Sperm epigenetic clock predicts pregnancy outcomes in the general population
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE185445 | GEO | 2022/07/06
REPOSITORIES: GEO
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Project description:DNA methylation microarray analysis was performed on human donor whole blood samples from patients with and without AMD. A total of 30 patient samples including 16 Normal, 3 AREDS grade 2 (early AMD) and 11 AREDS grade 3 (intermediate AMD) (AMD total, n = 14) were selected. Samples were obtained from individuals phenotyped according to the Age-Related Eye Disease Study (AREDS) classification. DNAm levels were measured using the EPIC-array (Illumina Inc., San Diego, CA, USA). Samples run on the EPIC-array were randomized and balanced for disease status and smoking status to minimise chip and row specific effects. The EPIC-array incorporated technical controls into the experimental design. In total, 500 ng (50 ng/μL) total peripheral whole blood-derived gDNA was bisulfite converted using the EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA) and hybridised to the EPIC-array according to the manufacturer’s instructions. Quality control analysis was performed using GenomeStudio (v2011.1). Raw IDAT files were then read into R (version 3.31) using the read.metharray.exp function within the minfi package. DNA methylation microarray data was collected in order to assess the estimated DNA methylation age using the Horvath multi-tissue, Hannum and Skin & Blood epigenetic clocks and to identify loci of differential methylation between the experimental groups.
2021-12-31 | E-MTAB-11279 | biostudies-arrayexpress
Project description:Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). We demonstrate that accurate age estimators can be built on the basis of highly conserved CpGs. However, the most accurate clock results from applying elastic net regression to all CpGs. While the anti-aging effect of calorie restriction could be detected with all types of epigenetic clocks, only ridge regression based clocks replicated the finding of slow epigenetic aging effects in dwarf mice. Overall, this study demonstrates that there are trade-offs when it comes to epigenetic clocks in mice. Highly accurate clocks might not be optimal for detecting the beneficial effects of anti-aging interventions.
2018-11-29 | GSE120136 | GEO
Project description:Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). We demonstrate that accurate age estimators can be built on the basis of highly conserved CpGs. However, the most accurate clock results from applying elastic net regression to all CpGs. While the anti-aging effect of calorie restriction could be detected with all types of epigenetic clocks, only ridge regression based clocks replicated the finding of slow epigenetic aging effects in dwarf mice. Overall, this study demonstrates that there are trade-offs when it comes to epigenetic clocks in mice. Highly accurate clocks might not be optimal for detecting the beneficial effects of anti-aging interventions.
2018-11-29 | GSE120132 | GEO
Project description:Epigenetic clocks are age predictors that use machine-learning models trained on DNA CpG methylation values to predict chronological or biological age. Increases in predicted epigenetic age relative to chronological age (epigenetic age acceleration) are connected to aging-associated pathologies, and changes in epigenetic age are linked to canonical aging hallmarks. However, epigenetic clocks rely on training data from bulk tissues whose cellular composition changes with age. We found that human naive CD8+ T cells, which decrease during aging, exhibit an epigenetic age 15–20 years younger than effector memory CD8+ T cells from the same individual. Importantly, homogenous naive T cells isolated from individuals of different ages show a progressive increase in epigenetic age, indicating that current epigenetic clocks measure two independent variables, aging and immune cell composition. To isolate the age-associated cell intrinsic changes, we created a new clock, the IntrinClock, that did not change among 10 immune cell types tested. IntrinClock showed a robust predicted epigenetic age increase in a model of replicative senescence in vitro and age reversal during OSKM-mediated reprogramming
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Project description:Markers of biological ageing have potential utility in primary care and public health. We developed a model of age based on untargeted metabolic profiling across multiple platforms, including nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry in urine and serum, within a large sample (N=2,239) from the UK Airwave cohort. We validated a subset of model predictors in a Finnish cohort including repeat measurements from 2,144 individuals. DNA methylation age was assessed for 1,110 participants using the Infinium HumanMethylation EPIC BeadChip. We investigated the determinants of accelerated ageing, including lifestyle and psychological risk factors for premature mortality. The metabolomic age model was well correlated with chronological age (mean r=0.86 across independent test sets). Increased metabolomic age acceleration (mAA) was associated after false discovery rate (FDR) correction with overweight/obesity, diabetes, heavy alcohol use and depression. DNA methylation age acceleration measures were uncorrelated with mAA. Increased DNA methylation phenotypic age acceleration (N = 1,110) was associated after FDR correction with heavy alcohol use, hypertension and low income. In conclusion, metabolomics is a promising approach for the assessment of biological age and appears complementary to established epigenetic clocks.
