Epigenetic age-predictions in mice using pyrosequencing, droplet digital PCR or barcoded bisulfite amplicon sequencing

AbstractAge-associated DNA methylation reflects aspects of biological aging - therefore epigenetic clocks for mice can help to elucidate the impact of treatments or genetic background on the aging process in this model organism. Initially, age-predictors for mice were trained on genome-wide DNA methylation profiles, whereas we have recently described a targeted assay based on pyrosequencing of DNA methylation at only three CG dinucleotides (CpGs). Here, we have re-evaluated pyrosequencing approaches in comparison to droplet digital PCR (ddPCR) and barcoded bisulfite amplicon sequencing (BBA-seq). At individual CpGs the correlation of DNA methylation with chronological age was slightly higher for pyrosequencing and ddPCR as compared to BBA-seq. On the other hand, BBA-seq revealed that neighboring CpGs tend to be stochastically modified in murine age-associated regions. Furthermore, the binary sequel of methylated and non-methylated CpGs in individual reads can be used for single-read predictions, which may reflect heterogeneity in epigenetic aging. In comparison to C57BL/6 mice the epigenetic age-predictions using BBA-seq were also accelerated in the shorter-lived DBA/2 mice, and in C57BL/6 mice with a lifespan quantitative trait locus of DBA/2 mice. Taken together, we describe further optimized and alternative targeted methods to determine epigenetic clocks in mice.

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Targeted methods for epigenetic age predictions in mice

Scientific Reports ◽

10.1038/s41598-020-79509-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Yang Han ◽

Miloš Nikolić ◽

Michael Gobs ◽

Julia Franzen ◽

Gerald de Haan ◽

...

Keyword(s):

Dna Methylation ◽

Model Organism ◽

Amplicon Sequencing ◽

Digital Pcr ◽

Biological Aging ◽

Epigenetic Aging ◽

Epigenetic Age ◽

Trait Locus ◽

Genomic Regions ◽

Cg Dinucleotides

AbstractAge-associated DNA methylation reflects aspect of biological aging—therefore epigenetic clocks for mice can elucidate how the aging process in this model organism is affected by specific treatments or genetic background. Initially, age-predictors for mice were trained for genome-wide DNA methylation profiles and we have recently described a targeted assay based on pyrosequencing of DNA methylation at only three age-associated genomic regions. Here, we established alternative approaches using droplet digital PCR (ddPCR) and barcoded bisulfite amplicon sequencing (BBA-seq). At individual CG dinucleotides (CpGs) the correlation of DNA methylation with chronological age was slightly higher for pyrosequencing and ddPCR as compared to BBA-seq. On the other hand, BBA-seq revealed that neighboring CpGs tend to be stochastically modified at murine age-associated regions. Furthermore, the binary sequel of methylated and non-methylated CpGs in individual reads can be used for single-read predictions, which may reflect heterogeneity in epigenetic aging. In comparison to C57BL/6 mice the single-read age-predictions using BBA-seq were also accelerated in the shorter-lived DBA/2 mice, and in C57BL/6 mice with a lifespan quantitative trait locus of DBA/2 mice. Taken together, we describe alternative targeted methods for epigenetic age predictions that provide new perspectives for aging-intervention studies in mice.

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The combined effect of obesity and aging on human sperm DNA methylation signatures: inclusion of BMI in the paternal germ line age prediction model

Scientific Reports ◽

10.1038/s41598-020-71979-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Albert Salas-Huetos ◽

Emma R. James ◽

Dallin S. Broberg ◽

Kenneth I. Aston ◽

Douglas T. Carrell ◽

...

Keyword(s):

