The role of extrachromosomal DNA in HER2-amplified breast cancer

PROJECT SUMMARY/ABSTRACT Breast cancer is a major cause of morbidity and mortality in the United States and is the second leading cause of cancer-related deaths among American women. Approximately 15% of newly diagnosed breast cancers in the US contain amplifications of the HER2 oncogene (HER2+). These HER2+ breast cancers are notoriously challenging to diagnose and treat due to their high levels of intratumoral heterogeneity, genome instability, and tendency to develop resistance to targeted anti-HER2 therapies such as trastuzumab. Extrachromosomal oncogene amplifications (extrachromosomal DNA or ecDNA) are increasingly appreciated as drivers of poor patient outcomes in many different cancer types but their role in breast cancer pathogenesis and the development of resistance to anti-HER2 therapy has yet to be explored. Furthermore, there are no established experimental models for studying HER2 ecDNA amplifications in breast cancer. We recently found that approximately one third of HER2 amplifications in breast cancer occur on ecDNA. We hypothesize that HER2 ecDNAs contribute to the genome instability and development of treatment resistance in HER2+ breast cancer, and therefore the identification of HER2 ecDNAs in breast cancer could be a clinically relevant finding. In this proposal we will address the role of HER2 ecDNA in breast cancer pathogenesis and treatment response using an innovative combination of patient samples, sequencing data, and organoid models. We will investigate the role of HER2 ecDNA in driving transcription replication conflict and replication stress (Aim 1), the role of HER2 ecDNA in the response to anti-HER2 therapies such as trastuzumab (Aim 2), and whether combined targeting of HER2 and the S phase checkpoint improves the response to trastuzumab (Aim 3). The completion of the proposed research will establish the role of ecDNA in HER+ breast cancer and establish breast cancer organoids as a new experimental system for the study of ecDNA biology. The applicant Natasha Weiser MD, PhD is a board-certified clinical pathologist at Stanford University with a world class mentoring team of Dr. Howard Chang, an expert in RNA biology and epigenomics, Dr. Paul Mischel, an expert in ecDNA, and Dr. Christina Curtis, an expert in breast cancer and organoid models. The proposal encompasses a five-year plan to enhance her research and professional skills with the goal of launching her independent career in academic pathology and cancer research. This award will facilitate the training required to reach her long-term career goals of (1) establishing herself as a leader in the field of academic pathology, (2) establishing a funded research program to understand ecDNA biology in the context of patient tumors, (3) being an excellent mentor to future scientists and physicians.