The use of DNA methylation clock in aging research

One of the key characteristics of aging is a progressive loss of physiological integrity, which weakens bodily functions and increases the risk of death. A robust biomarker is important for the assessment of biological age, the rate of aging, and a person's health status. DNA methylation clocks, novel biomarkers of aging, are composed of a group of cytosine-phosphate-guanine dinucleotides, the DNA methylation status of which can be used to accurately measure subjective age. These clocks are considered accurate biomarkers of chronological age for humans and other vertebrates. Numerous studies have demonstrated these clocks to quantify the rate of biological aging and the effects of longevity and anti-aging interventions. In this review, we describe the purpose and use of DNA methylation clocks in aging research.

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New Computational Approaches to Aging Research

Innovation in Aging ◽

10.1093/geroni/igaa057.2618 ◽

2020 ◽

Vol 4 (Supplement_1) ◽

pp. 736-736

Author(s):

Morgan E Levine

Keyword(s):

Aging Process ◽

Molecular Level ◽

Biological Aging ◽

Systems Dynamics ◽

Learning Approaches ◽

Biological Organization ◽

Aging Research ◽

Biomarkers Of Aging ◽

Age Related ◽

Novel Biomarkers

Abstract Aging is associated with numerous changes at all levels of biological organization. Harnessing this information to develop measures that accurately and reliably quantify the biological aging process will require systems biology approaches. This talk will illustrate how epigenetic data can be integrated with cellular, physiological, proteomic, and clinical data to model age-related changes that propagate up the levels—finally manifesting as age-related disease or death. I will also describe how network modeling and machine learning approaches (linear and non-linear) can be used to identify causal features in aging from which to generate novel biomarkers. Given the complexity of the biological aging process, modeling of systems dynamics over time will both lead to the development of better biomarkers of aging, and also inform our conceptualization of how alterations at the molecular level propagate up levels of organization to eventually influence morbidity and mortality risk.

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Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging

Genome Biology ◽

10.1186/s13059-021-02398-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Daniel L. McCartney ◽

Josine L. Min ◽

Rebecca C. Richmond ◽

Ake T. Lu ◽

Maria K. Sobczyk ◽

...

Keyword(s):

Dna Methylation ◽

Genome Wide Association Study ◽

Association Studies ◽

Genome Wide Association ◽

Biological Aging ◽

Genome Wide Association Studies ◽

Genetic Loci ◽

Biomarkers Of Aging ◽

Genome Wide ◽

Shared Genetic

Abstract Background Biological aging estimators derived from DNA methylation data are heritable and correlate with morbidity and mortality. Consequently, identification of genetic and environmental contributors to the variation in these measures in populations has become a major goal in the field. Results Leveraging DNA methylation and SNP data from more than 40,000 individuals, we identify 137 genome-wide significant loci, of which 113 are novel, from genome-wide association study (GWAS) meta-analyses of four epigenetic clocks and epigenetic surrogate markers for granulocyte proportions and plasminogen activator inhibitor 1 levels, respectively. We find evidence for shared genetic loci associated with the Horvath clock and expression of transcripts encoding genes linked to lipid metabolism and immune function. Notably, these loci are independent of those reported to regulate DNA methylation levels at constituent clock CpGs. A polygenic score for GrimAge acceleration showed strong associations with adiposity-related traits, educational attainment, parental longevity, and C-reactive protein levels. Conclusion This study illuminates the genetic architecture underlying epigenetic aging and its shared genetic contributions with lifestyle factors and longevity.

