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.