Abstract 1219: Integrative kinome exome sequencing and copy number profiling of ovarian clear cell carcinoma

Abstract

Abstract Introduction: High stage ovarian clear cell carcinoma (OCCC) is less responsive to chemotherapy and has a worse prognosis than other ovarian cancer subtypes. The most frequently mutated genes in OCCC have been characterized in recent years. These include deleterious mutations in the tumor suppressor gene ARID1A, epigenetic silencing and deleterious mutations in the PI3K antagonist PTEN as well as activating mutations in the PI3K catalytic subunit PIK3CA. Yet, therapeutic strategies that utilize these genetic aberrations are lacking. In the present study, we aimed to identify and validate new kinase targets in OCCC. Methods: To determine new mutations and copy number gains and losses, kinome sequencing was performed on DNA isolated from tumor samples (n=124) and matched controls (n=47) and high-coverage SNP analysis was implemented for 109 of the collected OCCC tumor samples. Inhibitor sensitivity screening was performed on 17 OCCC cell lines to validate potential kinase targets, following in vivo validation in OCCC patient-derived xenografts (PDX). Results: Mutations in ARID1A, PIK3CA, PTEN, KRAS and TP53 corresponded to frequencies found in literature. Most identified mutations could be designated to the PI3K/Akt/mTOR and MAPK signal transduction pathway, and HER family of receptor tyrosine kinases. The PI3K pathway related genes PIK3R1, ERBB3 and AKT1 were significantly mutated in our dataset and not described in OCCC before. EGFR, ERBB2 and PIK3CA emerged as most frequently amplified kinases. Combining mutations and copy number alterations in these pathways, 91% of all tumors were affected. The highly positive staining of p-S6 (90% of OCCC tumors) indeed suggests high mTORC1/2 activity in these tumors. Inhibitor screening demonstrated subsets of cell lines to be sensitive to EGFR or ERBB2 inhibition. Furthermore, the vast majority of OCCC cell lines was susceptible to inhibition of PI3K and MAPK downstream target mTORC1/2 using AZD8055, which efficacy was further demonstrated in several OCCC PDX models. In contrast, mTORC1 inhibition alone was less effective. Conclusion: Most kinase mutations and copy number alterations in OCCC can be related to PI3K and MAPK pathway activation. In vitro and in vivo data suggest mTORC1/2 inhibition as a novel treatment strategy in OCCC. Combinations of EGFR or ERBB2 inhibition with mTORC1/2 targeted therapy can be envisioned for OCCC tumors with EGFR or ERBB2 alterations. Supported by a grant from the Dutch Cancer Foundation: RUG 2012-5477 Citation Format: J.j. Caumanns, G.b.a Wisman, K Berns, T. Tomar, R.s.n. Fehrmann, R Bernards, A.g.j. Van der Zee, S De Jong. Integrative kinome exome sequencing and copy number profiling of ovarian clear cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1219. doi:10.1158/1538-7445.AM2017-1219