Epigenetic age-predictor for mice based on three CpG sites
- RWTH Aachen University Medical School, Germany
- University Hospital RWTH Aachen, Germany
- Ulm University, Germany
- University Medical Center Groningen, Netherlands
- Instituto Biodonostia, Spain
- Tecnun-University of Navarra, Spain
- Cincinnati Children's Hospital Burnet Campus, United States
Figures
Figure 1 with 1 supplement
Three CpG epigenetic age-predictor for mice.
(a–c) DNA methylation (DNAm) of three CpGs in the genes Prima1, Hsf4 and Kcns1 was analyzed by pyrosequencing in 24 C57BL/6 mice (training set). Coefficient of determination (R2) of DNAm versus chronological age is indicated. (d) Based on these age-associated DNAm changes a multivariable model for age prediction was calculated. (e–g) Subsequently, two independent validation sets were analyzed: 21 C57BL/6 mice from the University of Ulm and 19 C57BL/6 mice from the University of Groningen (validation sets 1 and 2, respectively). (h) Age predictions with the three-CpG-model revealed a high correlation with chronological age in the independent validation sets (MAD = mean absolute deviation; MAE = median absolute error).
Figure 1—figure supplement 1
Target sequences of pyrosequencing assays.
Sequences for the three genomic regions are depicted and CpG sites (red) are numbered by the dispensation order. The relevant CpGs with highest age-correlation are highlighted in bold.
Figure 2
Gender does not affect epigenetic age predictions in mice.
The deviations of predicted age by our three-CpG predictor versus chronological age did not reveal significant differences between female and male C57BL/6 mice (Mann–Whitney U test p=0.6).
Figure 3
Age-associated DNA methylation at the three CpG sites in different tissues.
Different tissues were isolated of three young (9.6 weeks) and three old mice (56.9 weeks) and DNAm was analyzed at the three relevant CpGs in (a) Prima1, (b) Hsf4, and (c) Kcns1. Epigenetic age-predictions using the 3 CpG model for blood demonstrated also significant differences between young and old mice in skin, intestine, brain, and testis (mean ± standard deviation; Student t-tests: *p<0.05; **p<0.01; ***p<0.001).
Figure 4
Epigenetic aging is accelerated in DBA/2 mice as compared to C57BL/6 mice.
(a–c) Age-related DNA methylation (DNAm) determined by pyrosequencing assay for three candidate CpGs on 33 of DBA/2 blood samples (14 mice from the University of Ulm and 19 mice from the University of Groningen; red). For comparison we provided measurements of the C57BL/6 mice (only from validation sets; blue). (d) Epigenetic age-predictions using the three CpG multivariable model for the C57BL/6 mice (blue; linear regression) and DBA/2 mice (red, logarithmic regression). Age-predictions in DBA/2 mice rather followed a logarithmic regression (R = Pearson correlation); (e) Based on the DNAm measurements in DBA/2 we adjusted the multivariate regression model for age-predictions of this mouse strain as described in the text (DBA/2 predictor).
Additional files
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Source data 1
Pyrosequencing raw data of mouse epigenetic aging predictor.
- https://doi.org/10.7554/eLife.37462.008
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Supplementary file 1
Age-associated DNAm in nine genomic regions of the training set.
- https://doi.org/10.7554/eLife.37462.009
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Supplementary file 2
Multivariable model based on 15 CpGs
- https://doi.org/10.7554/eLife.37462.010
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Supplementary file 3
Primers for pyrosequencing.
- https://doi.org/10.7554/eLife.37462.011
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Transparent reporting form
- https://doi.org/10.7554/eLife.37462.012
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Epigenetic age-predictor for mice based on three CpG sites
eLife 7:e37462.
https://doi.org/10.7554/eLife.37462
