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Tao X, Zhu Z, Wang L, Li C, Sun L, Wang W, Gong W. Biomarkers of Aging and Relevant Evaluation Techniques: A Comprehensive Review. Aging Dis 2024; 15:977-1005. [PMID: 37611906 PMCID: PMC11081160 DOI: 10.14336/ad.2023.00808-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023] Open
Abstract
The risk of developing chronic illnesses and disabilities is increasing with age. To predict and prevent aging, biomarkers relevant to the aging process must be identified. This paper reviews the known molecular, cellular, and physiological biomarkers of aging. Moreover, we discuss the currently available technologies for identifying these biomarkers, and their applications and potential in aging research. We hope that this review will stimulate further research and innovation in this emerging and fast-growing field.
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Affiliation(s)
- Xue Tao
- Department of Research, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China.
| | - Ziman Zhu
- Beijing Rehabilitation Medicine Academy, Capital Medical University, Beijing, China.
| | - Liguo Wang
- Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
| | - Chunlin Li
- School of Biomedical Engineering, Capital Medical University, Beijing, China.
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China.
| | - Liwei Sun
- School of Biomedical Engineering, Capital Medical University, Beijing, China.
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China.
| | - Wei Wang
- Department of Rehabilitation Radiology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China.
| | - Weijun Gong
- Department of Neurological Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China.
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Jackson P, Kempf MC, Goodin BR, A. Hidalgo B, Aroke EN. Neighborhood Environment and Epigenetic Age: A Scoping Review. West J Nurs Res 2023; 45:1139-1149. [PMID: 37902222 PMCID: PMC10748459 DOI: 10.1177/01939459231208304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
BACKGROUND Interest in how the neighborhood environment impacts age-related health conditions has been increasing for decades. Epigenetic changes are environmentally derived modifications to the genome that alter the way genes function-thus altering health status. Epigenetic age, a biomarker for biological age, has been shown to be a useful predictor of several age-related health conditions. Consequently, its relation to the neighborhood environment has been the focus of a growing body of literature. OBJECTIVE We aimed to describe the scope of the evidence on the relationship between neighborhood environmental characteristics and epigenetic age. METHODS Using scoping review following methods established by Arksey and O'Malley, we first defined our research questions and searched the literature in PubMed, PsycINFO, and EMBASE. Next, we selected the literature to be included, and finally, we analyzed and summarized the information. RESULTS Nine articles met the inclusion criteria. Most studies examined deprivation as the neighborhood characteristic of interest. While all studies were observational in design, the articles included diverse participants, including men and women, adults and children, and multiple ethnicities. Results demonstrated a relationship between the neighborhood environment and epigenetic age, whether the characteristic of interest is socioeconomic or physical. CONCLUSIONS Overall, studies concluded there was a relationship between neighborhood characteristics and epigenetic age, whether the characteristic of interest was socioeconomic or physical. However, findings varied based on how the neighborhood characteristic and/or epigenetic age was measured. Furthermore, a paucity of investigations on physical characteristics was noticeable and warrants increased attention.
