A breast tissue-specific epigenetic clock provides accurate chronological age predictions and reveals de-correlation of age and DNA methylation in tumor-adjacent and tumor samples

Abstract Epigenetic clocks have been widely used to estimate biological age across various tissues, but their accuracy in breast tissue remains suboptimal. Pan-tissue models such as Horvath’s and Hannum’s clocks, perform poorly in predicting chronological age in breast tissue, underscoring the need for a tissue-specific approach. In this study, we introduce a Breast Tissue-specific Epigenetic Clock (BTEC), developed using DNA methylation data from 553 healthy breast tissue samples across seven different studies. BTEC significantly outperformed pan-tissue clocks, demonstrating superior correlation with chronological age (r=0.88) and lower prediction errors (MAE=3.27 years) without requiring for dataset-specific regressions adjustments. BTEC’s chronological age predictions for tumor-adjacent samples showed distortions, with an average deviation of -1.76 years, which was even more pronounced in tumor samples, where the average difference between predicted and chronological age was -12.29 years. When analyzed by molecular subtype, the distortion was greater in the more aggressive HER2+ and TNBC tumors compared to HR+ tumors. The probes used by BTEC were associated with known oncogenes, genes involved in estrogen metabolism, cadherin binding and fibroblast growth factor binding. Despite the general rejuvenation observed in tumor tissue compared to normal breast, the correlation between BTEC’s predictions and cancer-related survival indicated that TNBC tumors with increased epigenetic ages had significant lower survival.