Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany.
Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany.
Int J Mol Sci. 2020 Aug 12;21(16):5778. doi: 10.3390/ijms21165778.
While ionizing radiation (IR) is a powerful tool in medical diagnostics, nuclear medicine, and radiology, it also is a serious threat to the integrity of genetic material. Mutagenic effects of IR to the human genome have long been the subject of research, yet still comparatively little is known about the genome-wide effects of IR exposure on the DNA-sequence level. In this study, we employed high throughput sequencing technologies to investigate IR-induced DNA alterations in human gingiva fibroblasts (HGF) that were acutely exposed to 0.5, 2, and 10 Gy of 240 kV X-radiation followed by repair times of 16 h or 7 days before whole-genome sequencing (WGS). Our analysis of the obtained WGS datasets revealed patterns of IR-induced variant (SNV and InDel) accumulation across the genome, within chromosomes as well as around the borders of topologically associating domains (TADs). Chromosome 19 consistently accumulated the highest SNVs and InDels events. Translocations showed variable patterns but with recurrent chromosomes of origin (e.g., Chr7 and Chr16). IR-induced InDels showed a relative increase in number relative to SNVs and a characteristic signature with respect to the frequency of triplet deletions in areas without repetitive or microhomology features. Overall experimental conditions and datasets the majority of SNVs per genome had no or little predicted functional impact with a maximum of 62, showing damaging potential. A dose-dependent effect of IR was surprisingly not apparent. We also observed a significant reduction in transition/transversion (Ti/Tv) ratios for IR-dependent SNVs, which could point to a contribution of the mismatch repair (MMR) system that strongly favors the repair of transitions over transversions, to the IR-induced DNA-damage response in human cells. Taken together, our results show the presence of distinguishable characteristic patterns of IR-induced DNA-alterations on a genome-wide level and implicate DNA-repair mechanisms in the formation of these signatures.
虽然电离辐射（IR）是医学诊断、核医学和放射学中强有力的工具，但它也是遗传物质完整性的严重威胁。IR 对人类基因组的诱变效应长期以来一直是研究的主题，但人们对 IR 暴露在 DNA 序列水平上对全基因组的影响仍然知之甚少。在这项研究中，我们采用高通量测序技术研究了急性暴露于 240 kV X 射线 0.5、2 和 10 Gy 后修复 16 小时或 7 天的人牙龈成纤维细胞（HGF）中的 IR 诱导的 DNA 改变，然后进行全基因组测序（WGS）。我们对获得的 WGS 数据集的分析揭示了 IR 诱导的变异（SNV 和 InDel）在整个基因组、染色体内部以及拓扑关联域（TAD）边界周围积累的模式。19 号染色体始终积累最高的 SNV 和 InDel 事件。易位显示出不同的模式，但具有可重复的染色体起源（例如，Chr7 和 Chr16）。IR 诱导的 InDel 数量相对增加，与 SNV 相比具有特征性特征，并且在没有重复或微同源特征的区域中，三联体缺失的频率相对较高。总体实验条件和数据集表明，大多数 SNV 对基因组没有或几乎没有预测的功能影响，最大数量为 62 个，显示出潜在的破坏性。IR 的剂量依赖性效应并不明显。我们还观察到 IR 依赖性 SNV 的转换/颠换（Ti/Tv）比值显著降低，这可能表明错配修复（MMR）系统的贡献，该系统强烈有利于修复转换而不是颠换，从而对人类细胞中的 IR 诱导的 DNA 损伤反应。总之，我们的结果表明，在全基因组水平上存在可区分的 IR 诱导的 DNA 改变的特征模式，并暗示 DNA 修复机制参与了这些特征的形成。
