Abstract 3409: T cell receptors and antibodies targeting shared indel-derived neoantigens

Abstract T cells play a pivotal role in cancer immunotherapy by recognizing neoantigens presented on HLA molecules, which are specifically expressed by cancer cells. While neoantigens are generally unique to individual cancers, shared antigens that are common in a subset of cancer patients, represent promising immunotherapeutic targets. Since frameshift insertions or deletions (indels) are reported to generate highly immunogenic neoantigens through novel open reading frames. However, few studies have explored shared neoantigens from frameshift indels, which are shred among multiple cancer patients. In this study, we analyzed frameshift neoantigens from frameshift indels in TCGA exome sequencing data, identifying 760 recurrent frameshift mutation clusters (FSCs) that shared frameshifted open reading frames and premature stop codons. Among these, we focused on two FSCs in the APC gene, which generate potential neoantigens (AS3 and AS10) presented the HLA-A24 molecule. We successfully identified the T cell receptor (TCR) sequences for APC frameshift neoantigens from healthy donor’s blood. Genetically engineered T cells expressing these TCRs demonstrated recognition and cytotoxic activity against target cells presenting these APC frameshift neoantigens. Additionally, we explored the development of an antibody targeting a complex formed by the APC shared neoantigen AS10 and the HLA-A24 molecule. Using phage display library screening, we isolated single-chain variable fragments (scFvs) that specifically recognized the AS10-HLA-A24 complex. A bispecific antibody (BsAb) was then designed to connect T cells via an anti-CD3 scFv to the AS10 neoantigen on HLA-A24. We found that the AS10 BsAb specifically recognized both the AS10-HLA-A24 complex and CD3 protein, and showed significant IFN-γ release and cytotoxicity against target cells expressing frameshift neoantigens. By focusing on recurrent frameshift mutations and shared neoantigens, this study provides compelling evidence for the development of more effective and broadly applicable immunotherapeutic strategies. Citation Format: Kazuma Kiyotani, Peng Zhao, Xiaojing Wu, Yusuke Nakamura. T cell receptors and antibodies targeting shared indel-derived neoantigens [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 3409.