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DNA Methylation Based Molecular Subtypes Predict Prognosis in Breast Cancer Patients

Cancer Control ◽

10.1177/1073274820988519 ◽

2021 ◽

Vol 28 ◽

pp. 107327482098851

Author(s):

Zeng-Hong Wu ◽

Yun Tang ◽

Yan Zhou

Keyword(s):

Breast Cancer ◽

Dna Methylation ◽

Molecular Subtypes ◽

Methylation Status ◽

The Cancer Genome Atlas ◽

Training Dataset ◽

Consensus Clustering ◽

Breast Cancer Patients ◽

Cancer Subtypes ◽

Novel Biomarkers

Background: Epigenetic changes are tightly linked to tumorigenesis development and malignant transformation’ However, DNA methylation occurs earlier and is constant during tumorigenesis. It plays an important role in controlling gene expression in cancer cells. Methods: In this study, we determining the prognostic value of molecular subtypes based on DNA methylation status in breast cancer samples obtained from The Cancer Genome Atlas database (TCGA). Results: Seven clusters and 204 corresponding promoter genes were identified based on consensus clustering using 166 CpG sites that significantly influenced survival outcomes. The overall survival (OS) analysis showed a significant prognostic difference among the 7 groups (p<0.05). Finally, a prognostic model was used to estimate the results of patients on the testing set based on the classification findings of a training dataset DNA methylation subgroups. Conclusions: The model was found to be important in the identification of novel biomarkers and could be of help to patients with different breast cancer subtypes when predicting prognosis, clinical diagnosis and management.

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Predictors of Biological Age: The Implications for Wellness and Aging Research

Gerontology and Geriatric Medicine ◽

10.1177/23337214211046419 ◽

2021 ◽

Vol 7 ◽

pp. 233372142110464

Author(s):

Trevor Lohman ◽

Gurinder Bains ◽

Lee Berk ◽

Everett Lohman

Keyword(s):

Dna Methylation ◽

Lifestyle Modification ◽

Biological Age ◽

Current Evidence ◽

Biological Aging ◽

Clinical Value ◽

Aging Research ◽

Mortality And Morbidity ◽

Morbidity Risk ◽

Pharmaceutical Interventions

As healthspan and lifespan research breakthroughs have become more commonplace, the need for valid, practical markers of biological age is becoming increasingly paramount. The accessibility and affordability of biological age predictors that can reveal information about mortality and morbidity risk, as well as remaining years of life, has profound clinical and research implications. In this review, we examine 5 groups of aging biomarkers capable of providing accurate biological age estimations. The unique capabilities of these biomarkers have far reaching implications for the testing of both pharmaceutical and non-pharmaceutical interventions designed to slow or reverse biological aging. Additionally, the enhanced validity and availability of these tools may have increasingly relevant clinical value. The authors of this review explore those implications, with an emphasis on lifestyle modification research, and provide an overview of the current evidence regarding 5 biological age predictor categories: Telomere length, composite biomarkers, DNA methylation “epigenetic clocks,” transcriptional predictors of biological age, and functional age predictors.

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Individual DNA Methylation Profile is Correlated with Age and can be Targeted to Modulate Healthy Aging and Longevity

Current Pharmaceutical Design ◽

10.2174/1381612825666191112095655 ◽

2019 ◽

Vol 25 (39) ◽

pp. 4139-4149 ◽

Cited By ~ 3

Author(s):

Francesco Guarasci ◽

Patrizia D'Aquila ◽

Alberto Montesanto ◽

Andrea Corsonello ◽

Dina Bellizzi ◽

...

Keyword(s):

Dna Methylation ◽

Mitochondrial Dna ◽

Aging Process ◽

Healthy Aging ◽

Nuclear Dna ◽

Epigenetic Modification ◽

Biological Aging ◽

Biomarkers Of Aging ◽

Age Related

: Patterns of DNA methylation, the best characterized epigenetic modification, are modulated by aging. In humans, different studies at both site-specific and genome-wide levels have reported that modifications of DNA methylation are associated with the chronological aging process but also with the quality of aging (or biological aging), providing new perspectives for establishing powerful biomarkers of aging. : In this article, the role of DNA methylation in aging and longevity has been reviewed by analysing literature data about DNA methylation variations occurring during the lifetime in response to environmental factors and genetic background, and their association with the aging process and, in particular, with the quality of aging. Special attention has been devoted to the relationship between nuclear DNA methylation patterns, mitochondrial DNA epigenetic modifications, and longevity. Mitochondrial DNA has recently been reported to modulate global DNA methylation levels of the nuclear genome during the lifetime, and, in spite of the previous belief, it has been found to be the target of methylation modifications. : Analysis of DNA methylation profiles across lifetime shows that a remodeling of the methylome occurs with age and/or with age-related decline. Thus, it can be an excellent biomarker of aging and of the individual decline and frailty status. The knowledge about the mechanisms underlying these modifications is crucial since it might allow the opportunity for targeted treatment to modulate the rate of aging and longevity.

