New targeted approaches for epigenetic age predictions

BMC Biology, vol. 18, pp. 71

Abstract

BACKGROUND: Age-associated DNA methylation changes provide a promising 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. RESULTS: In this study, we utilized 4647 Illumina BeadChip profiles of blood to select CpG sites that facilitate reliable age-predictions based on pyrosequencing. We demonstrate that the precision of DNA methylation measurements can be further increased with droplet digital PCR (ddPCR). In comparison, bisulfite barcoded amplicon sequencing (BBA-seq) gave slightly lower correlation between chronological age and DNA methylation at individual CpGs, while the age-predictions were overall relatively accurate. Furthermore, BBA-seq data revealed that the correlation of methylation levels with age at neighboring CpG sites follows a bell-shaped curve, often associated with a CTCF binding site. 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 a new approach 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. CONCLUSION: Targeted DNA methylation analysis at few age-associated CpGs by pyrosequencing, BBA-seq, and particularly ddPCR enables high precision of epigenetic age-predictions. Furthermore, we demonstrate that the stochastic evolution of age-associated DNA methylation patterns in BBA-seq data enables epigenetic clocks for individual DNA strands.

Authors 11

1. Yang Han Aachen Institute for Biomedical Engineering - Cell Biology

   RWTH Aachen University · Universitätsklinikum Aachen

   Affiliation as printed

   Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany

   Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany

2. Julia Franzen Aachen Institute for Biomedical Engineering - Cell Biology

   RWTH Aachen University · Universitätsklinikum Aachen

   Affiliation as printed

   Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany

   Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany

3. Thomas Stiehl

   Heidelberg University

   Affiliation as printed

   Interdisciplinary Center for Scientific Computing (IWR), Institute of Applied Mathematics, University of Heidelberg, Heidelberg, Germany

4. Michael Gobs Aachen Institute for Biomedical Engineering - Cell Biology

   RWTH Aachen University · Universitätsklinikum Aachen

   Affiliation as printed

   Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany

   Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany

5. Chao‐Chung Kuo Aachen Institute for Biomedical Engineering - Cell Biology

   RWTH Aachen University · Universitätsklinikum Aachen

   Affiliation as printed

   Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany

   Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany

   Institute for Biomedical Engineering – Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany

6. Miloš Nikolić Aachen Institute for Biomedical Engineering - Cell Biology

   RWTH Aachen University · Universitätsklinikum Aachen

   Affiliation as printed

   Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany

   Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany

7. Jan Hapala Aachen Institute for Biomedical Engineering - Cell Biology

   RWTH Aachen University · Universitätsklinikum Aachen

   Affiliation as printed

   Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany

   Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany

8. Barbara Elisabeth Koop

   Heinrich Heine University Düsseldorf

   Affiliation as printed

   Institute for Legal Medicine, Heinrich Heine University, Düsseldorf, Germany

9. Klaus Strathmann Aachen Institute for Transfusion Medicine

   RWTH Aachen University

   Affiliation as printed

   Institute for Transfusion Medicine, RWTH Aachen University Medical School, Aachen, Germany

10. Stefanie Ritz‐Timme

    Heinrich Heine University Düsseldorf

    Affiliation as printed

    Institute for Legal Medicine, Heinrich Heine University, Düsseldorf, Germany

11. Wolfgang Wagner corresponding Aachen Institute for Biomedical Engineering - Cell Biology

    RWTH Aachen University · Universitätsklinikum Aachen

    Affiliation as printed

    Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany. wwagner@ukaachen.de

    Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany. wwagner@ukaachen.de

    Institute for Biomedical Engineering – Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany