Circulating cell-free methylated DNA reveals tissue-specific, cellular damage from radiation treatment

Radiation therapy is an effective cancer treatment although damages to healthy tissues are common. Here we analyzed cell-free, methylated DNA released from dying cells into the circulation to evaluate radiation-induced cellular damages in different tissues. To map the circulating DNA fragments to human and mouse tissues, we established sequencing-based, cell-type specific reference DNA methylation atlases. We found that cell-type specific DNA blocks were mostly hypomethylated and located within signature genes of cellular identity. Cell-free DNA fragments were captured from serum samples by hybridization to CpG-rich DNA panels and mapped to the DNA methylation atlases. In a mouse model, thoracic radiation-induced tissue damages were reflected by dose-dependent increases in lung endothelial and cardiomyocyte methylated DNA in serum. The analysis of serum samples from breast cancer patients undergoing radiation treatment revealed distinct dose-dependent and 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, changes in cell-free methylated DNA can uncover cell-type specific effects of radiation and provide a readout of the biologically effective radiation dose received by healthy tissues.