Development of a DNA Adductome Database

摘要/摘要 频繁接触环境、饮食、内源性亲电体和活性氧中的化学物质 物种导致DNA的化学修饰，导致DNA加合物的形成。一些DNA 加合物可以在细胞分裂过程中诱导突变，当发生在基因组的关键区域时，可以导致 疾病，包括癌症。过去30年对DNA加合物的靶向分析表明， 人类基因组包含广泛的DNA加合物，其中许多被归因于生活方式因素，如 吸烟，吃熟透的熟肉，或通过氧化应激。随着高科技的发展， 分辨率质谱仪和新的扫描技术，非靶向的“组学”方法 已经可以在一次检测中同时筛选多个DNA加合物。然而， 由于缺乏可公开获取的大量数据，这一新兴领域的发展受到了阻碍。 用于DNA加合物鉴定和表征的光谱数据库。我们的目标是策划和开发一个 全面的DNA加合物标准数据库，从国际合作者和商业 消息来源。该数据库将免费提供，并可供公众搜索。 在目标1中，我们将建立广泛的dna加合物标准，通过我们的国内和国际 协作和商业来源。我们将优先考虑2‘-脱氧核糖核苷和碱基加合物 由环境和饮食毒物和内源性亲电体形成，但也获得修饰的RNA 从新兴的核糖核酸加合物分离领域中引用标准。我们将收集高分辨率的质谱图 这些标准通过两个常用的质谱计平台Orbitrap MS和Q-TOF MS进行加合。 在不同碰撞能下获得MS、MS2和MS3的光谱，以表征加合物结构。 在目标2中，我们将开发一个处理MS2和MS3数据的自动化工作流程，以快速精选 带有注释的单个DNA加合物，可以使用常见的 软件。生成的光谱库将以通用格式免费下载 研究团体成员对DNA加合物组特征的研究。 在可检索的参考文献中成功建立有效的DNA加合物质谱库 文库对于全面分析细胞DNA、尿液和其他组织中的DNA加合物组特征至关重要 生物基质。该数据库将促进DNA加合物在人类队列研究中的使用 增进我们对外部和内部暴露与疾病风险之间关系的理解。

Abstract/Summary The frequent exposure to chemicals in the environment, diet, endogenous electrophiles, and reactive oxygen species leads to the chemical modification of DNA, resulting in the formation of DNA adducts. Some DNA adducts can induce mutations during cell division, and when occurring in critical regions of the genome, can lead to disease, including cancer. The targeted analysis of DNA adducts over the past 30 years has revealed that the human genome contains a wide array of DNA adducts, many of which are attributed to life-style factors, such as smoking, the eating of well-done cooked meats, or through oxidative stress. With the advancement of high- resolution mass spectrometry instrumentation and new scanning technologies, untargeted “omics” approaches have become available to simultaneously screen for multiple DNA adducts in a single assay. However, the development of this emerging field of DNA adductomics is hindered by the lack of a publicly available mass spectral database for DNA adduct identification and characterization. Our goal is to curate and develop a comprehensive database of DNA adducts standards, obtained from international collaborators and commercial sources. The database will be freely available and searchable by the public. In Aim 1, we will establish an extensive collection of DNA adduct standards, via our domestic and international collaborations and commercial sources. We will prioritize 2'-deoxyribonucleoside and nucleobase adducts formed from environmental and dietary toxicants, and endogenous electrophiles, but also acquire modified RNA adduct standards from the emerging field of RNA adductomics. We will collect high-resolution mass spectra of these adduct standards via two commonly used mass spectrometer platforms, Orbitrap MS and Q-TOF MS. Spectra of MS, MS2 and MS3 will be acquired at various collision energies to characterize adduct structures. In Aim 2, we will develop an automated workflow to process MS2 and MS3 data to rapidly curate the spectra of individual DNA adducts with annotation, which can be submitted to a repository using commonly available software. The resulting spectral library will be freely available for download in common formats for characterization of DNA adductome profiles by members of the research community. The successful establishment of a validated DNA adduct mass spectral database in a searchable, reference library is critical for the comprehensive analysis of DNA adductome profiles from cellular DNA, urine, and other biological matrices. This database will facilitate the usage of DNA adductomics in human cohort studies and advance our understanding of the relationships between external and internal exposures and disease risk.