Abstract 3898: Integrating structural variants and single nucleotide variants to uncover evolutionary trajectories in melanoma
Authors: Xiwen Cui, Ayse G. Keskus, Salem Malikic, Yuelin Liu, Anton Goretsky, Chi-Ping Day, Farid R. Mehrabadi, Mikhail Kolmogorov, Glenn Merlino, S. Cenk Sahinalp
Journal: Cancer Research (2025)

Abstract Melanoma, a highly heterogeneous cancer, evolves through a complex interplay of genetic alterations, including both single nucleotide variants (SNVs) and structural variants (SVs). To study the evolutionary trajectory of melanoma, we established a model system composed of 24 single-cell-derived clonal sublines (C1-C24) from the M4 melanoma model, developed in a genetically engineered hepatocyte growth factor (HGF)-transgenic mouse. While SNVs have been extensively used to construct phylogenetic trees using Trisicell (Triple-toolkit for single-cell intratumor heterogeneity inference), a tool that analyzes intratumor heterogeneity and single-cell RNA mutations, the role and timing of SVs in melanoma evolution remain less well understood. This study integrates SV data with an SNV-driven phylogeny to investigate whether SV patterns align with SNV-based evolutionary trajectories in the mouse melanoma model, providing insights into the functional impact of SVs during tumor progression. We performed long-read sequencing on the 24 clonal sublines and detected SVs using Severus, a tool optimized for phasing in long-read sequencing. The SVs were mapped to the SNV-driven phylogeny using R and classified as either concordant (aligning with the SNV-based tree) or discordant (deviating from the SNV phylogeny). Gene ontology enrichment analysis revealed that concordant SVs were significantly enriched in genes associated with the hepatocyte growth factor receptor signaling pathway and the negative regulation of peptidyl-threonine phosphorylation, both of which represent core drivers of tumor progression. In contrast, discordant SVs were associated with a broader range of functional pathways, including the positive regulation of antigen receptor-mediated signaling and the regulation of natural killer cell-mediated cytotoxicity, though the exact mechanisms underlying these associations remain unclear. By integrating these SVs with an established SNV-driven phylogeny, this study highlights the distinct and critical roles SVs play in melanoma evolution. Concordant SVs appear to drive core oncogenic processes, while discordant SVs may contribute to other aspects of tumor evolution. These findings underscore the importance of considering SVs alongside SNVs to fully capture the complexity of melanoma evolution. Ongoing investigations will continue to explore the functional implications of these SVs and how the gene disruption patterns they cause shape the evolutionary trajectory of melanoma, offering potential targets for future therapeutic strategies. Citation Format: Xiwen Cui, Ayse G. Keskus, Salem Malikic, Yuelin Liu, Anton Goretsky, Chi-Ping Day, Farid R. Mehrabadi, Mikhail Kolmogorov, Glenn Merlino, S. Cenk Sahinalp. Integrating structural variants and single nucleotide variants to uncover evolutionary trajectories in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3898.