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Affiliation(s)
- Pamela Jackson
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Burel R. Goodin
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Bertha A. Hidalgo
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Edwin N. Aroke
- School of Nursing, University of Alabama at Birmingham, Birmingham, AL, USA
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Boekstein N, Barzilai N, Bertram A, Betts-LaCroix J, Fortney K, Helliwell SB, Hufford M, Mannick J, McLaughlin J, Mellon J, Morgen E, Regge N, Robinton DA, Sinclair DA, Young S, Starr R, Zhavoronkov A, Peyer J. Defining a longevity biotechnology company. Nat Biotechnol 2023; 41:1053-1055. [PMID: 37365260 DOI: 10.1038/s41587-023-01854-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Affiliation(s)
| | - Nir Barzilai
- American Federation for Aging Research (AFAR), New York, NY, USA
| | | | | | | | | | | | - Joan Mannick
- Tornado Therapeutics, Cambrian Bio Inc. PipeCo, New York, NY, USA
| | | | | | | | | | | | - David A Sinclair
- Genetics Department, Paul F. Glenn Center for Biology of Aging Research, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | | | - Risa Starr
- Longevity Biotechnology Association, New York, NY, USA
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Tamman AJF, Nagamatsu S, Krystal JH, Gelernter J, Montalvo-Ortiz JL, Pietrzak RH. Psychosocial Factors Associated With Accelerated GrimAge in Male U.S. Military Veterans. Am J Geriatr Psychiatry 2023; 31:97-109. [PMID: 36210262 DOI: 10.1016/j.jagp.2022.09.002] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 01/25/2023]
Abstract
OBJECTIVE Veterans are at high risk for health morbidities linked to premature mortality. Recently developed "epigenetic clock" algorithms, which compute intra-individual differences between biological and chronological aging, can help inform prediction of accelerated biological aging and mortality risk. To date, however, scarce research has examined potentially modifiable correlates of GrimAge, a novel epigenetic clock comprised of DNA methylation surrogates of plasma proteins and smoking pack-years associated with various morbidities and time-to-death. The objective of the study was to examine psychosocial correlates of this novel epigenetic clock. DESIGN Cross-sectional study. SETTING U.S. veteran population. PARTICIPANTS Participants were male, European American (EA), and derived from a nationally representative sample of U.S. veterans (N = 1,135, mean age = 63.3, standard deviation [SD] = 13.0). MEASUREMENTS We examined the prevalence of accelerated GrimAge and its association with a broad range of health, lifestyle, and psychosocial variables. RESULTS A total 18.3% of veterans had accelerated GrimAge (≥5 years greater GrimAge than chronological age; mean = 8.4 years acceleration, SD = 2.2). Fewer days of weekly physical exercise (relative variance explained [RVE] = 27%), history of lifetime substance use disorder (RVE = 21%), greater number of lifetime traumas (RVE = 19%), lower gratitude (RVE = 13%), reduced sleep quality (RVE = 7%), lower openness to experience (RVE = 7%), and unmarried/partnered status (RVE = 6%) were independently associated with increased odds of accelerated GrimAge. Increasing numbers of these risk factors were associated with greater odds of accelerated GrimAge, with greatest likelihood of acceleration for veterans with ≥3 risk factors (weighted 21.5%). CONCLUSIONS These results suggest that nearly 1-of-5 EA male U.S. veterans have accelerated GrimAge, and highlight a broad range of health, lifestyle, and psychosocial variables associated with accelerated GrimAge. Given that many of these factors are modifiable, these findings provide promising leads for risk stratification models of accelerated biological aging and precision medicine-based targets for interventions to mitigate risk for premature mortality in this population.
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Affiliation(s)
- Amanda J F Tamman
- Department of Psychiatry, Baylor College of Medicine (AJFT), Houston, TX.
