Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Serum MCC-seq]

Radiation therapy is an effective cancer treatment although damage to healthy tissues is common. Here we establish sequencing-based, cell-type specific DNA methylation reference maps of human and mouse tissues to infer the origins of cell-free DNA fragments released from dying cells into the circulation. We find cell-type specific DNA blocks mostly hypomethylated and located within genes intrinsic to cellular identity. In a mouse model, thoracic radiation-induced tissue damages were reflected by dose-dependent increases in lung endothelial, cardiomyocyte and hepatocyte methylated DNA in serum. The analysis of serum samples from breast cancer patients undergoing radiation treatment revealed distinct tissue-specific epithelial and endothelial responses to radiation across multiple organs. Strikingly, patients treated for right-sided breast cancers also showed increased hepatocyte and liver endothelial DNA in the circulation indicating the impact on liver tissues. Thus, cell-free methylated DNA in serum can uncover cell-type specific effects of radiation on healthy tissues and inform treatment. Tissue-of-origin analysis of cell-free DNA (cfDNA) using identified cell-type specific methylation patterns from reference WGBS data in healthy tissues. CfDNA from serum samples was analyzed by hybridization capture sequencing for changes in methylated cfDNA to uncover cellular damages. NOTE FROM SUBMITTER: Raw data are not available due to patient privacy concerns.