Abstract 2132: Tumor heterogeneity of CCNE1 copy number assessed by fluorescence in situ hybridization (FISH) in ovarian and uterine cancers and correlation with cyclin E protein expression
Authors: Petrone Adam , Aguado-Fraile Elia , Sethuraman Sunantha , Johnson Adrienne , Silverman Ian , Marshall Gary , Reis-Filho Jorge S. , Iafrate John , Veloso Artur , Rimkunas Victoria 
Published: April 2023

Abstract
Amplification of CCNE1 is a recurrent genetic alteration that has been associated with chemoresistance and poor prognosis in gynecological malignancies. We identified Protein Kinase, Membrane Associated Tyrosine/Threonine 1 (PKMYT1) as a novel synthetic lethal target in CCNE1 amplified cancers. In this genomic setting, PKMYT1 inhibition causes premature mitotic entry, mitotic catastrophe and, in turn, cell death. In pre-clinical models, correlation between CCNE1 copy number, cyclin E1 expression and sensitivity to PKMYT1 inhibition is imperfect. Thus, a deep understanding of CCNE1 amplification as a predictive biomarker for PKMYT1 inhibition is critical for refining patient selection strategies and strengthening our understanding of the mechanism of action. These learnings will be applied to correlative biomarker analyses in clinical trials evaluating RP-6306, a first-in-class, potent, and highly selective PKMYT1 inhibitor, in tumors with CCNE1 amplifications (NCT04855656, NCT05147272, NCT05147350). In this study, multiple features of CCNE1 were examined using a combination of whole genome and targeted next generation sequencing (NGS), FISH, and immunohistochemistry (IHC). Cyclin E1 levels were evaluated across tumor tissue microarrays spanning 5 tumor indications: triple-negative breast (n=100), colorectal (n=100), gastric (n=100), uterine (n=49), ovarian (n=100) cancers. The highest cyclin E1 protein levels were found in ovarian and uterine malignancies, consistent with indications with high prevalence of CCNE1 amplification (median H-score ovarian = 125; uterine = 100; gastric = 45; TNBC = 48 and CRC = 24). To explore CCNE1 amplification on a single cell level, we established a novel FISH assay using a subtelomeric q-arm control probe. The subtelomeric q-arm band is more frequently diploid than other regions on chromosome 19. Analytical validation of the FISH assay demonstrated sensitivity of 95%, specificity of 95.2%, and overall concordance of 95.1% when compared to a targeted sequencing panel (SNIPDx®). Within the uterine and ovarian cohorts, cancers harboring CCNE1 amplification were found to display higher cyclin E1 protein levels than non-amplified tumors (p-val=0.0002) and cyclin E1 expression was positively correlated with CCNE1 copy number (Spearman ρ=0.67; p-value=4.1e-05). Substantial intratumoral spatial heterogeneity of CCNE1 copy number when measured by FISH was observed across ovarian and uterine tumors. The potential impact of CCNE1 amplification heterogeneity, cyclin E1 protein levels and CCNE1 amplification fragment size on response to RP-6306 in preclinical models are currently being investigated and will be reported.
Citation Format: Adam Petrone, Elia Aguado-Fraile, Sunantha Sethuraman, Adrienne Johnson, Ian Silverman, Gary Marshall, Jorge S. Reis-Filho, John Iafrate, Artur Veloso, Victoria Rimkunas. Tumor heterogeneity of CCNE1 copy number assessed by fluorescence in situ hybridization (FISH) in ovarian and uterine cancers and correlation with cyclin E protein expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2132.