| | - Sheila Nagamatsu
- Department of Psychiatry, Yale School of Medicine (SN, JHK, JG, JLM-O, RHP), New Haven, CT
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine (SN, JHK, JG, JLM-O, RHP), New Haven, CT; U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System (JHK, JG, RHP), West Haven, CT
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine (SN, JHK, JG, JLM-O, RHP), New Haven, CT; U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System (JHK, JG, RHP), West Haven, CT
| | | | - Robert H Pietrzak
- Department of Psychiatry, Yale School of Medicine (SN, JHK, JG, JLM-O, RHP), New Haven, CT; U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System (JHK, JG, RHP), West Haven, CT; Department of Social and Behavioral Sciences, Yale School of Public Health (RHP), New Haven, CT
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Joshi D, Gonzalez A, Lin D, Raina P. The association between adverse childhood experiences and epigenetic age acceleration in the Canadian longitudinal study on aging (CLSA). Aging Cell 2023; 22:e13779. [PMID: 36650913 PMCID: PMC9924940 DOI: 10.1111/acel.13779] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/07/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023] Open
Abstract
Research examining the association between exposure to a wide range of adverse childhood experiences (ACEs) and accelerated biological aging in older adults is limited. The purpose of this study was to examine the association of ACEs, both as a cumulative score and individual forms of adversity, with epigenetic age acceleration assessed using the DNA methylation (DNAm) GrimAge and DNAm PhenoAge epigenetic clocks in middle and older-aged adults. This cross-sectional study analyzed baseline and first follow-up data on 1445 participants aged 45-85 years from the Canadian Longitudinal Study on Aging (CLSA) who provided blood samples for DNAm analysis. ACEs were assessed using a validated self-reported questionnaire. Epigenetic age acceleration was estimated by regressing each epigenetic clock estimate on chronological age. Cumulative ACEs score was associated with higher DNAm GrimAge acceleration (β: 0.07; 95% CI: 0.02, 0.11) after adjusting for covariates. Childhood exposure to parental separation or divorce (β: 0.06; 95% CI: 0.00, 0.11) and emotional abuse (β: 0.06; 95% CI: 0.00, 0.12) were associated with higher DNAm GrimAge acceleration after adjusting for other adversities and covariates. There was no statistical association between ACEs and DNAm PhenoAge acceleration. Early life adversity may become biologically embedded and lead to premature biological aging, in relation to DNAm GrimAge, which estimates risk of mortality. Strategies that increase awareness of ACEs and promote healthy child development are needed to prevent ACEs.
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Affiliation(s)
- Divya Joshi
- Department of Health Research Methods, Evidence, and ImpactMcMaster UniversityHamiltonOntarioCanada,Labarge Centre for Mobility in AgingMcMaster UniversityHamiltonOntarioCanada,McMaster Institute for Research on AgingMcMaster UniversityHamiltonOntarioCanada
| | - Andrea Gonzalez
- Labarge Centre for Mobility in AgingMcMaster UniversityHamiltonOntarioCanada,McMaster Institute for Research on AgingMcMaster UniversityHamiltonOntarioCanada,Department of Psychiatry and Behavioral NeurosciencesMcMaster UniversityHamiltonOntarioCanada,Offord Centre for Child StudiesHamiltonOntarioCanada
| | - David Lin
- Centre for Molecular Medicine and TherapeuticsBC Children's Hospital Research InstituteVancouverBritish ColumbiaCanada
| | - Parminder Raina
- Department of Health Research Methods, Evidence, and ImpactMcMaster UniversityHamiltonOntarioCanada,Labarge Centre for Mobility in AgingMcMaster UniversityHamiltonOntarioCanada,McMaster Institute for Research on AgingMcMaster UniversityHamiltonOntarioCanada,Department of Psychiatry and Behavioral NeurosciencesMcMaster UniversityHamiltonOntarioCanada
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Evaluation of Epigenetic Age Acceleration Scores and Their Associations with CVD-Related Phenotypes in a Population Cohort. BIOLOGY 2022; 12:biology12010068. [PMID: 36671760 PMCID: PMC9855929 DOI: 10.3390/biology12010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 01/04/2023]
Abstract
We evaluated associations between nine epigenetic age acceleration (EAA) scores and 18 cardiometabolic phenotypes using an Eastern European ageing population cohort richly annotated for a diverse set of phenotypes (subsample, n = 306; aged 45-69 years). This was implemented by splitting the data into groups with positive and negative EAAs. We observed strong association between all EAA scores and sex, suggesting that any analysis of EAAs should be adjusted by sex. We found that some sex-adjusted EAA scores were significantly associated with several phenotypes such as blood levels of gamma-glutamyl transferase and low-density lipoprotein, smoking status, annual alcohol consumption, multiple carotid plaques, and incident coronary heart disease status (not necessarily the same phenotypes for different EAAs). We demonstrated that even after adjusting EAAs for sex, EAA-phenotype associations remain sex-specific, which should be taken into account in any downstream analysis involving EAAs. The obtained results suggest that in some EAA-phenotype associations, negative EAA scores (i.e., epigenetic age below chronological age) indicated more harmful phenotype values, which is counterintuitive. Among all considered epigenetic clocks, GrimAge was significantly associated with more phenotypes than any other EA scores in this Russian sample.
