Abstract C105: A systematic evaluation of the therapeutic potential of base editing in cancer prevention and treatment
Authors: Merdler-Rabinowicz Rona , Dadush Ariel , Patiyal Sumeet , Daya Gulzar , Ray Lipika , Rajagopal Padma Sheila , Schaffer Alejandro A. , Ruppin Eytan , Levanon Erez Y. 
Published: December 2023

Base editing (BE) techniques offer efficient means to modify specific nucleotides in the genome. While current research mainly focuses on applying BE for treating genetic diseases caused by single-nucleotide variants (SNVs), its potential in cancer is worth exploring, as many tumors arise from an accumulation of various mutations. BE techniques primarily consist of a fusion between a Cas nuclease and a deaminase (Cas-BE), that enables A-to-G or C-to-T edits. This allows for the correction of G&gt;A and T&gt;C SNVs at the DNA or RNA level. Additionally, BE can correct C&gt;T and A&gt;G SNVs at the DNA level through the cellular DNA repair response. Precise targeting is aimed by a programmed guide RNA (gRNA), which engages in Watson-Crick base pairing with the desired region. However, a remaining concern is gRNA binding to additional locations in the genome, leading to unintended off-target edits. An alternative approach of RNA editing, involves utilizing the gRNA alone, harnessing the native Adenosine Deaminases Acting on RNA (ADAR) enzyme (Non-Cas-BE).  This eliminates the need for a vector vehicle and acting on the RNA level its effects are transient, thus potentially reducing off target permanent damage. Our first objective was to evaluate BE potential to reverse germline mutations in cancer predisposition genes (CPGs) as a strategy for cancer prevention. We analyzed the 64 CPGs recommended for pediatric genetic testing by NCBI, which are associated with cancer predisposition disorders. We extracted the known pathogenic SNVs reported in ClinVar within these genes, filtering those classified as neoplastic according to MedGen. Our findings indicate that among the 2820 SNVs examined, 54% display a suitable match for BE (34% for Cas-BE and 20% for Non-Cas-BE). To identify off-target sites, we utilized BLAST to compare the 40 nucleotides surrounding each mutation, resembling the gRNA, to the genome. Remarkably, our findings revealed that in 87% of BE correctable sites no off-target sites are detected, indicating that they are safe therapeutic targets. We further examined a list of pathogenic high-penetrance germline variants in adult patients who developed cancer, finding that among 250 SNVs reported, 59% could be addressed using BE. Second, we estimated the potential of BE to correct cancer driver mutations. Detecting the small subset of driver mutations within a tumor is indeed an open challenge, but once detected, correcting them holds considerable promise. We examined 5,913 driver mutations from 2,010 patients representing 36 cancer types, which underwent whole genome sequencing (WGS) in the PCWAG project, and found that 43% are suitable for BE, 16% by Non-Cas-BE. In 1,051 (52%) of the tumors at least one driver mutation is BE correctable, and in 208 (10%) all known driver mutations were BE correctable. Aligning with the swift incorporation of WGS in the field of oncology, this systematic exploration highlights the potential of BE to correct driver mutations for cancer prevention and treatment.

Citation Format: Rona Merdler-Rabinowicz, Ariel Dadush, Sumeet Patiyal, Gulzar Daya, Lipika Ray, Padma Sheila Rajagopal, Alejandro A. Schaffer, Eytan Ruppin, Erez Y. Levanon. A systematic evaluation of the therapeutic potential of base editing in cancer prevention and treatment [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C105.