Abstract 4304: Chromosome 3 dosage-loss informs on the unique biology underlying ultra high-risk uveal melanoma
Authors: Rose Johnathon Lynn , Srinivasan Sanjana , He Meng , Minelli Rosalba , Liu Chiu-Yi , Terranova Christopher , Gay Jason , Daniele Joseph R. , Dmitriy Loza , Peoples Michael , Soeung Melinda , Ramamoorthy Vandhana , Shah Parth , Soni Sanjay , Bristow Christopher , Wang Fangyang , Lopez Anastasia , Deckard Charles , Meyers Brooke , Perelli Luigi , Wani Khalida , Feng Ningping , Vellano Christopher P. , Marszalek Joe , Lazar Alexander J. , Futreal Andrew , Draetta Giulio F. , Woodman Scott E. , Heffernan Timothy , Genovese Giannicola , Carugo Alessandro , Giuliani Virginia 
Published: March 2024

Uveal melanoma (UM) is a rare and lethal tumor characterized by mutually exclusive activating mutations in GNAQ and GNA11, secondary mutations in EIF1AX, SF3B1 and BAP1, and a late-stage chromosome 3 copy-number (CN) loss event. Importantly, chromosome 3 CN loss is associated with BAP1 loss-of-function (LOF) and corresponds with tumor metastasis and poor patient prognosis. Understanding the biology underlying this chromosome 3 CN loss event is critical to informing on metastatic UM. To this end, we leveraged CRISPR-based centromere targeting to engineer multiple clones exhibiting chromosome 3 CN loss. We determined that dosage-loss of chromosome 3 was sufficient to develop multiple isogenic clones exhibiting genomic features of “ultra high-risk” UM, independent of BAP1 LOF. Leveraging this isogenic system, we evaluated in vitro and in vivo profiling, demonstrating site-specific liver metastasis only in orthotopic HR tumors, along with a significantly increased fitness in the liver. Next, we sought to inform on differential signaling pathways and therapeutic sensitivity between LR and HR models. Characterization of established UM oncogenic pathways identified a clear disengagement from classical MAPK and non-canonical Hippo signaling in the HR clones. These findings also correlate with a significant decrease in sensitivity to MEK and FAK inhibitors. In addition, we observed a PKC isoform swap from PKCε and PKCδ to PKCα, a feature observed in late-stage UM patient tumors. Interestingly, we also observed an increase in the expression of PRAME and NBS1 in HR models, both markers for poor prognosis in patients. Genome-anchored transcriptomic analysis also captured distinct profiles between the LR and HR clones, highlighting a significant increase in MYC associated targets upon chromosome 3 dosage-loss. This increase in MYC signaling coincides with site-specific 8q amplifications across the HR clones, implicating MYC as a core fitness driver in high-risk UM and a potential contributor to poor patient prognosis in monosomy 3 patients. Leveraging engineered models of chromosome 3 CN loss, and the subsequent induction of “ultra high-risk” UM, provides a unique opportunity to inform on the underlying biology of UM evolution and potential therapeutic strategies.

Citation Format: Johnathon Lynn Rose, Sanjana Srinivasan, Meng He, Rosalba Minelli, Chiu-Yi Liu, Christopher Terranova, Jason Gay, Joseph R. Daniele, Loza Dmitriy, Michael Peoples, Melinda Soeung, Vandhana Ramamoorthy, Parth Shah, Sanjay Soni, Christopher Bristow, Fangyang Wang, Anastasia Lopez, Charles Deckard, Brooke Meyers, Luigi Perelli, Khalida Wani, 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. Chromosome 3 dosage-loss informs on the unique biology underlying ultra high-risk 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 4304.