Evidence map›Paper›PMID 39806003›Full record

ArticleNature aging2025

Somatic mutation as an explanation for epigenetic aging.

Zane Koch, Adam Li, Daniel S Evans, Steven Cummings, Trey Ideker

Abstract read
In one paragraph

Article in Nature aging, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.

0numbers the graph read from it
0cells of the map it votes in
29citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

29 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. [Research Advances on Mechanisms and Interventions of DNA Methylation-Regulated Aging-Related Imbalance in Bone Metabolism].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2026
    Review
  5. Review
  6. Article
  7. Review
  8. Review
  9. Article
  10. The aging genome exhibits organized vulnerability to somatic mutations.bioRxiv : the preprint server for biology · 2026
    Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. Review
  16. Review
  17. Epigenetic networks coordinate DNA methylation across the genome.Molecular therapy : the journal of the American Society of Gene Therapy · 2025
    Review
  18. Article
  19. How to measure and model cardiovascular aging.Cardiovascular research · 2025
    Review
  20. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Zane KochProgram in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA.
Adam LiProgram in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA.
Daniel S EvansCalifornia Pacific Medical Center Research Institute, San Francisco, CA, USA.
Steven CummingsCalifornia Pacific Medical Center Research Institute, San Francisco, CA, USA. steven.cummings@ucsf.edu.ORCID http://orcid.org/0000-0001-8808-260X
Trey IdekerProgram in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA. tideker@health.ucsd.edu.ORCID http://orcid.org/0000-0002-1708-8454

Funding

Study of Muscle, Mobility and Aging: SOMMA2R01AG059416 · NIA · CALIFORNIA PACIFIC MED CTR RES INSTITUTE · PI STEVEN RON CUMMINGS, Peggy Mannen Cawthon · 2018 to 2026
$70.3M
TR&D 3 - Network Guided Machine LearningP41GM103504 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IDEKER, TREY · 2012 to 2024
$17.3M
The Cancer Cell Map Initiative v2.0U54CA274502 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Nevan J Krogan · 2022 to 2026
$14.2M
NCI NIH HHS U54 CA274502NIA NIH HHS R01 AG059416NIGMS NIH HHS P41 GM103504
6 · The paper itself

Abstract

DNA methylation marks have recently been used to build models known as epigenetic clocks, which predict calendar age. As methylation of cytosine promotes C-to-T mutations, we hypothesized that the methylation changes observed with age should reflect the accrual of somatic mutations, and the two should yield analogous aging estimates. In an analysis of multimodal data from 9,331 human individuals, we found that CpG mutations indeed coincide with changes in methylation, not only at the mutated site but with pervasive remodeling of the methylome out to ±10 kilobases. This one-to-many mapping allows mutation-based predictions of age that agree with epigenetic clocks, including which individuals are aging more rapidly or slowly than expected. Moreover, genomic loci where mutations accumulate with age also tend to have methylation patterns that are especially predictive of age. These results suggest a close coupling between the accumulation of sporadic somatic mutations and the widespread changes in methylation observed over the course of life.

Indexed as

AgingDNA MethylationEpigenesis, GeneticMutationAdultAgedCpG IslandsFemaleHumansMaleMiddle Aged

Identifiers

PMID39806003
PMCPMC12204751

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.