How epigenetic clocks tick: Unpacking the black box by deciphering biological pathways and transcriptomic signatures of accelerated aging

How epigenetic clocks tick: Unpacking the black box by deciphering biological pathways and transcriptomic signatures of accelerated aging | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article How epigenetic clocks tick: Unpacking the black box by deciphering biological pathways and transcriptomic signatures of accelerated aging Thalida Em Arpawong, Steve Cole, Harshanna Badhesha, Jung Ki Kim, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8844558/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 9 You are reading this latest preprint version Abstract Epigenetic clocks derived from DNA methylation robustly predict biological aging, health, and mortality, yet differ substantially in their predictive profiles. The biological processes underlying these differences remain poorly understood. Using data from 3,227 participants in the U.S. Health and Retirement Study, with contemporaneous DNA methylation and RNA-sequencing, we examined the five most widely used epigenetic clocks (Horvath, Hannum, PhenoAge, GrimAge, and DunedinPACE). Differential gene expression analyses identified clock-specific transcriptional signatures and enriched biological pathways, revealing substantial heterogeneity in the molecular processes captured by each clock. We further derived transcriptomic aging gene scores (TAGS), from differentially expressed genes of each age acceleration clock, and evaluated their associations with aging-related phenotypes. TAGS complemented DNAm clocks, and in several cases, showed stronger associations with age-related morbidities and mortality. Findings revealed more unique than common biological processes underlying clocks, illuminate their internal mechanisms, and advance their interpretability for aging research and clinical applications. Health sciences/Biomarkers Biological sciences/Computational biology and bioinformatics Health sciences/Diseases Biological sciences/Genetics Health sciences/Medical research Full Text Additional Declarations No competing interests reported. Supplementary Files MssSupplementaryInformation.docx MssSITablesS1aeDEGsfdr.01.xlsx MssSITablesS2aeGSEAfdr.25.xlsx MssSITablesS3GO75clusters.xlsx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 31 Mar, 2026 Reviews received at journal 25 Mar, 2026 Reviews received at journal 22 Mar, 2026 Reviewers agreed at journal 19 Mar, 2026 Reviewers agreed at journal 12 Mar, 2026 Reviewers invited by journal 12 Mar, 2026 Editor assigned by journal 12 Mar, 2026 Submission checks completed at journal 16 Feb, 2026 First submitted to journal 10 Feb, 2026 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8844558","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":606142844,"identity":"9e99cd6b-462a-46e0-b762-c93aafec9342","order_by":0,"name":"Thalida Em Arpawong","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAwElEQVRIiWNgGAWjYDADfgjFTIIWyQaStRgcIFYL/+yzBz/zVNyx23wj/eEHhgrrxAZCWiTO5SVL85x5lrztRo6xBMOZdMJaGM7wGEjnth1ONruRw8bA2HaYsBb5MzzGv0FajGekP2Ng/EeEFoMzPGYgW+wMJBLMGBgbiNBieIYvzfrPmcMJEmfeGEskHEs3JqhF7gzv4ZszKg7b87cDQ+xDjbUsQS0MDDxgEuKeBMLKEVrsiVM8CkbBKBgFIxIAAJLuPn/OodKBAAAAAElFTkSuQmCC","orcid":"","institution":"University of Southern California","correspondingAuthor":true,"prefix":"","firstName":"Thalida","middleName":"Em","lastName":"Arpawong","suffix":""},{"id":606142845,"identity":"1b72e4a6-866e-41fd-b709-2bded02d8359","order_by":1,"name":"Steve Cole","email":"","orcid":"","institution":"University of California","correspondingAuthor":false,"prefix":"","firstName":"Steve","middleName":"","lastName":"Cole","suffix":""},{"id":606142846,"identity":"1c56fa65-3cc9-4434-8778-c7c8fab076b8","order_by":2,"name":"Harshanna Badhesha","email":"","orcid":"","institution":"University of Southern California","correspondingAuthor":false,"prefix":"","firstName":"Harshanna","middleName":"","lastName":"Badhesha","suffix":""},{"id":606142847,"identity":"021e7ede-169b-4148-b822-bbe9823f919f","order_by":3,"name":"Jung Ki Kim","email":"","orcid":"","institution":"University of Southern California","correspondingAuthor":false,"prefix":"","firstName":"Jung","middleName":"Ki","lastName":"Kim","suffix":""},{"id":606142848,"identity":"be4a9d30-e5a1-47ac-808b-4803b72cea55","order_by":4,"name":"Christopher R. 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