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Regular, Intense Exercise Training as a Healthy Aging Lifestyle Strategy: Preventing DNA Damage, Telomere Shortening and Adverse DNA Methylation Changes Over a Lifetime

Frontiers in Genetics ◽

10.3389/fgene.2021.652497 ◽

2021 ◽

Vol 12 ◽

Author(s):

Maha Sellami ◽

Nicola Bragazzi ◽

Mohammad Shoaib Prince ◽

Joshua Denham ◽

Mohamed Elrayess

Keyword(s):

Dna Methylation ◽

Dna Damage ◽

Exercise Training ◽

Epigenetic Modification ◽

Methylation Status ◽

The Body ◽

Training Load ◽

Activity Level ◽

Biological Aging ◽

Age Related

Exercise training is one of the few therapeutic interventions that improves health span by delaying the onset of age-related diseases and preventing early death. The length of telomeres, the 5′-TTAGGGn-3′ tandem repeats at the ends of mammalian chromosomes, is one of the main indicators of biological age. Telomeres undergo shortening with each cellular division. This subsequently leads to alterations in the expression of several genes that encode vital proteins with critical functions in many tissues throughout the body, and ultimately impacts cardiovascular, immune and muscle physiology. The sub-telomeric DNA is comprised of heavily methylated, heterochromatin. Methylation and histone acetylation are two of the most well-studied examples of the epigenetic modifications that occur on histone proteins. DNA methylation is the type of epigenetic modification that alters gene expression without modifying gene sequence. Although diet, genetic predisposition and a healthy lifestyle seem to alter DNA methylation and telomere length (TL), recent evidence suggests that training status or physical fitness are some of the major factors that control DNA structural modifications. In fact, TL is positively associated with cardiorespiratory fitness, physical activity level (sedentary, active, moderately trained, or elite) and training intensity, but is shorter in over-trained athletes. Similarly, somatic cells are vulnerable to exercise-induced epigenetic modification, including DNA methylation. Exercise-training load, however, depends on intensity and volume (duration and frequency). Training load-dependent responses in genomic profiles could underpin the discordant physiological and physical responses to exercise. In the current review, we will discuss the role of various forms of exercise training in the regulation of DNA damage, TL and DNA methylation status in humans, to provide an update on the influence exercise training has on biological aging.

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DNAm-based signatures of accelerated aging and mortality in blood are associated with low renal function

Clinical Epigenetics ◽

10.1186/s13148-021-01082-w ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Pamela R. Matías-García ◽

Cavin K. Ward-Caviness ◽

Laura M. Raffield ◽

Xu Gao ◽

Yan Zhang ◽

...

Keyword(s):

