Assessing genome sequence integrity in normal human cells

摘要 人类体细胞每天暴露在DNA损伤剂中，来自内源和 和外源，导致广泛的DNA损伤，从DNA断裂和 在正常体细胞中，可能多达100,000个病变中的基本位置到巨大的加合物和交联物 一天。通过一系列复杂的基因组维护，几乎所有的损伤都能迅速修复 系统，尽管有错误。这样的错误会导致DNA突变，这种突变可能会因碱基而异 对较大基因组结构变异的替换和小的删除或插入，包括 染色体异常。突变是真正的分子终点，是丢失的直接指标 基因组序列的完整性。DNA突变会导致癌症，也与年龄有关- 与之相关的疾病以及衰老本身。为了研究人类的突变，应用最广泛的 分析是可选择的标记分析(例如，HGPRT)，但它们只能应用于能够 培养和克隆，当然只包含基因组的一小部分，排除了更多 突变负荷的全球评估。随着下一代测序的到来，体细胞 突变可以定量评估，但仅限于克隆谱系，如肿瘤，在这些克隆谱系中， 相当一部分细胞具有相同的突变。在正常组织中，体细胞突变是 丰度非常低，无法与测序错误区分开来。检测中的突变 正常的细胞和组织要么需要单细胞方法，要么需要极高的准确性 在测序的大宗DNA中区分真正的突变和人工制品。我们最近开发了和 验证了基于下一代测序的检测大多数(如果不是全部)类型的突变 使用散装DNA和基于单细胞的方法。在这里，我们建议进一步整合 将这些测试优化并验证为第一个基于下一代测序的突变分析 提供对正常人类细胞基因组序列完整性的全面洞察的系统。为 在这项提议中，该检测将量身定做，以测量烟草烟雾对人体的致突变作用 检验血液或口腔粘膜细胞突变反映基因组完整性丧失的假设 吸烟者和非吸烟者在人类肺中与肺癌的关系。在目标1中，我们将发展和 验证用于测量完整基因组图景的集成和自动化分析 体外暴露于烟草烟雾冷凝物的上皮细胞的不稳定性。在目标2中，我们将验证 人支气管、口腔和血细胞基因组序列完整性的综合检测 活体暴露与吸烟暴露和肺癌病例对照状态的关系。这个 在拟议的项目中开发的化验可能首次允许使用全球 以基因组序列完整性为终点评估个体患肺癌的风险 暴露在烟草烟雾中，反映在符合流行病学的非侵入性样本中 学习。

ABSTRACT Human somatic cells are exposed to DNA damaging agents on a daily basis from both endogenous and exogenous sources, resulting in a broad range of DNA lesions, varying from DNA breaks and abasic sites to bulky adducts and crosslinks, in normal somatic cells perhaps up to 100,000 lesions per day. Virtually all of that damage is quickly repaired through a complex set of genome maintenance systems, albeit with errors. Such errors result in DNA mutations, which can vary from base substitutions and small deletions or insertions to larger genome structural variation, including chromosomal aberrations. Mutations are true molecular end points, direct indicators of loss of genome sequence integrity. DNA mutations cause cancer and have also been implicated in age- related diseases as well as aging itself. To study mutations in humans, the most widely applied assays are selectable marker assays (e.g., HGPRT), but they can only be applied on cells that can be cultured and cloned, and of course comprise only a very small part of the genome, precluding a more global assessment of mutation loads. With the advent of next-generation sequencing, somatic mutations can be quantitatively assessed, but only in clonal lineages, such as tumors, in which a substantial fraction of cells harbor the same mutations. In normal tissues, somatic mutations are of very low abundance and cannot be distinguished from sequencing errors. Detecting mutations in normal cells and tissues requires either a single cell approach or extremely high accuracy in distinguishing a true mutation from an artifact in sequenced bulk DNA. We recently developed and validated next generation sequencing-based assays for detecting most if not all types of mutations using both bulk DNA and single cell-based approaches. Here we propose to integrate, further optimize and validate these assays into the first next-generation sequencing-based mutation analysis system that provides comprehensive insight in genome sequence integrity in normal human cells. For this proposal, the assay will be tailored to measuring the mutagenic effects of tobacco smoke for testing the hypothesis that mutations in blood or buccal mucosal cells reflect loss of genome integrity in human lung in smokers and non-smokers in relation to lung cancer. In Aim 1, we will develop and validate an integrated and automated assay for measuring the complete landscape of genome instability in epithelial cells exposed in vitro to tobacco smoke condensate. In Aim 2, we will validate the integrated assay for genome sequence integrity in human bronchial, buccal and blood cells exposed in vivo, in relation to tobacco smoke exposure and lung cancer case-control status. The assay developed in the proposed project would potentially allow, for the first time, the use of global genome sequence integrity as an endpoint to assess individual risk of lung cancer in relation to exposure to tobacco smoke, as reflected in non-invasive specimens amenable to epidemiologic studies.