Abstract 4356: An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell sequencing

Abstract Colorectal cancer (CRC), a complex and molecularly heterogenous disease that lacks robust predictive markers and targeted therapies, is the second leading cause of cancer death worldwide. In recent years, technological advances in short-read single-cell RNA sequencing (scRNA-seq) have been instrumental in deciphering tumor cell heterogeneities. However, most studies have focused on gene-level expression quantification without considering alterations in transcript structures arising from widespread alternative end processing and/or splicing which are frequently dysregulated in cancer. Here, we combined short- and long-read scRNA-seq of CRC patient samples to build the first isoform-resolution CRC transcriptomic atlas. We identified 394 dysregulated transcript structures in tumor epithelial cells, including 299 derived from the coupling of multiple alternative splicing events. Additionally, we characterized genes and isoforms associated with different colon epithelial lineages and tumor cell subpopulations exhibiting varying levels of stemness and differentiation, as well as their distinct prognostic implications. Finally, we built an algorithm by integrating mass spectrometry data and novel peptides derived from predicted open reading frames of recurrent tumor-specific transcripts to curate a panel of recurring neoepitopes. Overall, this study unveils the transcriptomic landscape of CRC and may drive the identification of neoantigens based on full-length transcriptomic atlases to aid future development of more universal neoantigen-based cancer vaccines. Citation Format: Zhongxiao Li, Bin Zhang, Jia Jia Chan, Hossein Tabatabaeian, Qing Yun Tong, Xiao Hong Chew, Xiaonan Fan, Charlene Chan, Patrick Driguez, Faith Cheong, Shi Wang, Bei En Siew, Ian Jse-Wei Tan, Kai-Yin Lee, Bettina Lieske, Wai-Kit Cheong, Dennis Kappei, Ker-Kan Tan, Xin Gao, Yvonne Tay. An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell 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(6_Suppl):Abstract nr 4356.