Cell-free, methylated DNA in blood samples reveals tissue-specific, cellular damage from radiation treatment

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. ### Competing Interest Statement Georgetown University filed a patent related to some of the approaches described in this manuscript. MEB and AW are named as inventors on this application and declare that as a potential conflict of interest. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.