Causally measuring aging and rejuvenation through transcriptomic damage

Aging is caused, fully in large part, by the progressive accumulation of damage, yet quantifying age-related damage across tissues and conditions remains a challenge. Here, we present a computational framework to quantify damage from standard RNA-sequencing data. It captures four classes of aberrant transcript structures, including premature termination upon intron retention, domain-disrupting splice variants, repeat elements, and gene fusion events, each reflecting distinct forms of RNA integrity loss. Using this method, we revealed a robust age-associated increase in transcriptomic damage across tissues. To integrate these measurements into a unified biomarker, we constructed a transcriptomic damage-based aging (tDamAge) clock using machine learning models trained across mouse tissues or human peripheral blood. It could predict age and detect transcriptomic shifts under both pro-aging and anti-aging conditions. Progeroid models exhibited accelerated tDamAge, whereas interventions such as caloric restriction, rapamycin, and methionine restriction lowered tDamAge. Cross-dataset analysis showed that diverse anti-aging interventions converge on shared transcriptomic signatures, particularly RNA processing and chromatin organization pathways, and these age-associated patterns could be reversed by interventions. We further identified elevated damage age acceleration in Alzheimer’s disease and observed rejuvenation-like reductions during embryonic development. Together, our findings establish transcriptomic damage as a causal, quantifiable and biologically interpretable feature of aging and demonstrate that tDamAge could detect age progression, acceleration, deceleration, and reversal.