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Engelbrecht HR, Merrill SM, Gladish N, MacIsaac JL, Lin DTS, Ecker S, Chrysohoou CA, Pes GM, Kobor MS, Rehkopf DH. Sex differences in epigenetic age in Mediterranean high longevity regions. FRONTIERS IN AGING 2022; 3:1007098. [PMID: 36506464 PMCID: PMC9726738 DOI: 10.3389/fragi.2022.1007098] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/21/2022] [Indexed: 11/24/2022]
Abstract
Sex differences in aging manifest in disparities in disease prevalence, physical health, and lifespan, where women tend to have greater longevity relative to men. However, in the Mediterranean Blue Zones of Sardinia (Italy) and Ikaria (Greece) are regions of centenarian abundance, male-female centenarian ratios are approximately one, diverging from the typical trend and making these useful regions in which to study sex differences of the oldest old. Additionally, these regions can be investigated as examples of healthy aging relative to other populations. DNA methylation (DNAm)-based predictors have been developed to assess various health biomarkers, including biological age, Pace of Aging, serum interleukin-6 (IL-6), and telomere length. Epigenetic clocks are biological age predictors whose deviation from chronological age has been indicative of relative health differences between individuals, making these useful tools for interrogating these differences in aging. We assessed sex differences between the Horvath, Hannum, GrimAge, PhenoAge, Skin and Blood, and Pace of Aging predictors from individuals in two Mediterranean Blue Zones and found that men displayed positive epigenetic age acceleration (EAA) compared to women according to all clocks, with significantly greater rates according to GrimAge (β = 3.55; p = 1.22 × 10-12), Horvath (β = 1.07; p = 0.00378) and the Pace of Aging (β = 0.0344; p = 1.77 × 10-08). Other DNAm-based biomarkers findings indicated that men had lower DNAm-predicted serum IL-6 scores (β = -0.00301, p = 2.84 × 10-12), while women displayed higher DNAm-predicted proportions of regulatory T cells than men from the Blue Zone (p = 0.0150, 95% Confidence Interval [0.00131, 0.0117], Cohen's d = 0.517). All clocks showed better correlations with chronological age in women from the Blue Zones than men, but all clocks showed large mean absolute errors (MAE >30 years) in both sexes, except for PhenoAge (MAE <5 years). Thus, despite their equal survival to older ages in these Mediterranean Blue Zones, men in these regions remain biologically older by most measured DNAm-derived metrics than women, with the exception of the IL-6 score and proportion of regulatory T cells.
