Genomic Biology of the Tandem Duplicator Phenotype in Mouse and Human Cancers

项目摘要 我们已经确定了一组基因组不稳定性配置称为串联复制表型 在~50%的三阴性乳腺癌、卵巢癌和子宫内膜癌中发现， 特定跨度大小的体细胞串联重复（TD）在全基因组范围内的大量分布。我们有 确定了这些配置的真正的遗传驱动因素，证明了Trp 53和Brca 1的缺失， 小鼠乳腺足以诱导具有TP 53中发现的短跨度TDP构型的肿瘤， BRCA 1缺陷的人类癌症，并表明在失去Brca 1后，TDs通过异常的 修复停滞的复制分叉。在这里，我们建议在体内部署计算分析的组合， 建模和体外实验，以深入了解不同的TDP 基因组构型出现并影响乳腺肿瘤发生的过程。具体来说，我们将调查 通过探索如何在不同TDP组中重新形成TD的分子机制 与DNA复制和分叉停滞相关的局部DNA特征有助于新TD的产生 在代表所有TDP组和所有TDP遗传驱动因素的大型泛癌症数据集（Aim 1A）中， BRCA 1活性的丧失可能调节在免疫排斥反应背景下形成的新生TD的扩散和位置。 短跨距TDP（目标1B）。我们将建立新的乳腺癌基因工程小鼠模型（GEMMs）， 癌症，以验证Ccne 1途径激活或Cdk 12活性丧失，两者均与Trp 53结合 功能丧失，诱导中等和长跨度TDP配置，模仿他们的人类同行， 根据TD跨度大小和分布（目标2A）以及基因组特征和遗传元件， 与TD形成相关并受TD形成影响（目的2B）。我们还将评估肿瘤细胞的肿瘤新抗原负荷。 新开发的GEMM中出现的TDP肿瘤，并测试免疫肿瘤学药物是否 最近出现的临床研究表明， （目标2A）。然后我们将使用同基因人类癌细胞系， 对于BRCA 1活性，以确定在不同细胞培养模式下从头TD形成的动力学。 扰动和作为BRCA 1状态的函数（目标3A）。最后，我们将使用新开发的GEMM， 了解乳腺中全基因组TD分布的进化路径，并辨别 TDP出现的动态，包括从头TD形成的速率和相对于时间轴的动态 乳腺肿瘤发生（Aim 3B）。如果成功的话，这一建议将揭示一个重要形式的根本原因， 人类癌症中基因组不稳定性的一个重要组成部分，TDP，定义了导致癌症形成的突变动力学， 这一条件，并产生模型系统，可以导致新的和定向治疗的发展 对抗癌细胞的生长

PROJECT SUMMARY We have identified a group of genome instability configurations called the Tandem Duplicator Phenotypes (TDPs) that are found in ~50% of triple negative breast, ovarian and endometrial cancers and are characterized by the massive genome-wide distribution of somatic tandem duplications (TDs) of specific span sizes. We have identified the bona fide genetic drivers of these configurations, demonstrated that loss of Trp53 and Brca1 in the mouse mammary gland is sufficient to induce tumors with the short-span TDP configuration found in TP53- and BRCA1-deficient human cancers, and shown that upon loss of Brca1, TDs are formed through the aberrant repair of stalled replication forks. Here, we propose to deploy a combination of computational analyses, in vivo modelling and in vitro experimentation to achieve a deep mechanistic understanding of how the distinct TDP genomic configurations emerge and impact the course of breast tumorigenesis. Specifically, we will investigate the molecular mechanisms leading to de novo TD formation across the different TDP groups by exploring how local DNA features associated with DNA replication and fork stalling contribute to the generation of new TDs across a large pan-cancer dataset representing all TDP groups and all TDP genetic drivers (Aim 1A) and how loss of BRCA1 activity may modulate the spread and location of the de novo TDs formed in the context of the short-span TDP (Aim 1B). We will establish new genetically engineered mouse models (GEMMs) of breast cancer to validate that activation of the Ccne1 pathway or loss of Cdk12 activity, both in conjunction with Trp53 loss of function, induces medium- and long-span TDP configurations that mimic their human counterparts both in terms of TD span size and distribution (Aim 2A) and of the genomic features and genetic elements that are associated with and affected by TD formation (Aim 2B). We will also assess the tumor neo-antigen load of the TDP tumors emerging from the newly developed GEMMs and test whether immuno-oncology agents are effective against mammary tumors with the TDP configuration, as suggested by recently emerging clinical observations (Aim 2A). We will then use isogenic human cancer cell lines that are either proficient or deficient for BRCA1 activity, to determine the dynamics of de novo TD formation under different modes of cellular perturbation and as a function of BRCA1 status (Aim 3A). Finally, we will use the newly developed GEMMs to understand the evolutionary path to genome-wide TD distribution in the mammary gland, and to discern the dynamics of TDP emergence, both in terms of the rate of de novo TD formation and with respect to the timeline of breast tumorigenesis (Aim 3B). If successful, this proposal will uncover the root causes of a significant form of genomic instability in human cancer, the TDP, define the mutational dynamics leading to cancer formation in this condition, and generate model systems that can lead to the development of new and directed therapeutics against cancer growth.