Abstract 2393: APOBEC3 enzymes induce chromosomal translocations in solid cancers

Introduction: Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) family of cytidine deaminases provides a defense for the host genome against exogenous viruses and endogenous retro-elements, but their enzymatic activity may cause host genomic instability via a conversion of cytosine to uracil during RNA and DNA editing. While it is well established that activation-induced cytidine deaminase (AID; a B-cell specific APOBEC family enzyme) induces genomic instability by initiating mutations and oncogenic chromosomal translocations involved in the development and progression of lymphoma, it is unclear whether APOBEC3 enzymes could play a similar role in non-hematopoietic cells. Recently, APOBEC-signature mutation (C-to-T transition) has been identified in almost half of all human cancers, including breast and lung cancers. However, enzymes that trigger chromosomal translocation in solid cancers are largely underdetermined. In this study, we investigated the role of APOBEC3 proteins in chromosomal translocation formation and validated APOBEC3-induced chromosomal translocations in solid cancers. Methods: We generated genome-wide chromosomal translocation maps of human APOBEC3 enzymes in both mouse and human cells by adapting the high-throughput, genome-wide translocation sequencing (HTGTS) technique. We exploited immortalized mouse fibroblasts carrying a 25x I-SceI meganuclease cassette targeted in the c-myc locus and also human MCF10A (breast), Beas-2B (lung), and PC-9 (non-small cell lung cancer) cells by generating DNA DSBs in either the c-myc locus or the EML4 locus by the CRISPR/Cas9 system. Results: All human APOBEC3 enzymes have cytidine deaminase activity on their preferred target motifs with different potency. By overexpressing APOBEC3 proteins in AID−/− B cell, we found that APOBEC3 enzymes, in contrast to AID, did not induce IgG1 class switch recombination (CSR) indicating a different mechanism of action between AID and other APOBEC3 enzymes. By HTGTS, we demonstrated that APOBEC3s and AID induced significantly higher number of translocations in novel hotspots compared to control fibroblasts. Strikingly, bioinformatics analysis of the junctions revealed that APOBEC3 proteins induce chromosomal translocations with similar frequency, but only partially overlap with AID. In addition, by analyzing individual genes or translocation targets, we observed similar but distinct effects on translocation frequency for each member of the APOBEC3 family. Interestingly, AID preferentially targets genomic regions associated with high transcriptional activity, but APOBEC3Cs do not. The analysis of HTGTS from human breast and lung cell lines revealed the similar pattern of translocations found in mouse fibroblasts. Remarkably, APOBEC3 off-target hotspots are distinct and unique in each cell type. Conclusions: We showed that human APOBEC3 enzymes enhance chromosomal translocations in non-hematopoietic cells with similar potency to AID, suggesting that APOBEC3 enzymes could be initiating genomic instability in solid tumors where AID is not expressed. Thus, APOBEC3 expression has to be tightly controlled in non-hematopoietic cells to limit its genotoxic effects. Citation Format: Taek-Chin Cheong, Qi Wang, Roberto Chiarle. APOBEC3 enzymes induce chromosomal translocations in solid cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2393.