Purpose Cyclin E1 (CCNE1) amplification is associated with primary treatment resistance and poor outcome in high grade serous ovarian cancer (HGSC). Here, we explore approaches to target CCNE1 amplified cancers and potential strategies to overcome resistance to targeted agents. Experiment Design To examine dependency on CDK2 in CCNE1 amplified HGSC, we utilised siRNA and conditional shRNA gene suppression, and chemical inhibition using dinaciclib, a small molecule CDK2 inhibitor. High throughput compound screening was used to identify selective synergistic drug combinations, as well as combinations that may overcome drug resistance. An observed relationship between CCNE1 and the AKT pathway was further explored in genomic data from primary tumors, and functional studies in fallopian tube secretory cells. Results We validate CDK2 as a therapeutic target by demonstrating selective sensitivity to gene suppression. However, we found that dinaciclib did not trigger amplicon-dependent sensitivity in a panel of HGSC cell lines. A high throughput compound screen identified synergistic combinations in CCNE1 amplified HGSC, including dinaciclib and AKT inhibitors. Analysis of genomic data from TCGA demonstrated co-amplification of CCNE1 and AKT2. Over-expression of Cyclin E1 and AKT isoforms, in addition to mutant TP53, imparted malignant characteristics in untransformed fallopian tube secretory cells, the dominant site of origin of HGSC. Conclusions These findings suggest a specific dependency of CCNE1 amplified tumors for AKT activity, and point to a novel combination of dinaciclib and AKT inhibitors that may selectively target patients with CCNE1 amplified HGSC.

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26Basal-like breast cancers (BLBC) are aggressive breast cancers that respond poorly 27 to targeted therapies and chemotherapies. In order to define therapeutically 28 targetable subsets of BLBC we examined two markers: cyclin E1 and BRCA1 loss. 29 In high grade serous ovarian cancer (HGSOC) these markers are mutually exclusive, 30 and define therapeutic subsets. We tested the same hypothesis for BLBC. 31Using a BLBC cohort enriched for BRCA1 loss, we identified convergence between 32 BRCA1 loss and high cyclin E1 expression, in contrast to HGSOC in which CCNE1 33 amplification drives increased cyclin E1 gene expression. Instead, BRCA1 loss 34 stabilized cyclin E1 during the cell cycle. Using siRNA we showed that BRCA1 loss 35 leads to stabilization of cyclin E1 by reducing phospho-cyclin E1-T62, and 36 conversely the overexpression of BRCA1 increased phospho-T62. Mutation of cyclin 37 E1-T62 to alanine increased cyclin E1 stability. We showed that tumors with high 38 cyclin E1/BRCA1 mutation in the BLBC cohort had decreased phospho-T62, 39 supporting this hypothesis. 40Since cyclin E1/CDK2 protects cells from DNA damage and cyclin E1 is elevated in 41 BRCA1 mutant cancers, we hypothesized that CDK2 inhibition would sensitize these 42 cancers to PARP inhibition. CDK2 inhibition induced DNA damage and synergized 43 with PARP inhibitors to reduce cell viability in BRCA1 mutated cell lines. Treatment 44 of BLBC patient-derived xenograft models with combination PARP and CDK2 45 inhibition led to tumor regression and increased survival. We conclude that BRCA1 46 status and high cyclin E1 have potential as predictive biomarkers to dictate the 47 therapeutic use of combination CDK inhibitors/PARP inhibitors in BLBC. 48 3 instability in cancer cells, and is frequently elevated in BLBC (9). Perplexingly, in 65 high grade serous ovarian cancer (HGSOC) cyclin E1 amplification and BRCA1/2 66 mutation are mutually exclusive, presumably because both aberrations drive 67 genomic instability and together they precipitate lethal genomic damage (10-12). 68We recently described two subsets of HGSOC, one where cyclin E1 gene 69 amplification and BRCA1 mutation were mutually exclusive, and another where high 70 cyclin E1 protein expression was due to post-transcriptional deregulation rather than 71 4 gene amplification, and was often concurrent with BRCA1/2 mutation (12). Cyclin E1 72 protein stability is regulated by a multi-step process of specific phosphorylation and 73 ubiquitination, leading to its cyclic expression and turnover (13). Key regulators in the 74 turnover of cyclin E1, such as the ubiquitin ligase component FBXW7 and the 75 deubiquitinase USP28, are frequently dysregulated in cancer (13-15) leading to 76 altered stability of the cyclin E1 protein. 77In this study, we examined whether BRCA1 loss and cyclin E1 gain occurred 78 concurrently or independently in breast cancer. We also explored the mechanisms 79 underpinning high cyclin E1 expression in BRCA1 mutated breast cancer including 80 gene amplification and p...

Basal-like breast cancers (BLBC) are aggressive breast cancers that respond poorly to targeted therapies and chemotherapies. In order to define therapeutically targetable subsets of BLBC we examined two markers: cyclin E1 and BRCA1 loss. In high grade serous ovarian cancer (HGSOC) these markers are mutually exclusive, and define therapeutic subsets. We tested the same hypothesis for BLBC. Using a BLBC cohort enriched for BRCA1 loss, we identified convergence between BRCA1 loss and high cyclin E1 protein expression, in contrast to HGSOC in which CCNE1 amplification drives increased cyclin E1. In cell lines, BRCA1 loss was associated with stabilized cyclin E1 during the cell cycle, and BRCA1 siRNA led to increased cyclin E1 in association with reduced phospho-cyclin E1 T62. Mutation of cyclin E1 T62 to alanine increased cyclin E1 stability. We showed that tumors with high cyclin E1/BRCA1 mutation in the BLBC cohort also had decreased phospho-T62, supporting this hypothesis. Since cyclin E1/CDK2 protects cells from DNA damage and cyclin E1 is elevated in BRCA1 mutant cancers, we hypothesized that CDK2 inhibition would sensitize these cancers to PARP inhibition. CDK2 inhibition induced DNA damage and synergized with PARP inhibitors to reduce cell viability in cell lines with homologous recombination deficiency, including BRCA1 mutated cell lines. Treatment of BRCA1 mutant BLBC patient-derived xenograft models with combination PARP and CDK2 inhibition led to tumor regression and increased survival. We conclude that BRCA1 status and high cyclin E1 have potential as predictive biomarkers to dictate the therapeutic use of combination CDK inhibitors/PARP inhibitors in BLBC.