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Affiliation(s)
- Hannah-Ruth Engelbrecht
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Sarah M. Merrill
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Gladish
- Department of Epidemiology and Population Health, School of Medicine, Stanford University, Palo Alto, CA, United States
| | - Julie L. MacIsaac
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - David T. S. Lin
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Simone Ecker
- UCL Cancer Institute, University College London, London, United Kingdom
| | | | - Giovanni M. Pes
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Michael S. Kobor
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,*Correspondence: Michael S. Kobor, ; David H. Rehkopf,
| | - David H. Rehkopf
- Department of Epidemiology and Population Health, School of Medicine, Stanford University, Palo Alto, CA, United States,*Correspondence: Michael S. Kobor, ; David H. Rehkopf,
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Epigenetic clock: A promising biomarker and practical tool in aging. Ageing Res Rev 2022; 81:101743. [PMID: 36206857 DOI: 10.1016/j.arr.2022.101743] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/13/2022] [Accepted: 09/30/2022] [Indexed: 01/31/2023]
Abstract
As a complicated process, aging is characterized by various changes at the cellular, subcellular and nuclear levels, one of which is epigenetic aging. With increasing awareness of the critical role that epigenetic alternations play in aging, DNA methylation patterns have been employed as a measure of biological age, currently referred to as the epigenetic clock. This review provides a comprehensive overview of the epigenetic clock as a biomarker of aging and a useful tool to manage healthy aging. In this burgeoning scientific field, various kinds of epigenetic clocks continue to emerge, including Horvath's clock, Hannum's clock, DNA PhenoAge, and DNA GrimAge. We hereby present the most classic epigenetic clocks, as well as their differences. Correlations of epigenetic age with morbidity, mortality and other factors suggest the potential of epigenetic clocks for risk prediction and identification in the context of aging. In particular, we summarize studies on promising age-reversing interventions, with epigenetic clocks employed as a practical tool in the efficacy evaluation. We also discuss how the lack of higher-quality information poses a major challenge, and offer some suggestions to address existing obstacles. Hopefully, our review will help provide an appropriate understanding of the epigenetic clocks, thereby enabling novel insights into the aging process and how it can be manipulated to promote healthy aging.
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Gao X, Huang J, Cardenas A, Zhao Y, Sun Y, Wang J, Xue L, Baccarelli AA, Guo X, Zhang L, Wu S. Short-Term Exposure of PM 2.5 and Epigenetic Aging: A Quasi-Experimental Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14690-14700. [PMID: 36197060 DOI: 10.1021/acs.est.2c05534] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Epigenetic age (EA) is an emerging DNA methylation-based biomarker of biological aging, but whether EA is causally associated with short-term PM2.5 exposure remains unknown. We conducted a quasi-experimental study of 26 healthy adults to test whether short-term PM2.5 exposure accelerates seven EAs with three health examinations performed before, during, and after multiple PM2.5 pollution waves. Seven EAs were derived from the DNA methylation profiles of the Illumina HumanMethylationEPIC BeadChip from CD4+ T-helper cells. We found that an increase of 10 μg/m3 in the 0-24 h personal PM2.5 exposure prior to health examinations was associated with a 0.035, 0.035, 0.050, 0.055, 0.052, and 0.037-unit increase in the changes of z-scored DNA methylation age acceleration (AA,Horvath), AA (Hannum), AA (GrimAge), DunedinPoAm, mortality risk score (MS), and epiTOC, respectively (p-values < 0.05). The same increase in the 24-48 h average personal PM2.5 exposure yielded smaller effects but was still robustly associated with the changes in AA (GrimAge), DunedinPoAm, and MS. Such acute aging effects of PM2.5 were mediated by the changes in several circulating biomarkers, including EC-SOD and sCD40L, with up to ∼28% mediated proportions. Our findings demonstrated that short-term PM2.5 exposure could accelerate aging reflected by DNA methylation profiles via blood coagulation, oxidative stress, and systematic inflammation.
