Abstract 1649: Large scale multi-omics concordance study of cyclin E1 identifies high expressing tumors lacking CCNE1 gene alterations across multiple tumor indications
Authors: Sophie E. Willis, Gemma N. Jones, Shaan Gill, Emma V. Jones, Amelia Raymond, Barrett Nuttall, Sophie Kirschner, Sakshi Gulati, Paola Marco-Casanova, Benedetta Lombardi, David Jenkins, Felicia S. Ng, James Hadfield, Paul Waring, Helen K. Angell, Heike Laman
Journal: Cancer Research (2024)

Abstract Cyclin E1 is a key regulator of the G1/S transition and is thought to cause excessive entry into the cell cycle. CCNE1 is amplified in a range of tumor indications, and its amplification is associated with poorer prognosis and resistance to chemotherapy. Cyclin E1 is also being investigated as a potential biomarker for inhibitors targeting the replication stress response. Understanding the best way to quantify cyclin E1 overexpression is fundamental to support patient selection approaches for these inhibitors. In many cases, gene amplification correlates with increased cyclin E1 protein expression; however, there are a proportion of high-grade serous ovarian cancer and basal-like breast cancer cases where cyclin E1 protein overexpression does not correlate with gene amplification. In this study, we investigate if this phenomenon is observed in other cancers and some of the potential mechanisms causing cyclin E1 overexpression. We used a multi-omics approach to assess cyclin E1 expression in 1417 formalin-fixed paraffin-embedded (FFPE) patient tumor resections across 6 indications (SCCHN, Bladder, NSCLC, TNBC, Ovarian &amp; SCLC). We used copy number variation (CNV) determined by next generation sequencing (NGS), NanoString nCounter RNA analysis and protein expression by immunohistochemistry (IHC). 830 were evaluable for all 3 methods and demonstrated CCNE1 gene amplification by NGS (CNV normalized log2 ratio ≥1.5) in 3.3% cases. Using a threshold of mRNA z-score &amp;gt;2, 17% cases had high CCNE1 mRNA and 29% had high cyclin E1 protein (H-score ≥100). 15.7% (130/830) cases had high protein expression without gene amplification or gain, crucially this was found across all 6 indications (n=20/102 SCCHN, n=29/166 Bladder, n=34/232 NSCLC, n=15/76 SCLC, n=15/143 TNBC &amp; n=17/118 Ovarian). Impaired protein degradation has been proposed as a mechanism that may result in high Cyclin E1 expression. From a panel of 1600 genes, we assessed the relationship between cyclin E1 and mRNA expression of 57 genes involved in the ubiquitin-proteasome pathway in 1239 samples across the 6 indications. We assessed mutations which could impair ubiquitination in 915 samples across the 6 indications. We also assessed the methylation status of 893 genes associated with ubiquitin ligases or deubiquitinases in a cohort of 170 TNBC samples. Further investigation into other mechanisms causing cyclin E1 overexpression is required. IHC provides an ideal platform to build our understanding of cyclin E1 expression spatially. Our results indicate that assessing Cyclin E1 protein overexpression instead of CCNE1 gene amplification could greatly broaden the population of patients who could benefit from replication stress response kinase inhibitors, as cyclin E1 overexpression correlates with genomic instability and replication stress. Citation Format: Sophie E. Willis, Gemma N. Jones, Shaan Gill, Emma V. Jones, Amelia Raymond, Barrett Nuttall, Sophie Kirschner, Sakshi Gulati, Paola Marco-Casanova, Benedetta Lombardi, David Jenkins, Felicia S. Ng, James Hadfield, Paul Waring, Helen K. Angell, Heike Laman. Large scale multi-omics concordance study of cyclin E1 identifies high expressing tumors lacking CCNE1 gene alterations across multiple tumor indications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1649.