Do Quynh-Trang, Tzeng Shun-Fen, Wang Chih-Yen, Wu Chih-Hsing, Kafeenah Husam, Chen Shu-Hui
Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
Commun Biol. 2025 Mar 11;8(1):357. doi: 10.1038/s42003-025-07657-0.
Genotoxic estrogen metabolites generate various DNA lesions; however, their target genes and carcinogenic mechanisms remain unexplored. Here, genome-wide sequencing using click probe enrichment coupled with liquid chromatography-tandem mass spectrometry (Click-Probe-Seq/LC-MS) is developed to identify damaged genes and characterize the released and stable adducts induced by 4-hydroxy-17β-estradiol (4OHE2) in MCF-7 cell chromatin. The data reveal that guanine nucleobases in the GC-rich transcription-relevant domain are the main target sites. Moreover, the damage abundance positively correlates with DNase hypersensitive sites, suggesting that 4OHE2 preferentially attacks accessible chromatin regions beyond the estrogen receptor (ER) binding sites. Cell-based studies indicate that accumulated 4OHE2 suppresses gene transcription, causes ineffective damage repair, and decreases cell viability, differing from the uncontrolled cell growth caused by extensive ER signaling. The Click-Probe-Seq/LC-MS approach reveals the first chromatin damage map induced by an endogenous metabolite, exposing a previously unexplored landscape in cancer research that is applicable to other genotoxic species.
具有基因毒性的雌激素代谢产物会产生多种DNA损伤；然而，它们的靶基因和致癌机制仍未得到探索。在此，我们开发了一种全基因组测序方法，即利用点击探针富集结合液相色谱-串联质谱技术（Click-Probe-Seq/LC-MS），以鉴定受损基因，并表征4-羟基-17β-雌二醇（4OHE2）在MCF-7细胞染色质中诱导产生的释放型和稳定型加合物。数据显示，富含鸟嘌呤的与转录相关结构域中的鸟嘌呤碱基是主要靶位点。此外，损伤丰度与DNA酶超敏位点呈正相关，这表明4OHE2优先攻击雌激素受体（ER）结合位点之外的可及染色质区域。基于细胞的研究表明，积累的4OHE2会抑制基因转录，导致损伤修复无效，并降低细胞活力，这与广泛的ER信号传导所导致的细胞生长失控不同。Click-Probe-Seq/LC-MS方法揭示了由内源性代谢产物诱导产生的首张染色质损伤图谱，展现了癌症研究中一个此前未被探索的领域，该领域适用于其他具有基因毒性的物质。