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Affiliation(s)
- Xu Gao
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing100191, China
| | - Jing Huang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing100191, China
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, California94720, United States
| | - Yan Zhao
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing100191, China
| | - Yanyan Sun
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, and Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing100069, China
| | - Jiawei Wang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing100191, China
| | - Lijun Xue
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing100191, China
| | - Andrea A Baccarelli
- Laboratory of Environmental Precision Health, Mailman School of Public Health, Columbia University, New York, New York10032, United States
| | - Xinbiao Guo
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing100191, China
| | - Ling Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, and Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing100069, China
| | - Shaowei Wu
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an710061, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, Shaanxi710061, China
- Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi710061, China
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Hamlat EJ, Adler NE, Laraia B, Surachman A, Lu AT, Zhang J, Horvath S, Epel ES. Association of subjective social status with epigenetic aging among Black and White women. Psychoneuroendocrinology 2022; 141:105748. [PMID: 35397259 DOI: 10.1016/j.psyneuen.2022.105748] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Subjective social status (SSS), an individual's assessment of their own social status in relation to others, is associated with health and mortality independently of objective SES; however, no studies have tested whether SSS influences epigenetic aging. The current study examines if SSS is associated with epigenetic age acceleration in both Black and White women, independently of objective SES measured during both childhood and adulthood. METHOD For 9- and 10-year-old Black and White girls, parental education and annual household income was obtained. At ages 39-42, 361 participants (175 Black, 186 White) reported their current education, household income, and SSS, and provided saliva to assess age acceleration using the GrimAge epigenetic clock. Linear regression estimated the association of SSS with epigenetic age acceleration, controlling for objective SES (current education, current income, parents' education, income during childhood), smoking, and counts of cell types. RESULTS When all objective SES variables were included in the model, SSS remained significantly associated with epigenetic age acceleration, b = - 0.31, p = .003, ß = - 0.15. Black women had significantly greater age acceleration than White women, (t(359) = 5.20, p > .001, d = 0.55) but race did not moderate the association between SSS and epigenetic age acceleration. CONCLUSIONS Women who rated themselves lower in SSS had greater epigenetic age acceleration, regardless of income and education. There was no difference by race for this association.
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Affiliation(s)
- Elissa J Hamlat
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, USA.
| | - Nancy E Adler
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, USA
| | - Barbara Laraia
- School of Public Health, University of California, Berkeley, USA
| | - Agus Surachman
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, USA
| | - Ake T Lu
- Department of Human Genetics, University of California, Los Angeles, USA
| | - Joshua Zhang
- Department of Human Genetics, University of California, Los Angeles, USA
| | - Steve Horvath
- Department of Human Genetics, University of California, Los Angeles, USA; Department of Biostatistics, University of California, Los Angeles, USA
| | - Elissa S Epel
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, USA
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Epigenetic Age Acceleration Is Not Associated with Age-Related Macular Degeneration. Int J Mol Sci 2021; 22:ijms222413457. [PMID: 34948253 PMCID: PMC8705580 DOI: 10.3390/ijms222413457] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Abstract
DNA methylation age (DNAm age) estimation is a powerful biomarker of human ageing. To date, epigenetic clocks have not been evaluated in age-related macular degeneration (AMD). Here, we perform genome-wide DNA methylation analyses in blood of AMD patients with a documented smoking history (14 AMD, 16 Normal), identifying loci of differential methylation (DML) with a relaxed p-value criterion (p ≤ 10−4). We conduct DNAm age analyses using the Horvath-multi tissue, Hannum and Skin & Blood epigenetic clocks in both blood and retinal pigment epithelium (RPE). We perform Ingenuity Pathway Analysis Causal Network Analysis (IPA CNA) on the topmost significantly differentially methylated CpG probes in blood and RPE. Results show poor performance of epigenetic clocks in RPE. Epigenetic age acceleration (EAA) was not observed in AMD. However, we observe positive EAA in blood of smokers, and in smokers with AMD. DML analysis revealed hypomethylation at cg04953735 within RPTOR (p = 6.51 × 10−5; Δβ = −11.95%). IPA CNA in the RPE also identified RPTOR as the putative master regulator, predicted to be inhibited in AMD. In conclusion, this is the first study evaluating an association of epigenetic ageing in AMD. We posit a role for RPTOR as a common master regulator of methylation changes in the RPE in AMD.
