase 1, contributing to changes in gene expression. In fact, it can modulate methylation patterns of promoters/enhancers consequently leading to multiple phenotypic changes. Here, we provide evidence and discuss the potential roles of exercise-induced ROS in altering cytosine methylation patterns during muscle adaptation processes.
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Affiliation(s)
- Zsolt Radak
- Research Center for Molecular Exercise Science, Hungarian University of Sport Science, 1123, Budapest, Hungary; Faculty of Sport Sciences, Waseda University, Tokorozawa, 359-1192, Japan.
| | - Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
| | - Lei Zhou
- Research Center for Molecular Exercise Science, Hungarian University of Sport Science, 1123, Budapest, Hungary
| | - Soroosh Mozaffaritabar
- Research Center for Molecular Exercise Science, Hungarian University of Sport Science, 1123, Budapest, Hungary
| | - Yaodong Gu
- Faculty of Sports Science, Ningbo University, Ningbo, China
| | - Ricardo A Pinho
- Laboratory of Exercise Biochemistry in Health, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Xu Zheng
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, Jilin, China; Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, Jilin, China; Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
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18
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Yu D, Li M, Linghu G, Hu Y, Hajdarovic KH, Wang A, Singh R, Webb AE. CellBiAge: Improved single-cell age classification using data binarization. Cell Rep 2023; 42:113500. [PMID: 38032797 PMCID: PMC10791072 DOI: 10.1016/j.celrep.2023.113500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Aging is a major risk factor for many diseases. Accurate methods for predicting age in specific cell types are essential to understand the heterogeneity of aging and to assess rejuvenation strategies. However, classifying organismal age at single-cell resolution using transcriptomics is challenging due to sparsity and noise. Here, we developed CellBiAge, a robust and easy-to-implement machine learning pipeline, to classify the age of single cells in the mouse brain using single-cell transcriptomics. We show that binarization of gene expression values for the top highly variable genes significantly improved test performance across different models, techniques, sexes, and brain regions, with potential age-related genes identified for model prediction. Additionally, we demonstrate CellBiAge's ability to capture exercise-induced rejuvenation in neural stem cells. This study provides a broadly applicable approach for robust classification of organismal age of single cells in the mouse brain, which may aid in understanding the aging process and evaluating rejuvenation methods.
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Affiliation(s)
- Doudou Yu
- Molecular Biology, Cell Biology, and Biochemistry Graduate Program, Brown University, Providence, RI 02912, USA; Data Science Institute, Brown University, Providence, RI 02912, USA
| | - Manlin Li
- Data Science Institute, Brown University, Providence, RI 02912, USA
| | - Guanjie Linghu
- Data Science Institute, Brown University, Providence, RI 02912, USA
| | - Yihuan Hu
- Data Science Institute, Brown University, Providence, RI 02912, USA
| | | | - An Wang
- Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ritambhara Singh
- Department of Computer Science, Brown University, Providence, RI 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.
| | - Ashley E Webb
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA; Center on the Biology of Aging, Brown University, Providence, RI 02912, USA; Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA; Center for Translational Neuroscience, Brown University, Providence, RI 02912, USA.
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19
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Cuomo M, Coretti L, Costabile D, Della Monica R, De Riso G, Buonaiuto M, Trio F, Bravaccio C, Visconti R, Berni Canani R, Chiariotti L, Lembo F. Host fecal DNA specific methylation signatures mark gut dysbiosis and inflammation in children affected by autism spectrum disorder. Sci Rep 2023; 13:18197. [PMID: 37875530 PMCID: PMC10598023 DOI: 10.1038/s41598-023-45132-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
The gut-brain axis involves several bidirectional pathway communications including microbiome, bacterial metabolites, neurotransmitters as well as immune system and is perturbed both in brain and in gastrointestinal disorders. Consistently, microbiota-gut-brain axis has been found altered in autism spectrum disorder (ASD). We reasoned that such alterations occurring in ASD may impact both on methylation signatures of human host fecal DNA (HFD) and possibly on the types of human cells shed in the stools from intestinal tract giving origin to HFD. To test this hypothesis, we have performed whole genome methylation analysis of HFD from an age-restricted cohort of young children with ASD (N = 8) and healthy controls (N = 7). In the same cohort we have previously investigated the fecal microbiota composition and here we refined such analysis and searched for eventual associations with data derived from HFD methylome analysis. Our results showed that specific epigenetic signatures in human fecal DNA, especially at genes related to inflammation, associated with the disease. By applying methylation-based deconvolution algorithm, we found that the HFD derived mainly from immune cells and the relative abundance of those differed between patients and controls. Consistently, most of differentially methylated regions fitted with genes involved in inflammatory response. Interestingly, using Horvath epigenetic clock, we found that ASD affected children showed both epigenetic and microbiota age accelerated. We believe that the present unprecedented approach may be useful for the identification of the ASD associated HFD epigenetic signatures and may be potentially extended to other brain disorders and intestinal inflammatory diseases.
