Abstract 94: Advanced preclinical modeling reveals unique monosomy 3 associated biology in late-stage uveal melanoma

Abstract

Abstract Uveal melanoma (UM) is a rare and lethal malignancy with very limited therapeutic options characterized by mutually exclusive activating mutations in GNAQ and GNA11, resulting in overactive proliferative signaling of Gαq/11 heterotrimeric G proteins. Additionally, tumors typically present with mutually exclusive mutations in one of three proteins with little functional overlap: BAP1, SF3B1, or EIF1AX. Metastatic progression of late-stage uveal melanoma is highly associated with chromosome 3 copy-loss, a unique chromosomal event (monosomy 3 or M3). However, the underlying biology of this distinct copy-loss event, and whether this event directly contributes towards the metastatic phenotype observed in late-stage disease, has largely been unexplored partially due to a lack of available models in the field. Here, using CRISPR-based centromere targeting we artificially created multiple isogenic clones exhibiting monosomy 3 (M3) from a well characterized disomy 3 (D3) UM cell model. Remarkably, the selective loss of one copy of chromosome 3 was sufficient to recapitulate clinical hallmarks of metastatic UM, including pigmentation loss, alterations in cell morphology and expression of late-stage disease markers. In addition, we also show how chromosome 3 copy-loss increases invasive potential and site-specific liver metastasis upon orthotopic implantation. Furthermore, successful development of this isogenic system has allowed for a comprehensive understanding of the molecular signaling, transcriptomic changes and chromatin-level modifications directly regulated by chromosome 3 copy-loss. Specifically, the monosomy 3 event emerged as the major contributor towards the molecular variance across D3 vs. M3 UM contexts and the primary driving force underpinning the large-scale epigenomic rewiring observed in M3 isogenic clones via transposase-accessible chromatin with sequencing (ATACseq). These observations together supported a scenario where the epigenomic rewiring associated to a selective genomic alteration, in this case the loss of one copy of chromosome 3, directs the acquisition of a new and aggressive phenotype. Current studies are focused on defining how these epigenomic alterations contribute towards the metastatic phenotype and identifying context-specific vulnerabilities associated with chromosome 3 copy-loss to develop novel therapeutics strategies to treat late-stage metastatic disease. Citation Format: Johnathon L. Rose, Sanjana Srinivasan, Meng He, Rosalba Minelli, Chiu-Yi Liu, Jason Gay, Joseph R. Daniele, Michael Peoples, Melinda Soeung, Vandhana Ramamoorthy, Anastasia Lopez, Charles Deckard, Brooke Meyers, Edoardo Del Poggetto, Daniel Zamler, Justin Huang, Luigi Perelli, Khalida Wani, Christopher Bristow, Ningping Feng, Christopher P. Vellano, Joe Marszalek, Alexander J. Lazar, Andrew Futreal, Giulio F. Draetta, Scott E. Woodman, Timothy Heffernan, Giannicola Genovese, Alessandro Carugo, Virginia Giuliani. Advanced preclinical modeling reveals unique monosomy 3 associated biology in late-stage uveal melanoma [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 94.