DNA copy number alterations (CNAs) are oncogenic drivers for many types of human cancer. For some cancers, e.g. certain ovarian, breast and endometrial cancers, it is very likely that CNAs, comprise the bulk of genetic alterations responsible for their highly malignant properties. CNAs may also be responsible for driving squamous carcinoma of the lung and for subsets of gastric and esophageal cancers. Relatively little attention is being paid to understanding this class of genetic alterations. More importantly, from a cancer treatment perspective, there is no roadmap for determining whether they induce selective dependencies that could be utilized for developing new therapeutics. As our group and others have discovered in the past several years, the vast majority of CNAs contain multiple driver genes, and this makes it considerably more difficult to study how they impact cancer progression compared to single-gene events. The overall goal of this project is to develop new tools and models to investigate multigenic CNAs so that they can be more readily studied and utilized in developing new therapeutics.
In Aim 1, we will combine CRISPR/Cas9 and Cre-Lox genome engineering to accurately model multigenic CNAs and determine how they impact oncogenic phenotypes in normal mammary epithelial cells, similar to how mutations in single-gene alterations such as PIK3CA are currently studied. Once we have validated these new cell models, we will screen for induced dependencies.
In Aim 2, we will develop and implement computational methods to extract information about specific CNAs from the warehouse of information present in large-scale integrated cancer genome datasets. We have extensive preliminary results that validate this approach, including the prediction of CNA-selective dependencies. Lastly, to truly understand how multigenic CNAs play a role in cancer, we must functionally probe the interactions between multiple drivers. We previously demonstrated that these interactions were key features of the oncogenicity of the 14q13 amplicon in lung cancer and 11q13 amplicon in liver cancer. Thus, our final goal is to develop and implement generalizable methods to study genetic interactions between multiple drivers (Aim 3). Our proposal is based on the premise that CNAs are important drivers in cancer but that the current research approach needs to be improved. The clinical effectiveness of targeted treatments for patients with HER2-amplified breast cancers underscores the enormous translational potential of CNAs. By developing the tools and models for CNAs described in this proposal, we will make a significant impact on understanding multigenic CNAs and will lay the groundwork for identifying associated dependencies and therapeutic strategies.

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Project Summary Copy number alterations are important drivers in cancer but current research approaches are based on methods developed for single gene alterations such as mutational activation of KRAS. Our proposal is to develop methods that take into account the multigenic nature of copy number alterations. We will apply these methods to the study of breast cancer with the goal of finding selective dependencies that can form the basis of new targeted therapeutic strategies.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
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Cancer Genetics Study Section (CG)
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Li, Jerry
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State University New York Stony Brook
Schools of Medicine
Stony Brook
United States
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