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Hamlat EJ, Prather AA, Horvath S, Belsky J, Epel ES. Early life adversity, pubertal timing, and epigenetic age acceleration in adulthood. Dev Psychobiol 2021; 63:890-902. [PMID: 33423276 DOI: 10.1002/dev.22085] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/05/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Given associations linking early life adversity, pubertal timing, and biological aging, we examined the direct and indirect effects of early life trauma on adult biological aging (via age of menarche). METHODS Participants were premenopausal women (N = 183). Path models evaluated whether early life trauma predicted early pubertal timing and thereby, adult epigenetic age acceleration (indexed via four epigenetic clocks: Horvath DNAm Age, Hannum DNAm Age, DNAm PhenoAge, and DNAm GrimAge). Secondary analyses explored the effects of type of trauma (abuse and neglect) and adult chronic stress status (caregiver of child with autism and non-caregiver). RESULTS Early life trauma and earlier age at menarche independently predicted accelerated aging based on one of the four epigenetic clocks, DNAm GrimAge, though early life trauma was not associated with age of menarche. Childhood abuse, but not neglect, predicted faster epigenetic aging; results did not differ by chronic stress status. CONCLUSIONS Early trauma and early menarche appear to exert independent effects on DNAm GrimAge, which has been shown to be the strongest epigenetic predictor of mortality risk. This study identifies a potential correlate or determinant of accelerated epigenetic aging-menarcheal age. Future research should address the limitations of this study by using racially diverse samples.
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Affiliation(s)
| | | | | | - Jay Belsky
- University of California, Davis, CA, USA
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13
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Matsuyama S. Mechanisms of aging, age-associated diseases, and lifespan determination. Exp Biol Med (Maywood) 2020; 245:1529-1531. [PMID: 32903037 DOI: 10.1177/1535370220955146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Shigemi Matsuyama
- Division of Hematology and Oncology, Department of Medicine School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Case Comprehensive Cancer Center, Cleveland, OH, 44106, USA
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14
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Matsuyama M, Søraas A, Yu S, Kim K, Stavrou EX, Caimi PF, Wald D, deLima M, Dahl JA, Horvath S, Matsuyama S. Analysis of epigenetic aging in vivo and in vitro: Factors controlling the speed and direction. Exp Biol Med (Maywood) 2020; 245:1543-1551. [PMID: 32762265 DOI: 10.1177/1535370220947015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
IMPACT STATEMENT Aging is associated with DNA methylation (DNAm) changes. Recent advancement of the whole-genome DNAm analysis technology allowed scientists to develop DNAm-based age estimators. A majority of these estimators use DNAm data from a single tissue type such as blood. In 2013, a multi-tissue age estimator using DNAm pattern of 353 CpGs was developed by Steve Horvath. This estimator was named "epigenetic clock", and the improved version using DNAm pattern of 391 CpGs was developed in 2018. The estimated age by epigenetic clock is named DNAmAge. DNAmAge can be used as a biomarker of aging predicting the risk of age-associated diseases and mortality. Although the DNAm-based age estimators were developed, the mechanism of epigenetic aging is still enigmatic. The biological significance of epigenetic aging is not well understood, either. This minireview discusses the current understanding of the mechanism of epigenetic aging and the future direction of aging research.