Dna Methylation ◽

African American ◽

Kidney Disease ◽

Meta Analysis ◽

Methylation Status ◽

Serum Urate ◽

Biological Aging ◽

Epigenetic Biomarkers ◽

Age Related ◽

New Findings

Abstract Background The difference between an individual's chronological and DNA methylation predicted age (DNAmAge), termed DNAmAge acceleration (DNAmAA), can capture life-long environmental exposures and age-related physiological changes reflected in methylation status. Several studies have linked DNAmAA to morbidity and mortality, yet its relationship with kidney function has not been assessed. We evaluated the associations between seven DNAm aging and lifespan predictors (as well as GrimAge components) and five kidney traits (estimated glomerular filtration rate [eGFR], urine albumin-to-creatinine ratio [uACR], serum urate, microalbuminuria and chronic kidney disease [CKD]) in up to 9688 European, African American and Hispanic/Latino individuals from seven population-based studies. Results We identified 23 significant associations in our large trans-ethnic meta-analysis (p < 1.43E−03 and consistent direction of effect across studies). Age acceleration measured by the Extrinsic and PhenoAge estimators, as well as Zhang’s 10-CpG epigenetic mortality risk score (MRS), were associated with all parameters of poor kidney health (lower eGFR, prevalent CKD, higher uACR, microalbuminuria and higher serum urate). Six of these associations were independently observed in European and African American populations. MRS in particular was consistently associated with eGFR (β = − 0.12, 95% CI = [− 0.16, − 0.08] change in log-transformed eGFR per unit increase in MRS, p = 4.39E−08), prevalent CKD (odds ratio (OR) = 1.78 [1.47, 2.16], p = 2.71E-09) and higher serum urate levels (β = 0.12 [0.07, 0.16], p = 2.08E−06). The “first-generation” clocks (Hannum, Horvath) and GrimAge showed different patterns of association with the kidney traits. Three of the DNAm-estimated components of GrimAge, namely adrenomedullin, plasminogen-activation inhibition 1 and pack years, were positively associated with higher uACR, serum urate and microalbuminuria. Conclusion DNAmAge acceleration and DNAm mortality predictors estimated in whole blood were associated with multiple kidney traits, including eGFR and CKD, in this multi-ethnic study. Epigenetic biomarkers which reflect the systemic effects of age-related mechanisms such as immunosenescence, inflammaging and oxidative stress may have important mechanistic or prognostic roles in kidney disease. Our study highlights new findings linking kidney disease to biological aging, and opportunities warranting future investigation into DNA methylation biomarkers for prognostic or risk stratification in kidney disease.

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Acceleration of Biological Aging and Underestimation of Subjective Age Are Risk Factors for Severe COVID-19

Biomedicines ◽

10.3390/biomedicines9080913 ◽

2021 ◽

Vol 9 (8) ◽

pp. 913

Author(s):

Tatiana N. Berezina ◽

Stanislav Rybtsov

Keyword(s):

Risk Factors ◽

Risk Group ◽

Rapid Assessment ◽

Accelerated Aging ◽

Risk Groups ◽

Biological Aging ◽

Risk Of Infection ◽

Subjective Age ◽

Risk Of Death ◽

Subjective Aging

In an epidemic, it is important to have methods for reliable and rapid assessment of risk groups for severe forms of the disease for their priority vaccination and for the application of preventive lockdown measures. The aim of this study was to investigate risk factors for severe forms of COVID-19 in adults using indicators of biological and subjective aging. Longitudinal studies evaluated the severity of the disease and the number of cases. Respondents (447) were divided into “working group” and “risk group” (retirees with chronic diseases). During the lockdown period (in mid-2020), accelerated aging was observed in the group of workers (by 3.9–8 years for men and an increase at the tendency level for women). However, the respondents began to feel subjectively younger (by 3.3–7.2 years). In the risk group, there were no deviations from the expected biopsychological aging. The number of cases at the end of 2020 was 31% in workers and 0% in the risk group. Reasonably, the risk group followed the quarantine rules more strictly by 1.5 times. In working men, indicators of relative biological and relative subjective aging (measured in both 2019 and mid-2020) significantly influenced the incidence at the end of 2020. In women, only the indicators obtained in mid-2020 had a significant impact. The relative biological aging of an individual tested in the middle of 2020 had a direct impact on the risk of infection (p < 0.05) and on the probability of death (p < 0.0001). On the contrary, an increase in the relative subjective (psychological) aging index reduced the risk of infection (at the tendency level, p = 0.06) and the risk of death (p < 0.0001). Both the risk of infection and the risk of death increased with calendar age at the tendency level. Conclusions: Indicators of individual relative biological and subjective aging affect the probability of getting COVID-19 and its severity. The combination of high indicators of biological aging and underestimated indicators of subjective aging is associated with increased chances of developing severe forms of the disease.

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