Abstract 3488: Decoding splicing isoforms and adaptive evolution in melanoma brain metastases through single cell long-read RNA sequencing

Abstract Melanoma brain metastasis (MBM) is the third most common origin of metastasis to the brain, with a median overall survival of 8. 9 months. Alternative splicing plays a critical role in cancer pathogenesis through altered protein coding complexity in tumor cells, which however has been poorly studied in MBM due to technical limitations. Long-read single cell RNA sequencing has the unique strength of measuring transcript isoforms and mutations simultaneously in individual cells due to its capacity of measuring full-length transcripts. In this study, we employed high throughout single cell long-read RNA sequencing (scNanoRNAseq) onto patient-matched MBM and extracranial metastasis (ECM) tumor pairs to evaluate the extent to which splicing isoforms impact adaptive clonal evolution in MBM. Our results showed that MBM tumors had distinct genetic alterations and ecological cellular compositions compared to matched ECM tumors, indicating that tumor clones were adaptively expanded in brain microenvironment. Comparative isoform analysis revealed that hundreds of genes expressed different combinations of isoforms (DCIs) involved in glucose and lipid metabolic pathways. Interestingly, our data demonstrated that ~10% of splicing related genes themselves were alternatively spliced including both spliceosome members and splicing activators. Furthermore, we calculated temporal changes of isoform usages along with tumor cell evolutionary lineages to quantify their impact on adaptive clonal expansion in MBM. Taken together, our work improves the understanding of transcriptional and splicing dynamics inherent in the adaptive evolution of MBM, providing evidence for developing new therapeutics targeting tumor cell-specific and MBM-specific splicing isoforms. Citation Format: Lina Lu, Cheng-Kai Shiau, Kazutaka Fukumura, Hsiaoyun Lin, Yueying He, Timothy Pan, Lisa Norberg, Jennifer Ritchie, Jason T. Huse, Ruli Gao. Decoding splicing isoforms and adaptive evolution in melanoma brain metastases through single cell long-read RNA sequencing 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 (6Suppl): Abstract nr 3488.