TIME-Seq Enables Highly-Efficient Epigenetic Age Predictions in Large-Scale Human and Mouse Longevity Studies

Abstract

Epigenetic “clocks” based on DNA methylation (DNAme) are the most robust and widely-used aging biomarkers, but prevailing clock methods are expensive and laborious. Here, we describe Tagmentation-based Indexing for Methylation Sequencing (TIME-Seq), a highly-scalable approach for low-cost epigenetic clocks. With TIME-Seq, we predict age in 3,556 human and mouse samples from nine tissue- and cell-types. We show that TIME-Seq clocks are accurate and robust, enriched for Polycomb Repressive Complex 2 (PRC2)-regulated loci, and benchmark favorably against conventional methods despite being up to 100-fold less expensive. In parallel, we discovered a new approach to predict age from shallow sequencing (e.g., 0.01x clock-depth) by adapting scAge for bulk analysis. Using dietary interventions and gene therapy, we find that TIME-Seq clocks reflect diverse interventions in multiple tissues. Finally, by collecting 810 blood samples from 60 mice in seven months, we observe dynamic epigenetic age-deceleration after treatment with lifespan-extending drugs, rapamycin and acarbose. Our methods will accelerate aging research by enabling efficient clock measurement in larger-scale human and animal studies.

Note:
Funding Information: This work was supported by the National Institutes of Health grant to The Jackson Laboratory Nathan Shock Center of Excellence in the Basic Biology of Aging (AG038070). P.T.G was supported by the National Science Foundation Graduate Research Fellowship (DGE1745303) and the NIH-NIA F99/K00 award (AG073499), and A.E.K was supported by a Diamond/AFAR Postdoctoral Transition Award in Aging (DIAMOND19036) and an NIA K99/R00 Fellowship (K99AG070102). N.N.H. and M.K.E. are supported by the Intramural Research Program (IRP) of the National Institute on Aging (NIA), National Institutes of Health. This work was also funded by NIH/NIA (R01AG019719 to D.A.S; P01AG055369 to S.J.M.; AG065403 and AG047200 to V.N.G) and the Glenn Foundation for Medical Research (to D.A.S.). The LEAP experiment was supported by a Longevity Impetus Grant to P.T.G.

Declaration of Interests: P.T.G. and D.A.S. are named inventors on a patent application related to TIME-Seq methods filed by Harvard Medical School and licensed to Tally Health. D.A.S is a founder, investor, and equity owner for Tally Health and P.T.G. has received minor equity compensation as a consultant to Tally Health. Additional info on D.A.S. affiliations not directly related to this work can be found at sinclair.hms.harvard.edu/david-sinclairs-affiliations. A.T., C.K, V.N.G. are named inventors on a patent application related to scAge filed by Brigham and Women’s Hospital. All other authors have nothing to disclose.

Ethics Approval Statement: Sample handling, data analysis, and study design were approved by the Mass General Brigham Institutional Review Board (protocol number 2021P003059).

All mouse experiments were approved by the Institutional Animal Care and Use Committee of the Harvard Medical Area Standing Committee on Animals.

Keywords: Epigenetics, aging, DNA methylation, biomarkers, epigenetic clocks, human research, rapamycin, acarbose, dietary interventions, high-fat diet, caloric restriction