Abstract 3541: A novel chimeric RNA as a source of neoantigens in CRC

Abstract Colorectal cancer (CRC) is the second-leading cause of cancer-related death worldwide, affecting over 100, 000 men and women in the United States every year. There is an unmet need for early biomarker discovery and the identification of novel therapeutic targets in CRC. Chimeric RNAs and their protein products are well-established as ideal biomarkers and drug targets for malignant cancers. Additionally, cancer-specific fusion proteins present attractive targets for neoantigen vaccines. Using RNA-seq from The Cancer Genome Atlas (TCGA) database, we have identified a chimeric RNA prevalent in approximately 50% of CRC samples, but absent in non-cancer colon tissue. This transcript correlates with worse overall survival, is expressed as early as stage I CRC, and is present in both microsatellite stable and instable disease. This chimeric RNA arises from readthrough transcription and cis-splicing between adjacent genes, producing a previously unidentified chimeric protein. Importantly, this protein includes a splice variant of the 5’ gene, leading to a frameshift in the 3’ gene and resulting in a novel 101 amino acid peptide sequence. This sequence is not detected by mass spectrometry in any healthy tissue but is present in multiple CRC cases within the Clinical Proteome Tumor Analysis Consortium (CPTAC) data portal. Using an antibody generated against the frameshift sequence, we have confirmed this protein is expressed in patient CRC samples, regardless of disease stage, sex, age, race, or microsatellite instability status. Finally, we have demonstrated that T cells from healthy donors and patients with CRC exhibit activation following co-culture with autologous dendritic cells pulsed with peptides derived from this protein. Additionally, these T cells display cytotoxicity against HLA-matched CRC cell lines. These findings highlight the potential of chimeric RNAs and their protein products as both biomarkers and therapeutic targets, presenting a previously unexplored class of tumor antigens as an innovative strategy for improving patient outcomes. Citation Format: Sarah A. Lynch, Amanda M. Lulu, Samir Lalani, Justin Elfman, Craig L. Slingluff, Hui Li. A novel chimeric RNA as a source of neoantigens in CRC [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 3541.