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.
Using sequencing analyses of human cancer genomes, we previously identified a form of extensive chromosomal rearrangement called the Tandem Duplicator Phenotype (TDP), which is found in ~50% of triple- negative breast cancers, as well as ovarian and endometrial cancers. To understand how different types of TDPs are formed in mammary tissues and then evolve in established breast tumors, our research will use genome sequencing analyses and exploit genetically engineered mouse models and cultured human breast cancer cells. The insights we gain into TDP formation and evolution will ultimately support clinical development of new TDP- targeting cancer treatments.