Consequences of retrotransposition on genome integrity

项目摘要 转座因子是人类遗传变异的主要来源，也通过引起体细胞突变而导致人类疾病。转座在人类癌症中的活性已得到充分证实。由L1元件编码的RNA结合蛋白ORF 1 p的表达以及L1和其他转座子的插入在癌细胞和癌症基因组中是常见的。然而，逆转录转座是否以及如何有助于癌症基因组进化和促进肿瘤发生仍不清楚。在这里，我们假设反转录转座可能会促进癌症的演变，除了插入引起长距离的基因组重排。该假设是基于原发性癌症基因组中的基因组观察以及来自我们的体外实验的分子和基因组数据来制定的。为了验证这一假设，我们将结合联合收割机体外模型的实验方法（目标1）与计算分析（目标2）的逆转录转座和逆转录转座相关的重排在原发性癌症和癌前细胞（目标2）。具体来说，我们提出LINE-1插入的非规范分辨率可以导致DNA断裂和长距离DNA重排，并且这些重排的子集通过产生经历重排波的无着丝粒或双着丝粒染色体来进一步破坏基因组的稳定。为了验证这一点，我们首先评估DNA损伤及其对L1 ORF 2 p（Aim 1a）的内切核酸酶（EN）和逆转录酶（RT）活性的依赖性。然后，我们使用最先进的Look-Seq方法（结合了细胞生物学和全基因组测序）来确定ORF 2 p诱导的DNA损伤的直接和下游基因组后果（Aim 1b和1c）。联合收割机。补充这些在体外分析的逆转录转座，我们建议分析散装癌症基因组（目标2b）和单个癌前细胞基因组（目标2c），以明确评估的流行插入和长距离重排，承担逆转录转座的标志。我们专注于食管癌，逆转录转座的患病率极高（>90%的癌症）和称为Barrett食管（BE）的癌前疾病，其中LINE-1逆转录转座也已被观察到。拟议的工作包括开发新的生物信息学软件包，用于鸟枪法癌症测序数据中的联合重排和转座检测，这将使研究遗传变异，基因组不稳定性和体细胞基因组进化的研究人员受益（Aim 2a）。总之，拟议的研究将彻底表征LINE-1逆转录转座和基因组不稳定性之间的关系，以及逆转录转座在癌症演变中的作用。这些知识可能会导致癌症预防和治疗的新途径。

Project Summary Transposable elements are a major source of human genetic variation and also contribute to human diseases by causing somatic mutations. The activity of transposition in human cancers is well established. Both expression of the RNA binding protein ORF1p encoded by the L1 element and insertions of L1 and other transposons are commonplace in cancer cells and cancer genomes. However, whether and how retrotransposition contributes to cancer genome evolution and promotes tumorigenesis remain unclear. Here, we hypothesize that retrotransposition may promote cancer evolution by causing long-range genomic rearrangements in addition to insertions. This hypothesis is formulated based on both genomic observations in primary cancer genomes and molecular and genomic data from our in vitro experiments. To test this hypothesis, we will combine experimental approaches in in vitro models (Aim 1) with computational analyses (Aim 2) of retrotransposition and retrotransposition-associated rearrangements in primary cancers and precancer cells (Aim 2). Specifically, we propose that non-canonical resolution of LINE-1 insertions can cause DNA breaks and long-range DNA rearrangements, and a subset of these rearrangements further destabilizes genomes by generating acentric or dicentric chromosomes that undergo waves of rearrangements. To test this, we first assess DNA damage and its dependence on the endonuclease (EN) and reverse transcriptase (RT) activities of L1 ORF2p (Aim 1a). We then determine both immediate and downstream genomic consequences of ORF2p-induced DNA damage using state-of-the-art Look-Seq approaches that combine cell biology and whole-genome sequencing (Aim 1b and 1c). Complementing these in vitro analyses of retrotransposition, we propose to analyze bulk cancer genomes (Aim 2b) and single pre-cancer cell genomes (Aim 2c) to definitively assess the prevalence of insertions and long-range rearrangements that bear the hallmarks of retrotransposition. We focus on esophageal cancers with an extremely high prevalence of retrotransposition (in >90% of cancers) and the precancer condition known as Barrett's Esophagus (BE), where LINE-1 retrotransposition has also been observed previously. The proposed work includes development of new bioinformatic packages for joint rearrangement and transposition detection in shotgun cancer sequencing data that will benefit researchers studying genetic variation, genome instability, and somatic genome evolution (Aim 2a). Together, the proposed studies will thoroughly characterize the relationships between LINE-1 retrotransposition and genome instability writ large and the roles of retrotransposition in cancer evolution. This knowledge may lead to new avenues of cancer prevention and therapeutics.