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Affiliation(s)
- Mariella Cuomo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy
| | - Lorena Coretti
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano 49, 80131, Naples, Italy
| | - Davide Costabile
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy
- SEMM-European School of Molecular Medicine, University of Naples "Federico II", Naples, Italy
| | - Rosa Della Monica
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy
| | - Giulia De Riso
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy
| | - Michela Buonaiuto
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy
| | - Federica Trio
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy
| | - Carmela Bravaccio
- Department of Translational Medical Science - Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Roberta Visconti
- Institute for the Experimental Endocrinology and Oncology "G. Salvatore", Italian National Council of Research, Via S. Pansini 5, 80131, Naples, Italy
| | - Roberto Berni Canani
- Department of Translational Medical Science - Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Lorenzo Chiariotti
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy.
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy.
- SEMM-European School of Molecular Medicine, University of Naples "Federico II", Naples, Italy.
| | - Francesca Lembo
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano 49, 80131, Naples, Italy.
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20
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Chen Q, Dwaraka VB, Carreras-Gallo N, Mendez K, Chen Y, Begum S, Kachroo P, Prince N, Went H, Mendez T, Lin A, Turner L, Moqri M, Chu SH, Kelly RS, Weiss ST, Rattray NJ, Gladyshev VN, Karlson E, Wheelock C, Mathé EA, Dahlin A, McGeachie MJ, Smith R, Lasky-Su JA. OMICmAge: An integrative multi-omics approach to quantify biological age with electronic medical records. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562114. [PMID: 37904959 PMCID: PMC10614756 DOI: 10.1101/2023.10.16.562114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Biological aging is a multifactorial process involving complex interactions of cellular and biochemical processes that is reflected in omic profiles. Using common clinical laboratory measures in ~30,000 individuals from the MGB-Biobank, we developed a robust, predictive biological aging phenotype, EMRAge, that balances clinical biomarkers with overall mortality risk and can be broadly recapitulated across EMRs. We then applied elastic-net regression to model EMRAge with DNA-methylation (DNAm) and multiple omics, generating DNAmEMRAge and OMICmAge, respectively. Both biomarkers demonstrated strong associations with chronic diseases and mortality that outperform current biomarkers across our discovery (MGB-ABC, n=3,451) and validation (TruDiagnostic, n=12,666) cohorts. Through the use of epigenetic biomarker proxies, OMICmAge has the unique advantage of expanding the predictive search space to include epigenomic, proteomic, metabolomic, and clinical data while distilling this in a measure with DNAm alone, providing opportunities to identify clinically-relevant interconnections central to the aging process.