Dna Methylation ◽

Germ Line ◽

Age Groups ◽

Human Sperm ◽

Absolute Error ◽

Epigenetic Aging ◽

Epigenetic Age ◽

Sperm Dna ◽

Epigenetic Age Acceleration ◽

The Impact

Abstract Male aging and obesity have both been shown to contribute to declines in fertility in men. Recent work in aging has shown consistent epigenetic changes to sperm as a man ages. In fact, our lab has built a tool that utilizes DNA methylation signatures from sperm to effectively predict an individual’s age. Herein, we performed this preliminary cohort study to determine if increased BMI accelerates the epigenetic aging in sperm. A total of 96 participants were divided into four age groups (22–24, 30, 40–41, and > 48 years of age) and additionally parsed into two BMI sub-categories (normal and high/obese). We found no statistically significant epigenetic age acceleration. However, it is important to note that within each age category, high BMI individuals were predicted to be older on average than their actual age (~ 1.4 years), which was not observed in the normal BMI group. To further investigate this, we re-trained a model using only the present data with and without BMI as a feature. We found a modest but non-significant improvement in prediction with BMI [r2 = 0.8814, mean absolute error (MAE) = 3.2913] compared to prediction without BMI (r2 = 0.8739, MAE = 3.3567). Future studies with higher numbers of age-matched individuals are needed to definitively understand the impact of BMI on epigenetic aging in sperm.

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The Epigenetic Pacemaker is a more sensitive tool than penalized regression for identifying moderators of epigenetic aging

10.1101/2021.10.05.463222 ◽

2021 ◽

Author(s):

Colin Farrell ◽

Kalsuda Lapborisuth ◽

Chanyue Hu ◽

Kyle Pu ◽

Sagi Snir ◽

...

Keyword(s):

Dna Methylation ◽

Penalized Regression ◽

Chronological Age ◽

Data Set ◽

Epigenetic State ◽

Age Related ◽

Epigenetic Aging ◽

Epigenetic Age ◽

The Impact ◽

The Relationship

Epigenetic clocks, DNA methylation based chronological age prediction models, are commonly employed to study age related biology. The error between the predicted and observed age is often interpreted as a form of biological age acceleration and many studies have measured the impact of environmental and other factors on epigenetic age. Epigenetic clocks are fit using approaches that minimize the error between the predicted and observed chronological age and as a result they reduce the impact of factors that may moderate the relationship between actual and epigenetic age. Here we compare the standard methods used to construct epigenetic clocks to an evolutionary framework of epigenetic aging, the epigenetic pacemaker (EPM) that directly models DNA methylation as a function of a time dependent epigenetic state. We show that the EPM is more sensitive than epigenetic clocks for the detection of factors that moderate the relationship between actual age and epigenetic state (ie epigenetic age). Specifically, we show that the EPM is more sensitive at detecting sex and cell type effects in a large aggregate data set and in an example case study is more sensitive sensitive at detecting age related methylation changes associated with polybrominated biphenyl exposure. Thus we find that the pacemaker provides a more robust framework for the study of factors that impact epigenetic age acceleration than traditional clocks based on linear regression models.

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Effects of Smoking Cessation on Epigenetic Aging

Innovation in Aging ◽

10.1093/geroni/igab046.2518 ◽

2021 ◽

Vol 5 (Supplement_1) ◽

pp. 673-673

Author(s):

Brian Chen ◽

Weiye Wang ◽

Nichole Rigby ◽

Randal Olson ◽

Steve Sabes

Keyword(s):

Dna Methylation ◽

Experimental Studies ◽

Biological Aging ◽

Multiple Time ◽

Epigenetic Aging ◽

Epigenetic Age ◽

Epigenetic Age Acceleration ◽

Aging Rates ◽

Multiple Time Points ◽

Over Time

Abstract “Epigenetic clocks” have become widely used to assess individual rates of biological aging. However, experimental data are limited in humans to identify potential confounding factors that may influence one’s rate of epigenetic aging and multiple health outcomes. We examined multiple epigenetic aging measures among regular smokers who quit smoking for two weeks. DNA methylation markers were assessed in both whole blood and saliva at multiple time points using a customized DNA methylation microarray. Generally, no changes in epigenetic aging rates were detected in the two week observation period with the exception of pronounced decreases over time in rate of Hannum’s clock and Extrinsic Epigenetic Age Acceleration in blood DNA. In saliva DNA, decreases over time were detected in the rates of the GrimAge and DNAmPhenoAge clocks, but we saw an increase in the rate of the Skin and Blood Clock. Additional experimental studies of other common exposures may be useful to better characterize factors that may affect the observed “rate” of epigenetic aging.

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New Targeted Approaches for Epigenetic Age Predictions

10.1101/799031 ◽

2019 ◽

Cited By ~ 1

Author(s):

Yang Han ◽

Julia Franzen ◽

Thomas Stiehl ◽

Michael Gobs ◽

Chao-Chung Kuo ◽

...

