DNA Methylation Signatures of Cellular Senescence Are Not Reversed by Senolytic Treatment

Epigenetic clocks are commonly used aging biomarkers based on DNA methylation that predict long-term morbidity and mortality risk. Increased cellular senescence with age is also posited to contribute to age-related disease and mortality. However, prior studies have found that existing epigenetic clocks show inconsistent associations with cellular senescence and no reductions after senolytic treatment. We hypothesize this reflects that senescence-related CpGs are a small proportion of age-related CpGs, and that an epigenetic clock focused on a core senescence signal conserved across different cell types and different senescence inducers would be a better tool for monitoring senescence and senolytic treatment compared to traditional epigenetic clocks. In our study, we find that senescence, age and mortality risk intersect at a small subset of the DNA methylome (9363 CpGs out of 396,333 analyzed; 2.4%). Utilizing these CpGs, we generated three different epigenetic clocks trained to predict in vitro senescence, age, and mortality, respectively. Surprisingly, all three of these predictors stayed the same or even accelerated after senolytic treatment in both in vivo and in vitro data. Our findings not only call into question whether cellular senescence can be captured by DNA methylation but also challenge the assumption that aging biomarkers decrease after geroscience interventions.