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Longitudinal prediction of DNA methylation to forecast epigenetic outcomes

ABSTRACT: Longitudinal prediction of DNA methylation to forecast epigenetic outcomes

PROVIDER: PRJNA1068624 | ENA |

REPOSITORIES: ENA

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Longitudinal prediction of DNA methylation to forecast epigenetic outcomes

Project description:We introduce a probabilistic and longitudinal machine learning framework based on multi-mean Gaussian processes (GPs), accounting for individual and gene correlations across time. This method provides future predictions of DNA methylation status at different individual ages while accounting for uncertainty.

2025-05-14 | GSE254135 | GEO

Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes

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Project description:Prediction of neurological outcomes shortly after cardiac arrest would represent a major breakthrough. We tested the ability of gene expression profiles of blood cells to predict outcome in cardiac arrest patients. 35 consecutive cardiac arrest patients treated with therapeutic hypothermia (33Â°C for 24h) were included in this prospective monocentre study. Cerebral Performance Category (CPC) was determined at discharge and 6 months later. All patients had blood sampling at the end of hypothermia. Gene expression profiles of blood cells were determined using 25,000~gene microarray in two groups of patients: good outcome (CPC 1-2) and bad outcome (CPC 3-5).

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Developmental Dynamics of Blood DNA Methylation in Dairy Cattle from Birth to Adulthood: a longitudinal study based on enzymatic methyl-sequencing (EM-seq).

Project description:DNA methylation is a key epigenetic mechanism involved in the regulation of gene expression, development, and ageing. It is also one of the most promising biomarkers for biological age prediction, particularly through the development of epigenetic clocks. In this study, we analyzed DNA methylation dynamics in Holstein Friesian dairy cattle across three developmental stages: birth, weaning, and adulthood, using enzymatic methyl-sequencing (EM-seq) data obtained from longitudinal blood samples collected from six female individuals. The results revealed variable methylation profiles across developmental stages, particularly in promoter regions. Differential methylation analysis highlighted marked epigenetic remodeling between birth and weaning (662,571 differentially methylated CpG sites, DMCs), as well as between weaning and adulthood (190,437 DMCs), with a global trend toward hypomethylation in adulthood. Furthermore, estimation of blood cell proportions by deconvolution indicated that methylation variations were partly associated with changes in cellular composition during development, suggesting that age alone did not fully explain the observed variability. Finally, a subset of CpG sites showing consistent and unidirectional methylation changes was identified, representing potential candidates for epigenetic aging biomarkers. These results may contribute to improving epigenetic age prediction models, particularly in young animals, a developmental stage that remains underrepresented in current epigenetic clocks. Overall, this study showed that DNA methylation dynamics in cattle result from an interaction between intrinsic aging processes, immune system maturation, and changes in cellular composition, and provided new insights into epigenetic age estimation in dairy cattle.

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DNA methylation of longitudinal samples from The Swedish Adoption/Twin Study of Aging (SATSA)

Project description:The methylation data were measured from longitudinal blood samples to study the longitudinal change of methylation in association with age.

2018-10-20 | E-MTAB-7309 | biostudies-arrayexpress

Longitudinal study of DNA methylation during the first 5 years of life

Project description:Background: Early life epigenetic programming influences adult health outcomes. Moreover, DNA methylation levels have been found to change more rapidly during the first years of life. Our aim was the identification and characterization of the CpG sites that are modified with time during the first years of life. We hypothesize that these DNA methylation changes would lead to the detection of genes that might be epigenetically modulated by environmental factors during early childhood and which, if disturbed, might contribute to susceptibility to diseases later in life. Methods: The study of the DNA methylation pattern of 485577 CpG sites was performed on 30 blood samples from 15 subjects, collected both at birth and at 5 years old, using IlluminaÂ® Infinium 450 k array. To identify differentially methylated CpG (dmCpG) sites, the methylation status of each probe was examined using linear models and the Empirical Bayes Moderated t test implemented in the limma package of R/Bioconductor. Surogate variable analysis was used to account for batch effects. Results: DNA methylation levels significantly changed from birth to 5 years of age in 6641 CpG sites. Of these, 36.79 % were hypermethylated and were associated with genes related mainly to developmental ontology terms, while 63.21 % were hypomethylated probes and associated with genes related to immune function. Conclusions: Our results suggest that DNA methylation alterations with age during the first years of life might play a significant role in development and the regulation of leukocyte-specific functions. This supports the idea that blood leukocytes experience genome remodeling related to their interaction with environmental factors, underlining the importance of environmental exposures during the first years of life and suggesting that new strategies should be take into consideration for disease prevention. Longitudinal study including 15 samples

2016-06-15 | E-GEOD-83334 | biostudies-arrayexpress

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