High grade serous ovarian cancer (HGSC) accounts for 80% of ovarian cancer mortality, and no targeted therapies are available for this disease. Previous studies have searched for mutations and gene fusions that drive HGSC, but the clinically actionable discoveries have been underwhelming. Although mutations and gene fusions have been a significant focus of cancer genetics, other types of understudied genomic aberrations are known to be cancer-driving, such as Intragenic genetic rearrangements (IGRs) that result in exons within genes being duplicated or deleted. Some IGRs have been reported to drive growth in tumors, such as EGFR and ERBB2 exon rearrangements that are known to cause activation of these kinases. Analysis of TCGA Pan-cancer copy number data revealed that HGSC exhibits a higher frequency of unbalanced IGR events than all other cancers. More interestingly, our analyses of TCGA copy number data have revealed recurrent exon duplications in the ephrin-receptor protein-tyrosine kinase EPHA3 that may be present in up to 8.3% of HGSC tumors. EPHA3 is overexpressed in a number of cancer types, where it has been proposed as a cancer driver and therapeutic target. The in-frame duplication we detected is predicted to cause the resultant protein to contain an extra fibronectin type 3 domain, which could possibly lead to activation of EPHA3. We have verified the presence of this aberrant transcript in two ovarian cancer cell lines, including a HGSC cell line. Specific knockdown of this aberrant transcript in the HGSC cell line potently reduced cell viability suggesting that it may drive cancer cell growth. We hypothesize that EPHA3 intragenic rearrangements may play a key role in activating this tyrosine kinase, which may promote HGSC progression and recurrence and thus constitute a viable therapeutic target. This proposal seeks to assess the incidence of EPHA3 exon duplications in HGSC, explore its association with tumor recurrence and chemoresistance, characterize the underlying genomic aberrations and protein products, examine its function in activating EPHA3 signaling and HGSC progression, and evaluate the therapeutic effect of EPHA3 inhibitors in vitro. The EPHA3 exon duplication, if validated, could provide a powerful biomarker for effective EPHA3-targeted therapy in HGSC. More important, small molecule EPHA3 kinase inhibitors are already commercially available, and a monoclonal antibody targeting EPHA3 has been found to be safe and clinically active in a phase I clinical trial for hematologic malignancies. Thus, successful accomplishment of this project could pave the way for new precision medicine against EPHA3 rearrangements, which would benefit a substantial population of HGSC patients.
High-grade serous ovarian cancer (HGSC) accounts for up to 80% of ovarian cancer mortality, and overall survival has not been improved for decades due to the lack of actionable genetic drivers. Our genome-wide analysis of copy number data revealed a potential intragenic duplication of the receptor tyrosine kinase EPHA3, which will be investigated in this project to assess its therapeutic role in HGSC progression and recurrence. Successful accomplishment of this project could pave the way to a new precision medicine targeting EPHA3, which would benefit a substantial population of patients suffering from this deadly disease.