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Affiliation(s)
- Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Kevin Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Yulu Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Sofina Begum
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicole Prince
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Aaron Lin
- TruDiagnostic, Inc., Lexington, KY USA
| | | | - Mahdi Moqri
- Division of Genetics, Dept. of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Su H. Chu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Rachel S. Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicholas J.W Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde, Glasgow, UK
| | - Vadim N. Gladyshev
- Division of Genetics, Dept. of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Karlson
- Department of Personalized Medicine, Mass General Brigham and Harvard Medical School, Boston, MA, USA
| | - Craig Wheelock
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Ewy A. Mathé
- Division of Preclinical Innovation, National Center for Advancing Translational Science, National Institutes of Health, Rockville, MD, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michae J. McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Jessica A. Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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21
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Naue J. Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications. Genes Genomics 2023; 45:1239-1261. [PMID: 37253906 PMCID: PMC10504122 DOI: 10.1007/s13258-023-01392-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals. OBJECTIVE This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application. METHODS The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics. CONCLUSION The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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22
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Jokai M, Torma F, McGreevy KM, Koltai E, Bori Z, Babszki G, Bakonyi P, Gombos Z, Gyorgy B, Aczel D, Toth L, Osvath P, Fridvalszky M, Teglas T, Posa A, Kujach S, Olek R, Kawamura T, Seki Y, Suzuki K, Tanisawa K, Goto S, Kerepesi C, Boldogh I, Ba X, Davies KJA, Horvath S, Radak Z. DNA methylation clock DNAmFitAge shows regular exercise is associated with slower aging and systemic adaptation. GeroScience 2023; 45:2805-2817. [PMID: 37209203 PMCID: PMC10643800 DOI: 10.1007/s11357-023-00826-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/10/2023] [Indexed: 05/22/2023] Open
Abstract
DNAmPhenoAge, DNAmGrimAge, and the newly developed DNAmFitAge are DNA methylation (DNAm)-based biomarkers that reflect the individual aging process. Here, we examine the relationship between physical fitness and DNAm-based biomarkers in adults aged 33-88 with a wide range of physical fitness (including athletes with long-term training history). Higher levels of VO2max (ρ = 0.2, p = 6.4E - 4, r = 0.19, p = 1.2E - 3), Jumpmax (p = 0.11, p = 5.5E - 2, r = 0.13, p = 2.8E - 2), Gripmax (ρ = 0.17, p = 3.5E - 3, r = 0.16, p = 5.6E - 3), and HDL levels (ρ = 0.18, p = 1.95E - 3, r = 0.19, p = 1.1E - 3) are associated with better verbal short-term memory. In addition, verbal short-term memory is associated with decelerated aging assessed with the new DNAm biomarker FitAgeAcceleration (ρ: - 0.18, p = 0.0017). DNAmFitAge can distinguish high-fitness individuals from low/medium-fitness individuals better than existing DNAm biomarkers and estimates a younger biological age in the high-fit males and females (1.5 and 2.0 years younger, respectively). Our research shows that regular physical exercise contributes to observable physiological and methylation differences which are beneficial to the aging process. DNAmFitAge has now emerged as a new biological marker of quality of life.
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Affiliation(s)
- Matyas Jokai
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Ferenc Torma
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
- Sports Neuroscience Division, Advanced Research Initiative for Human High Performance (ARIHHP), Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Tsukuba, 305-8574, Japan
- Laboratory of Exercise Biochemistry and Neuroendocrinology, Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Tsukuba, 305-8574, Japan
| | - Kristen M McGreevy
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Erika Koltai
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Zoltan Bori
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Gergely Babszki
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Peter Bakonyi
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Zoltan Gombos
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Bernadett Gyorgy
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Dora Aczel
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Laszlo Toth
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Peter Osvath
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Marcell Fridvalszky
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Timea Teglas
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Aniko Posa
- Interdisciplinary Excellence Center, Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, 6700, Szeged, Hungary
| | - Sylwester Kujach
- Department of Physiology, Faculty of Physical Education, Gdansk University of Physical Education and Sport, Gdańsk, Poland
| | - Robert Olek
- Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Poland
| | - Takuji Kawamura
- Faculty of Sport Sciences, Waseda University, Tokorozawa, 2-579-15, Japan
| | - Yasuhiro Seki
- Faculty of Sport Sciences, Waseda University, Tokorozawa, 2-579-15, Japan
| | - Katsuhiko Suzuki
- Faculty of Sport Sciences, Waseda University, Tokorozawa, 2-579-15, Japan
| | - Kumpei Tanisawa
- Faculty of Sport Sciences, Waseda University, Tokorozawa, 2-579-15, Japan
| | - Sataro Goto
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary
| | - Csaba Kerepesi
- Institute for Computer Science and Control (SZTAKI), Eötvös Loránd Research Network, Budapest, Hungary
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin, China
| | - Kelvin J A Davies
- Ethel Percy Andrus Gerontology Centre of the Leonard Davis School of Gerontology; Division of Molecular & Computational Biology, Department of Biological Sciences, of the Dornsife College of Letters, Arts, and Sciences; and Department of Biochemistry & Molecular Medicine of the USC Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089-0191, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Zsolt Radak
- Research Institute of Sport Science, Hungarian University of Sport Science, Budapest, Hungary.
