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

项目总结 我们已经确定了一组基因组不稳定配置，称为串联复制子表型 (TDPs)在约50%的三阴性乳腺癌、卵巢癌和子宫内膜癌中发现，其特征是 由于特定跨度大小的体细胞串联复制(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遗传驱动因素，证明了Trp53和BRCA1在 小鼠乳腺足以诱发肿瘤，具有TP53-和TDP的短跨距构型 BRCA1缺失的人类癌症，并表明当BRCA1丢失时，TDS通过异常形成 修复停滞的复制分叉。在这里，我们建议在活体内部署计算分析的组合 建模和体外实验，以实现对不同的TDP如何产生深刻的机制理解 基因组构型的出现影响了乳腺肿瘤的发生过程。具体地说，我们将调查 通过探索不同TDP基团从头形成TD的分子机制 与DNA复制和分叉失速相关的局部DNA特征有助于产生新的TD 跨越代表所有TDP组和所有TDP基因驱动因素的大型泛癌症数据集(目标1A)以及如何 BRCA1活性的丧失可能调制在以下背景下形成的从头TD的扩散和位置 短跨度TDP(目标1B)。我们将建立新的乳房基因工程小鼠模型(GEMM) 肿瘤验证Ccne1通路激活或CDK12活性丧失，两者都与Trp53结合 功能丧失，导致中跨和长跨TDP配置模仿它们的人类同行 就TD跨度大小和分布(目标2A)以及符合以下条件的基因组特征和遗传要素而言 与TD的形成有关并受其影响(目标2B)。我们还将评估肿瘤新抗原的载量 从新开发的GEMM中出现TDP肿瘤并测试免疫肿瘤学试剂是否 最近出现的临床研究表明，对具有TDP构型的乳腺肿瘤有效 观察(目标2 A)。然后，我们将使用相同基因的人类癌细胞系，这些细胞系要么熟练，要么缺乏 对于BRCA1活性，确定不同细胞模式下从头形成TD的动力学 扰动和作为BRCA1状态的函数(目标3A)。最后，我们将使用新开发的GEMM来 了解全基因组TD在乳腺中分布的进化路径，并识别 从从头形成TD的速度和相对于时间线的角度，TDP出现的动力学 乳房肿瘤发生(目标3B)。如果成功，这项提议将揭示一种重要形式的根本原因 人类癌症基因组不稳定性的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的治疗方法的发展 对抗癌症的生长。

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.