Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Reference Cell-type RNA-seq]. Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Reference Cell-type RNA-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. Overall design: Transcriptomic profiling of gene expression reflective of cellular identity in sorted cell populations from healthy tissue donors.

放射治疗是临床有效的癌症治疗手段，但其常会对健康组织造成损伤。本研究构建了基于测序技术的人类与小鼠组织的细胞类型特异性DNA甲基化参考图谱，旨在推断死亡细胞释放进入循环系统的循环游离DNA (cell-free DNA) 片段的组织来源。研究发现，细胞类型特异性DNA区段大多呈低甲基化状态，且定位于与细胞固有身份密切相关的基因内部。在小鼠模型中，胸部辐射诱发的组织损伤可通过血清中肺内皮细胞、心肌细胞与肝细胞甲基化DNA的剂量依赖性升高得到反映。对接受放射治疗的乳腺癌患者血清样本进行分析后发现，多个器官的上皮细胞与内皮细胞对辐射呈现出组织特异性的差异化应答。尤为值得关注的是，接受右侧乳腺癌治疗的患者外周循环中肝细胞与肝内皮细胞DNA水平同样升高，这表明辐射对肝脏组织存在影响。综上，血清中的循环游离甲基化DNA能够揭示辐射对健康组织的细胞类型特异性效应，可为临床治疗提供参考依据。整体实验设计：对来自健康组织供体的分选细胞群体中反映细胞身份的基因表达进行转录组分析。