- Faculty of Sport Sciences, Waseda University, Tokorozawa, 2-579-15, Japan.
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23
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Pośpiech E, Pisarek A, Rudnicka J, Noroozi R, Boroń M, Masny A, Wysocka B, Migacz-Gruszka K, Lisman D, Pruszkowska-Przybylska P, Kobus M, Szargut M, Dowejko J, Stanisz K, Zacharczuk J, Zieliński P, Sitek A, Ossowski A, Spólnicka M, Branicki W. Introduction of a multiplex amplicon sequencing assay to quantify DNA methylation in target cytosine markers underlying four selected epigenetic clocks. Clin Epigenetics 2023; 15:128. [PMID: 37563670 PMCID: PMC10416531 DOI: 10.1186/s13148-023-01545-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND DNA methylation analysis has proven to be a powerful tool for age assessment. However, the implementation of epigenetic age prediction in diagnostics or routine forensic casework requires appropriate laboratory methods. In this study, we aimed to compare the performance of large-scale DNA methylation analysis protocols that show promise in terms of accuracy, throughput, multiplexing capacity, and high sensitivity. RESULTS The protocols were designed to target a predefined panel of 161 genomic CG/CA sites from four known estimators of epigenetic age-related parameters, optimized and validated using artificially methylated controls or blood samples. We successfully targeted 96% of these loci using two enrichment protocols: Ion AmpliSeq™, an amplicon-based method integrated with Ion Torrent S5, and SureSelectXT Methyl-Seq, a hybridization-based method followed by MiSeq FGx sequencing. Both protocols demonstrated high accuracy and robustness. Although hybridization assays have greater multiplexing capabilities, the best overall performance was observed for the amplicon-based protocol with the lowest variability in DNA methylation at 25 ng of starting DNA, mean observed marker coverage of ~ 6.7 k reads, and accuracy of methylation quantification with a mean absolute difference between observed and expected methylation beta value of 0.054. The Ion AmpliSeq method correlated strongly with genome-scale EPIC microarray data (R = 0.91) and showed superiority in terms of methylation measurement accuracy. Method-to-method bias was accounted for by the use of linear transformation, which provided a highly accurate prediction of calendar age with a mean absolute error of less than 5 years for the VISAGE and Hannum age clocks used. The pace of aging (PoAm) and the mortality risk score (MRS) estimators included in our panel represent next-generation clocks, were found to have low to moderate correlations with the VISAGE and Hannum models (R < 0.75), and thus may capture different aspects of epigenetic aging. CONCLUSIONS We propose a laboratory tool that allows the quantification of DNA methylation in cytosines underlying four different clocks, thus providing broad information on epigenetic aging while maintaining a reasonable number of CpG markers, opening the way to a wide range of applications in forensics, medicine, and healthcare.
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Affiliation(s)
- Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.
| | - Aleksandra Pisarek
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Joanna Rudnicka
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | | | - Bożena Wysocka
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Kamila Migacz-Gruszka
- Department of Dermatology, Collegium Medicum of the Jagiellonian University, Krakow, Poland
| | - Dagmara Lisman
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | | | - Magdalena Kobus
- Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszynski University in Warsaw, Warsaw, Poland
| | - Maria Szargut
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Joanna Dowejko
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Kamila Stanisz
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Julia Zacharczuk
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Aneta Sitek
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | | | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
- Institute of Forensic Research, Krakow, Poland
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