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

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Abstract

Radiation therapy is an effective cancer treatment, although damage to healthy tissues is common. Here we analyzed cell-free, methylated DNA released from dying cells into the circulation to evaluate radiation-induced cellular damage 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 damage was reflected by dose-dependent increases in lung endothelial and cardiomyocyte methylated DNA in serum. The analysis of serum samples from patients with breast cancer 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.

Authors

Megan E. McNamara, Netanel Loyfer, Amber J. Kiliti, Marcel O. Schmidt, Sapir Shabi-Porat, Sidharth S. Jain, Sarah Martinez Roth, A. Patrick McDeed IV, Nesreen Shahrour, Elizabeth Ballew, Yun-Tien Lin, Heng-Hong Li, Anne Deslattes Mays, Sonali Rudra, Anna T. Riegel, Keith Unger, Tommy Kaplan, Anton Wellstein