Abstract 2847: Patterns of APOBEC3-mediated chromosomal rearrangements in solid cancers
Authors: Taek-Chin Cheong, Qi Wang, Ahram Jang, Elif Karaca-Atabay, Jake June-Koo Lee, Roberto Chiarle
Journal: Cancer Research (2025)

Abstract Chromosomal translocations are complex biological processes that require the formation of DNA double-strand breaks (DSBs) at two different loci, followed by the joining of the broken ends by DNA repair mechanisms. In B-cell lymphoma, chromosomal translocations are directed by the on- or off-target activity of activation-induced cytidine deaminase (AID) that converts cytosine to uracil in single-stranded DNA (ssDNA), facilitating DSBs when two unpaired nicks are close together. However, no such enzymes have been discovered in solid tumors. While AID, a B-cell-specific APOBEC enzyme, is responsible for somatic hypermutations and chromosomal translocations in B-cell malignancies, apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3; A3) enzymes have been primarily studied for their mutagenic potential in solid cancers. In this study, we present detailed characterizations of A3-induced chromosomal translocations in multiple cell models. While shared features of AID- and A3-driven translocations are expected because they deaminate cytosine at similar consensus sequences which should result in similar patterns of DNA DSB hotspots, their translocation patterns are partially distinct. As expected, AID generated focal DSB clusters (FDCs) near transcription start site (TSS) regions, but AID also induced new types of FDCs in the gene body and in both TSS and gene body, as well as dispersed DSB cluster (DDC)-type translocations. Interestingly, A3s enhanced FDCs and DDCs in fibroblasts with the similar level of AID, but A3s were only able to induce FDCs in the gene body, not in the TSS region. Both AID- and A3-mediated chromosomal translocations were enriched in genomic regions associated with early-replicating constant timing regions (CTRs), A compartments, and topologically associated domain (TAD) boundaries. Moreover, we revealed an enrichment of A3-attributed mutational signatures at the vicinity of A3-induced chromosomal rearrangements and the oncogene amplification boundaries in patient samples. Finally, we found that A3 expression significantly increased the number of oncogenic tyrosine kinase (TK) fusions, such as ALK, RET, ROS1, and NTRK1 fusions that are recurrently found in non-small cell lung cancer (NSCLC). Furthermore, deletion of APOBEC3 genes significantly decreased the number of oncogenic TK fusions. This study highlights that A3 enzymes induce chromosomal translocations and the formation oncogenic TK fusions in human cancers, with their translocation patterns distinct from but partially shared with those induced by AID, suggesting A3s as promising therapeutic targets for reducing genomic instability in cancer patients. Citation Format: Taek-Chin Cheong, Qi Wang, Ahram Jang, Elif Karaca-Atabay, Jake June-Koo Lee, Roberto Chiarle. Patterns of APOBEC3-mediated chromosomal rearrangements in solid cancers [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 2847.