Jiang Yang, Mingard Cécile, Huber Sabrina M, Takhaveev Vakil, McKeague Maureen, Kizaki Seiichiro, Schneider Mirjam, Ziegler Nathalie, Hürlimann Vera, Hoeng Julia, Sierro Nicolas, Ivanov Nikolai V, Sturla Shana J
Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland.
Pharmacology and Therapeutics, Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
ACS Cent Sci. 2023 Feb 22;9(3):362-372. doi: 10.1021/acscentsci.2c01100. eCollection 2023 Mar 22.
Chemical modifications to DNA bases, including DNA adducts arising from reactions with electrophilic chemicals, are well-known to impact cell growth, miscode during replication, and influence disease etiology. However, knowledge of how genomic sequences and structures influence the accumulation of alkylated DNA bases is not broadly characterized with high resolution, nor have these patterns been linked with overall quantities of modified bases in the genome. For benzo(a) pyrene (BaP), a ubiquitous environmental carcinogen, we developed a single-nucleotide resolution damage sequencing method to map in a human lung cell line the main mutagenic adduct arising from BaP. Furthermore, we combined this analysis with quantitative mass spectrometry to evaluate the dose-response profile of adduct formation. By comparing damage abundance with DNase hypersensitive sites, transcription levels, and other genome annotation data, we found that although overall adduct levels rose with increasing chemical exposure concentration, genomic distribution patterns consistently correlated with chromatin state and transcriptional status. Moreover, due to the single nucleotide resolution characteristics of this DNA damage map, we could determine preferred DNA triad sequence contexts for alkylation accumulation, revealing a characteristic DNA damage signature. This new BaP damage signature had a profile highly similar to mutational signatures identified previously in lung cancer genomes from smokers. Thus, these data provide insight on how genomic features shape the accumulation of alkylation products in the genome and predictive strategies for linking single-nucleotide resolution in vitro damage maps with human cancer mutations.
DNA碱基的化学修饰，包括与亲电化学物质反应产生的DNA加合物，众所周知会影响细胞生长、复制过程中的错误编码以及影响疾病病因。然而，关于基因组序列和结构如何影响烷基化DNA碱基积累的知识，尚未在高分辨率下得到广泛表征，这些模式也未与基因组中修饰碱基的总量联系起来。对于苯并(a)芘（BaP）这种普遍存在的环境致癌物，我们开发了一种单核苷酸分辨率的损伤测序方法，以在人肺细胞系中绘制由BaP产生的主要诱变加合物图谱。此外，我们将该分析与定量质谱相结合，以评估加合物形成的剂量反应曲线。通过将损伤丰度与DNase超敏位点、转录水平和其他基因组注释数据进行比较，我们发现尽管总体加合物水平随着化学暴露浓度的增加而上升，但基因组分布模式始终与染色质状态和转录状态相关。此外，由于这种DNA损伤图谱具有单核苷酸分辨率的特点，我们可以确定烷基化积累的优选DNA三联体序列背景，揭示出一种特征性的DNA损伤特征。这种新的BaP损伤特征与先前在吸烟者肺癌基因组中鉴定出的突变特征高度相似。因此，这些数据为基因组特征如何塑造基因组中烷基化产物的积累提供了见解，并为将单核苷酸分辨率的体外损伤图谱与人类癌症突变联系起来提供了预测策略。