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Affiliation(s)
- Mieko Matsuyama
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Arne Søraas
- Department of Microbiology, Oslo University Hospital, Case Comprehensive Cancer Center, Oslo 0372, Norway
| | - Sarah Yu
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Kyuhyeon Kim
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Evi X Stavrou
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Paolo F Caimi
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - David Wald
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA.,Department of Microbiology, Oslo University Hospital, Case Comprehensive Cancer Center, Oslo 0372, Norway
| | - Marcos deLima
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - John A Dahl
- Department of Microbiology, Oslo University Hospital, Case Comprehensive Cancer Center, Oslo 0372, Norway
| | - Steve Horvath
- Department of Pathology, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Shigemi Matsuyama
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
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15
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Lowe R, Danson AF, Rakyan VK, Yildizoglu S, Saldmann F, Viltard M, Friedlander G, Faulkes CG. DNA methylation clocks as a predictor for ageing and age estimation in naked mole-rats, Heterocephalus glaber. Aging (Albany NY) 2020; 12:4394-4406. [PMID: 32126024 PMCID: PMC7093186 DOI: 10.18632/aging.102892] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/25/2020] [Indexed: 01/07/2023]
Abstract
The naked mole-rat, Heterocephalus glaber (NMR), the longest-lived rodent, is of significance and interest in the study of biomarkers for ageing. Recent breakthroughs in this field have revealed ‘epigenetic clocks’ that are based on the temporal accumulation of DNA methylation at specific genomic sites. Here, we validate the hypothesis of an epigenetic clock in NMRs based on changes in methylation of targeted CpG sites. We initially analysed 51 CpGs in NMR livers spanning an age range of 39-1,144 weeks and found 23 to be significantly associated with age (p<0.05). We then built a predictor of age using these sites. To test the accuracy of this model, we analysed an additional set of liver samples, and were successfully able to predict their age with a root mean squared error of 166 weeks. We also profiled skin samples with the same age range, finding a striking correlation between their predicted age versus their actual age (R=0.93), but which was lower when compared to the liver, suggesting that skin ages slower than the liver in NMRs. Our model will enable the prediction of age in wild-caught and captive NMRs of unknown age, and will be invaluable for further mechanistic studies of mammalian ageing.
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Affiliation(s)
- Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Amy F Danson
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Centre for Genomic Health, Queen Mary University of London, London, UK
| | - Selin Yildizoglu
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Frédéric Saldmann
- Fondation pour la Recherche en Physiologie, Brussels, Belgium.,Service de Physiologie et Explorations Fonctionnelles, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Melanie Viltard
- Fondation pour la Recherche en Physiologie, Brussels, Belgium
| | - Gérard Friedlander
- Service de Physiologie et Explorations Fonctionnelles, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université Paris Descartes, Faculté de Médecine, Paris, France.,INSERM UMR_S1151 CNRS UMR8253 Institut Necker-Enfants Malades (INEM), Paris, France
| | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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16
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Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JPJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK. DNA methylation aging clocks: challenges and recommendations. Genome Biol 2019; 20:249. [PMID: 31767039 PMCID: PMC6876109 DOI: 10.1186/s13059-019-1824-y] [Citation(s) in RCA: 459] [Impact Index Per Article: 91.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK.
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Stephan Beck
- Medical Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, London, UK.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
| | - Steve Horvath
- Department of Human Genetics, Gonda Research Center, David Geffen School of Medicine, Los Angeles, CA, USA.
- Department of Biostatistics, School of Public Health, University of California-Los Angeles, Los Angeles, CA, USA.
| | - Trey Ideker
- San Diego Center for Systems Biology, University of California-San Diego, San Diego, CA, USA.
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.
- The Wellcome Trust Sanger Institute, Cambridge, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK.
| | | | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany.
| | - Kang Zhang
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau.
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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17
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Abstract
Increasing numbers of studies implicate abnormal DNA methylation in cancer and many non-malignant diseases. This is consistent with numerous findings about differentiation-associated changes in DNA methylation at promoters, enhancers, gene bodies, and sites that control higher-order chromatin structure. Abnormal increases or decreases in DNA methylation contribute to or are markers for cancer formation and tumour progression. Aberrant DNA methylation is also associated with neurological diseases, immunological diseases, atherosclerosis, and osteoporosis. In this review, I discuss DNA hypermethylation in disease and its interrelationships with normal development as well as proposed mechanisms for the origin of and pathogenic consequences of disease-associated hypermethylation. Disease-linked DNA hypermethylation can help drive oncogenesis partly by its effects on cancer stem cells and by the CpG island methylator phenotype (CIMP); atherosclerosis by disease-related cell transdifferentiation; autoimmune and neurological diseases through abnormal perturbations of cell memory; and diverse age-associated diseases by age-related accumulation of epigenetic alterations.
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center and Tulane Center for Bioinformatics and Genomics, Tulane University Health Sciences Center , New Orleans , LA , USA
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