Abstract PR016: Investigating vulnerabilities associated with chromosome arm aneuploidy in cancer

Abstract Aneuploidy – loss or gain of whole chromosomes or chromosome arms, is rare and poorly tolerated in normal cells but occurs in ∼90% of solid tumors; however, the mechanisms through which specific aneuploidies affect cancer development are unclear. Additionally, generating mammalian models of specific chromosome arm alterations is technically difficult, limiting further study. Cancers have tumor, cell, and tissue type-specific patterns of chromosome arm copy-number alterations that influence tumor evolution and sensitivity to anti-cancer therapies. Squamous cell carcinomas (SCCs) affecting lung, head and neck, esophageal, and cervical tissues have been shown to feature conserved early losses and gains of arms 3p and 3q, respectively, and are associated with relatively few oncogenic drivers and treatment options. These aneuploidies are particularly well established in lung SCC and have been shown to promote tumorigenesis, metastasis, and poor prognosis. To study cancer vulnerabilities associated with chromosome 3 arm aneuploidies, we used CRISPR-Cas9 to delete a 3p copy in human immortalized lung epithelial cell lines—the lung SCC cell-of-origin. A subset of clones duplicated a wild type chromosome 3 copy, transitioning to 3q gain and providing us with independent models for chromosome 3 wild type, 3p loss, and 3q gain. Next, we performed a CRISPRi screen and found that 3q gain cells are more sensitive to knockdown of sterol regulatory element-binding factor 1 (SREBF1)—a master regulator of cholesterol and fatty acid biosynthesis, its co-factor SREBP cleavage activating protein (SCAP), and downstream target HMG-CoA reductase (HMGCR)—the rate-limiting enzyme for cholesterol synthesis. 3q gain cells also showed up-regulated fatty acid metabolites, ceramides, triglycerides, and phosphatidylinositols. After performing a chemical screen, 3q gain cells showed reduced proliferation, increased apoptosis, and DNA damage in response to statins (HMGCR inhibitors). Statins have previously been shown to induce tumor-specific apoptosis and reduced cancer risk, although these studies have associated with variable efficacy and underlying mechanisms. We hypothesize that 3q gain is a biomarker of statin response and sensitivity in squamous cancers. We aim to study the mechanism through which aneuploidy alters lipid metabolism and contributes to cancer. Investigating aneuploidy-induced vulnerabilities will help us understand how cancers exploit aneuploidies to promote tumorigenesis and to elucidate novel and specific therapeutic targets for cancers with shared copy-number profiles. Citation Format: Nadja Zhakula-Kostadinova, Sejal Jain, Laura Byron, Matthew L. Meyerson, Alison M. Taylor. Investigating vulnerabilities associated with chromosome arm aneuploidy in cancer abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR016.