In a News and Views commentary entitled “To BE or not to BE, that is the question”, Dr. Li Yang at CAS-MPG Partner Institute for Computational Biology (PICB) of Chinese Academy of Sciences, together with Dr. Jia Chen at School of Life Science and Technology (SLST) and Dr. Bei Yang at Shanghai Institute for Advanced Immunochemical Studies (SIAIS) of ShanghaiTech University, commented three recent studies published in Science and Nat Biotechnol aboutaccuracy of base editing. The commentary was published online in Nat Biotechnol on April 18, 2019.
Base editors (BEs) were recently developed by combining different nucleoside deaminase family members with the CRISPR-Cas9 system and have been used for targeted C-to-T/A-to-G base editing in various cells or living organisms. Since BEs catalyze the deamination of cytidine or adenosine at target sites without generating DSBs and that the majority of human pathogenic variants are single mutations, BEs were thought to be promising tools to correct these disease-related point mutations. However, several recent studies showed that cytosine base editors, specifically a commonly-used cytosine base editor3 (BE3), but not adenine base editors, induce elevated levels of genome-wide off-target substitutions (Zuo et al., 2019, Science; Jin et al., 2019, Science; Kim et al., 2019, Nat Biotechnol), therefore raising concerns about the safety of base editing on cytosines.
In this News and Views commentary, the authors indicated that the detected off-target editing may be caused directly by the rat APOBEC1 moiety of BE3. The authors further hypothesized that the use of native or engineered APOBEC deaminases with relatively low DNA binding or catalytic activity may help to reduce unexpected off-target substitutions. Meanwhile, deamination activity-reduced BEs might lead to inefficient on-target editing, as high on-target activity is essential for broad applications of base editing, especially for therapeutic-related applications in somatic cells. In this scenario, it will be more prudent to adopt strategies other than using activity-reduced deaminases when developing high-precision BEs going forward.
Figure 1 Cas9- and BE-mediated editing. a, Gene editing and p53-mediated DNA damage response induced by Cas9. b, sgRNA-dependent on-target and off-target base editing induced by BE3. c, sgRNA-independent off-target editing induced by BE3.