Circulating cell-free methylated DNA reveals tissue-specific, cellular damage from radiation treatment
Megan E. McNamara, … , Tommy Kaplan, Anton Wellstein
Megan E. McNamara, … , Tommy Kaplan, Anton Wellstein
Published June 15, 2023
Citation Information: JCI Insight. 2023;8(14):e156529. https://doi.org/10.1172/jci.insight.156529.
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Research Article Genetics Oncology

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

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

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Figure 3

Cell-type-specific DNA blocks are mostly hypomethylated, enriched at intragenic regions and developmental transcription factor (TF) binding motifs.

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Cell-type-specific DNA blocks are mostly hypomethylated, enriched at int...
(A and B) Heatmaps of differentially methylated cell-type-specific blocks identified from reference WGBS data compiled from healthy cell types and tissues in human (A) and mouse (B). Each cell in the plot marks the methylation score of 1 genomic region (rows) at each of the 20 cell types in human and 9 in mouse (columns). Up to 100 blocks with the highest methylation score are shown per cell type. The methylation score represents the number of fully unmethylated or methylated read pairs/total coverage for hypo- and hypermethylated blocks, respectively. (C) Schematic diagram depicting location of human cell-type-specific hypo- and hypermethylated blocks. Genomic annotations of cell-type-specific methylation blocks were determined by analysis using HOMER. (D) Distribution of human (left) and mouse (right) cell-type-specific methylation blocks relative to genomic regions used in the hybridization capture probes. Captured blocks with less than 5% variance across cell types represent blocks without cell-type specificity and were used as background. *P < 0.05 by χ2 test (degrees of freedom = 4). (E) Total number and top 5 TF binding sites enriched among cell-type-specific differentially methylated blocks (DMBs) in human (top) and mouse (bottom), using HOMER motif analysis (cumulative hypergeometric distribution statistic). As above, captured blocks with less than 5% variance across cell types were used as background.