Abstract 1758: Chromosome 3 copy number loss alone drives tumor evolution to aggressive disease in uveal melanoma
Authors: Srinivasan Sanjana , Rose Johnathon , Minelli Rosalba , Terranova Christopher , Shah Parth , Daniele Joseph R. , Peoples Michael , He Meng , Liu Chiu-Yi , Gay Jason , Soeung Melinda , Soni Sanjay , Wang Fangyang , Bristow Christopher , Wani Khalida , Perelli Luigi , Loza Dmitry , Feng Ningping , Tarabichi Maxime , Van Loo Peter , Futreal Andrew , Woodman Scott , Lazar Alexander , Vellano Christopher P. , Marszalek Joseph , Draetta Giulio F. , Heffernan Timothy , Carugo Alessandro , Genovese Giannicola , Giuliani Virginia 
Published: March 2024

Uveal Melanoma (UM) is a rare tumor characterized by mutations in GNAQ or GNA11, followed by a mutation in BAP1, SF3B1 or EIF1AX. Notably, a large subset of BAP1 mutant patients present with a unique chromosome 3 copy-number (CN) loss and higher likelihood of metastases. The biology underlying the causes and consequences of Monosomy 3 (M3), and its role in metastases is largely unexplored. This can be partially attributed to the relatively few numbers of preclinical models of UM, and the inability to delineate M3 from BAP1 loss. To address this, we derived a preclinical isogenic model of chromosome 3 CN loss through CRISPR-based centromere targeting in a well characterized UM cell line lacking a BAP1 mutation. Clones with and without chromosome 3 loss were derived from these efforts. Recent studies have evaluated genomic events in primary UM and described five CN aberration-based subtypes expanding beyond M3, with the fifth subtype being called the “ultra-high-risk UM” based on poor survival and extremely high metastatic rate. Whole genome sequencing across our clones confirmed chromosome 3 CN loss, and in addition to this, recapitulated all of the core genomic features characteristic of the ultra-high-risk UM group. In comparison, our models without chromosome 3 CN loss maintained a genomic profile more characteristic of lower risk UM subtypes. The genomic landscape of our isogenic low risk (LR) and high risk (HR) clones suggest that chromosome 3 CN loss alone in the absence of BAP1 mutations can be the driver for acquisition of downstream genomic events seen in aggressive UM. Further, using single cell DNA sequencing on the parental model, LR and HR clones, we confirmed that chromosome 3 CN loss in our clones was engineered, and not a pre-existing subclone in the parental cell line. Bulk RNAseq on our LR and HR clones demonstrate concordance with genomic regions of losses and gains, while also highlighting upregulation of pathways such as cell cycle and DNA damage response in the HR clones. Next, we developed patient derived xenograft (PDX) models demonstrating differential behavior in paired in vivo settings, where HR clones had higher fitness advantage and metastatic potential, specifically to the mouse liver. This modeling has enabled us to employ spatial transcriptomics in a PDX setting, adapt existing methodology to infer chromosomal copy number events in our system and inform transcriptional and genomic phenotypes akin to the aggressive HR clones. Thus, using our engineered preclinical models, we demonstrate that chromosome 3 loss, in the absence of BAP1 mutations is capable of driving aggressive disease in UM, characterized by genomic evolution, transcriptional reprogramming and in vivo invasiveness.

Citation Format: Sanjana Srinivasan, Johnathon Rose, Rosalba Minelli, Christopher Terranova, Parth Shah, Joseph R. Daniele, Michael Peoples, Meng He, Chiu-Yi Liu, Jason Gay, Melinda Soeung, Sanjay Soni, Fangyang Wang, Christopher Bristow, Khalida Wani, Luigi Perelli, Dmitry Loza, Ningping Feng, Maxime Tarabichi, Peter Van Loo, Andrew Futreal, Scott Woodman, Alexander Lazar, Christopher P. Vellano, Joseph Marszalek, Giulio F. Draetta, Timothy Heffernan, Alessandro Carugo, Giannicola Genovese, Virginia Giuliani. Chromosome 3 copy number loss alone drives tumor evolution to aggressive disease in uveal melanoma [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 1758.