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Project description:DNA methylation is a reaction that results in the formation of 5-methylcytosine when a methyl group is added to the cytosine’s C5 position. As organisms age, DNA methylation patterns change in a reproducible fashion. This phenomenon has established DNA methylation as a valuable biomarker in aging studies. Epigenetic clocks based on weighted combinations of methylation sites have been developed to accurately predict the age of an individual from their methylome. However, many epigenetic clocks, particularly those that utilize penalized regression, model the changes in methylation linearly with age. Moreover, these models, which use methylation levels as features, are not robust to missing data and do not account for the count-based nature of bisulfite sequence data. Additionally, the models are generally not interpretable. To overcome these challenges, we present BayesAge, an extension of the previously developed scAge approach that was developed for the analysis of single cell DNA methylation datasets. BayesAge utilizes maximum likelihood estimation (MLE) to infer ages, models count data using binomial distributions, and uses LOWESS smoothing to capture the non-linear dynamics between methylation and age. Our approach is designed for use with bulk bisulfite sequencing datasets. BayesAge outperforms scAge in several respects. Specifically, BayesAge’s age residuals are not age associated, thus providing a less biased representation of epigenetic age variation across populations. Moreover, BayesAge enables the estimation of error bounds on age inference and, when run on downsampled data, its coefficient of determination between predicted and actual ages surpasses both scAge and penalized regression.
2024-03-20 | GSE261769 | GEO
Project description:Chronological aging correlates with epigenetic modifications at specific loci, calibrated to species lifespan. Such ‘epigenetic clocks’ appear conserved among mammals, but whether they are cell-autonomous and restricted by maximal organismal lifespan remains unknown. We used a multi-lifetime murine model of repeat vaccination and memory T cell transplantation to test whether epigenetic aging tracks with cellular replication, and if such clocks continue ‘counting’ beyond species lifespan. We found that memory T cell epigenetic clocks tick independently of host age and continue through four lifetimes. Instead of recording chronological time, T cells recorded proliferative experience through modification of cell cycle regulatory genes. Applying this epigenetic profile across a range of human T cell contexts, we found that naïve T cells appeared ‘young’ regardless of organism age, while in pediatric patients, T-cell acute lymphoblastic leukemia (T-ALL) appeared to have epigenetically aged for up to 200 years. Thus, T cell epigenetic clocks measure replicative history and can continue to accumulate well-beyond organismal lifespan.
2024-05-06 | GSE263941 | GEO
Project description:We aim to improve anti-ageing drug discovery, currently achieved through laborious and lengthy longevity analysis. Recent studies demonstrated that the most accurate molecular method to measure human age is based on CpG methylation profiles, as exemplified by several epigenetics clocks that can accurately predict an individual’s age. Here, we developed CellAge, a new epigenetic clock that measures subtle ageing changes in primary human cells in vitro. As such it provides a unique tool to measure effects of relatively short pharmacological treatments on ageing. We validated our CellAge clock against known longevity drugs such as rapamycin and trametinib. Moreover, we uncovered novel anti-ageing drugs, torin2 and Dactolisib (BEZ-235), demonstrating the value of our approach as a screening and discovery platform for anti-ageing strategies. CellAge outperforms other epigenetic clocks in measuring subtle ageing changes in primary human cells in culture. The tested drug treatments reduced senescence and other ageing markers, further consolidating our approach as a screening platform. Finally, we showed that the novel anti-ageing drugs we uncovered in vitro, indeed increased longevity in vivo. Our method expands the scope of CpG methylation profiling from measuring human chronological and biological age from human samples in years, to accurately and rapidly detecting anti-ageing potential of drugs using human cells in vitro, providing a novel accelerated discovery platform to test sought after geroprotectors.
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Project description:Infertility is one of the most common reproductive health disorders affecting 16% of couples in the U.S. Most concerning are the new meta-analysis data showing that sperm counts among men in developed countries have declined over 50% in the past four decades. With no sign of reversing this downward trajectory, we may not only be facing a fertility crisis, but low sperm count also has wider public health implications, including increased risks in morbidity and mortality. Given this dramatic decrease in sperm quality over a short period, genetic influences are likely not attributable, but rather, environmental factors encountered over the life-course. The objective of this pilot project is to determine the feasibility of generating metabolomic data from human seminal plasma collected as part of the ongoing SEEDS cohort.
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Project description:Chronological age prediction from DNA methylation sheds light on human aging, indicates poor health and predicts lifespan. Previous studies developed methylation clocks based on linear regression models on methylation array data. While accurate, these models are limited to fixed-rate changes in methylation levels across age. Moreover, the high cost of methylation arrays, compared to targeted-PCR sequencing, hinders widespread utility of such predictors. We present an AI-based alternative termed GP-age, which uses a non-parametric approach based on Gaussian Process Regression of a large cohort of ~12K blood methylomes. Given a new blood sample, methylation levels are compared to the cohort samples, which are then weighted to predict the query age. Using only 30 CpG sites, our approach outperforms state-of-the-art methylation clocks that use hundreds of sites, with a median error of 2.1 years (on held-out data). Our model was also applied to sequencing-based data yielding highly accurate predictions. Overall, we provide an accessible alternative to current array-based methylation clocks, with future applications in aging research, forensic profiling, and monitoring epigenetic processes in transplantation medicine and cancer.
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