Keyword(s):

Dna Methylation ◽

Cost Effective ◽

Amplicon Sequencing ◽

Digital Pcr ◽

Ctcf Binding ◽

Ctcf Binding Site ◽

High Throughput Analysis ◽

Cpg Sites ◽

Targeted Analysis ◽

Epigenetic Age

AbstractAging causes epigenetic modifications, which are utilized as a biomarker for the aging process. While genome-wide DNA methylation profiles enable robust age-predictors by integration of many age-associated CG dinucleotides (CpGs), there are various alternative approaches for targeted measurements at specific CpGs that better support standardized and cost-effective high-throughput analysis. In this study, we utilized 4,650 Illumina BeadChip datasets of blood to select the best suited CpG sites for targeted analysis. DNA methylation analysis at these sites with either pyrosequencing or droplet digital PCR (ddPCR) revealed a high correlation with chronological age. In comparison, bisulfite barcoded amplicon sequencing (BBA-seq) gave slightly lower precision at individual CpGs. However, BBA-seq data revealed that the correlation of methylation levels with age at neighboring CpG sites follows a bell-shaped curve, often accompanied by a CTCF binding site at the peak. We demonstrate that within individual BBA-seq reads the DNA methylation at neighboring CpGs is not coherently modified but reveals a stochastic pattern. Based on this, we have developed an alternative model for epigenetic age predictions based on the binary sequel of methylated and non-methylated sites in individual reads, which reflects heterogeneity in epigenetic aging within a sample. Thus, the stochastic evolution of age-associated DNA methylation patterns, which seems to resemble epigenetic drift, enables epigenetic clocks for individual DNA strands.

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Epigenetic Clocks Are Not Accelerated in COVID-19 Patients

International Journal of Molecular Sciences ◽

10.3390/ijms22179306 ◽

2021 ◽

Vol 22 (17) ◽

pp. 9306

Author(s):

Julia Franzen ◽

Selina Nüchtern ◽

Vithurithra Tharmapalan ◽

Margherita Vieri ◽

Miloš Nikolić ◽

...

Keyword(s):

Dna Methylation ◽

Risk Factor ◽

Acute Respiratory Distress Syndrome ◽

Distress Syndrome ◽

Amplicon Sequencing ◽

Chronological Age ◽

Blood Samples ◽

Telomere Attrition ◽

Epigenetic Aging ◽

Epigenetic Age

Age is a major risk factor for severe outcome of the 2019 coronavirus disease (COVID-19). In this study, we followed the hypothesis that particularly patients with accelerated epigenetic age are affected by severe outcomes of COVID-19. We investigated various DNA methylation datasets of blood samples with epigenetic aging signatures and performed targeted bisulfite amplicon sequencing. Overall, epigenetic clocks closely correlated with the chronological age of patients, either with or without acute respiratory distress syndrome. Furthermore, lymphocytes did not reveal significantly accelerated telomere attrition. Thus, these biomarkers cannot reliably predict higher risk for severe COVID-19 infection in elderly patients.

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A New Monocyte Epigenetic Clock Reveals Effects of Alcohol Consumption on Epigenetic Aging in Three Independent Cohorts

10.1101/2021.03.22.436488 ◽

2021 ◽

Author(s):

Xiaoyu Liang ◽

Rajita Sinha ◽

Amy C. Justice ◽

Mardge H. Cohen ◽

Bradley E. Aouizerat ◽

...

Keyword(s):

