Kinome directed target discovery and validation in unique ovarian clear cell carcinoma models

Abstract

Advanced stage ovarian clear cell carcinoma (OCCC) is unresponsive to conventional platinum-based chemotherapy. Efforts to improve OCCC chemotherapy responses have focused on combining platinum with other chemotherapeutic agents or targeted therapies, but have unfortunately not led to higher survival rates. SWI/SNF chromatin remodeling complexes are important regulators of chromatin structure and gene transcription. Multiple SWI/SNF subunits are genetically altered in cancer. The SWI/SNF DNA targeting subunit ARID1A is frequently mutated with the highest mutation frequency found in OCCC. Kinases are important for the regulation of proliferation and apoptosis signaling. A number of kinases are mutated in OCCC, including PIK3CA and KRAS, and are known to promote tumor growth. The aim of this thesis was to identify new therapeutic targets for OCCC patients. To this end, we searched for specific kinase vulnerabilities in OCCC with deleterious mutations in ARID1A using kinome-centered shRNA based synthetic lethality screening in ARID1A wild-type and mutant OCCC cell lines. The identified synthetic lethal hit was validated in vitro and in vivo and we found causal evidence for the observed synthetic lethal interaction with ARID1A loss. In addition, we searched for new kinase alterations in a large group of OCCC tumors and cell lines and subsequently tested the druggability of downstream affected pathways in vitro and in patient-derived xenograft (PDX) models of OCCC. Based on the heterogeneous pattern of mutations across PI3K/AKT/mTOR and MAPK proliferation pathways in OCCC, we searched for effective combinations of PI3K/AKT/mTOR and MAPK kinase inhibitors in low-dose concentrations to simultaneously target key kinases in OCCC. Finally, we described the establishment of OCCC PDX models and compared genomic and histopathology characteristics between paired patient and PDX OCCC tumors to determine the level of similarity. In conclusion, new therapeutic targets in OCCC have been identified and a low-dose treatment strategy was preclinically tested in unique OCCC models in this thesis. These results may advance the treatment of OCCC