Alcohol Consumption ◽

Hiv Infection ◽

Clinical Decision Making ◽

Clinical Decision ◽

Biological Age ◽

Biological Aging ◽

Epigenetic Clock ◽

Excessive Alcohol Consumption ◽

Epigenetic Age ◽

The Impact

AbstractBackgroundExcessive alcohol consumption increases the risk of aging-related comorbidities and mortality. Assessing the impact of alcohol consumption on biological age is important for clinical decision-making and prevention. Evidence shows that alcohol alters monocyte function, and age is associated with DNA methylome and transcriptomic changes among monocytes. However, no monocyte-based epigenetic clock is currently available. In this study, we developed a new monocyte-based DNA methylation clock (MonoDNAmAge) by using elastic net regularization. The MonoDNAmAge was validated by benchmarking using epigenetic age acceleration (EAA) in HIV infection. Using MonoDNAmAge clock as well as four established clocks (i.e., HorvathDNAmAge, HannumDNAmAge, PhenoDNAmAge, GrimDNAmAge), we then evaluated the effect of alcohol consumption on biological aging in three independent cohorts (N=2,242).ResultsMonoDNAmAge, comprised of 186 CpG sites, was highly correlated with chronological age (rtraining=0.96, p<2.20E-16; rtesting=0.86, p=1.55E-141). The MonoDNAmAge clock predicted an approximately 10-year age acceleration from HIV infection in two cohorts. Quadratic regression analysis showed a nonlinear relationship between MonoDNAmAge and alcohol consumption in the Yale Stress Center Community Study (YSCCS, pmodel=4.55E-08, px2 =7.80E-08) and in the Veteran Aging Cohort Study (VACS, pmodel=1.85E-02, px2 =3.46E-02). MonoDNAmAge and light alcohol consumption showed a negative linear relationship in the Women’s Interagency HIV Study (WIHS, β=-2.63, px=2.82E-06). Heavy consumption increased EAAMonoDNAmAge up to 1.60 years in the VACS while light consumption decreased EAAMonoDNAmAge to 2.66 years in the WIHS. These results were corroborated by the four established epigenetic clocks.ConclusionsWe observed a nonlinear effect of alcohol consumption on epigenetic age that is estimated by a novel monocyte-based “clock” in three distinct cohorts, highlighting the complex effects of alcohol consumption on biological age.

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The costs of competition: high social status males experience accelerated epigenetic aging in wild baboons

10.1101/2020.02.22.961052 ◽

2020 ◽

Cited By ~ 1

Author(s):

Jordan A. Anderson ◽

Rachel A. Johnston ◽

Amanda J. Lea ◽

Fernando A. Campos ◽

Tawni N. Voyles ◽

...

Keyword(s):

Dominance Rank ◽

Natural Populations ◽

Life History Strategy ◽

Male Dominance ◽

Biological Aging ◽

Epigenetic Clock ◽

Epigenetic Aging ◽

Epigenetic Age ◽

Aging Rates ◽

Young Life

AbstractAging, for virtually all life, is inescapable. However, within populations, biological aging rates vary. Understanding sources of variation in this process is central to understanding the biodemography of natural populations. We constructed a DNA methylation-based age predictor for an intensively studied wild baboon population in Kenya. Consistent with findings in humans, the resulting “epigenetic clock” closely tracks chronological age, but individuals are predicted to be somewhat older or younger than their known ages. Surprisingly, these deviations are not explained by the strongest predictors of lifespan in this population, early adversity and social integration. Instead, they are best predicted by male dominance rank: high-ranking males are predicted to be older than their true ages, and epigenetic age tracks changes in rank over time. Our results argue that achieving high rank for male baboons—the best predictor of reproductive success—imposes costs consistent with a “live fast, die young” life history strategy.

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An epigenetic aging analysis of randomized metformin and weight loss interventions in overweight postmenopausal breast cancer survivors

Clinical Epigenetics ◽

10.1186/s13148-021-01218-y ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Jamaji C. Nwanaji-Enwerem ◽

Felicia Fei-Lei Chung ◽

Lars Van der Laan ◽

Alexei Novoloaca ◽

Cyrille Cuenin ◽

...

Keyword(s):

Breast Cancer ◽

Weight Loss ◽

Cancer Survivors ◽

Breast Cancer Survivors ◽

Controlled Trial ◽

Postmenopausal Breast Cancer ◽

Biological Aging ◽

Epigenetic Aging ◽

Epigenetic Age ◽

Registration Number

AbstractMetformin and weight loss relationships with epigenetic age measures—biological aging biomarkers—remain understudied. We performed a post-hoc analysis of a randomized controlled trial among overweight/obese breast cancer survivors (N = 192) assigned to metformin, placebo, weight loss with metformin, or weight loss with placebo interventions for 6 months. Epigenetic age was correlated with chronological age (r = 0.20–0.86; P < 0.005). However, no significant epigenetic aging associations were observed by intervention arms. Consistent with published reports in non-cancer patients, 6 months of metformin therapy may be inadequate to observe expected epigenetic age deceleration. Longer duration studies are needed to better characterize these relationships.Trial Registration: Registry Name: ClincialTrials.Gov.Registration Number: NCT01302379.Date of Registration: February 2011.URL:https://clinicaltrials.gov/ct2/show/NCT01302379

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