Stepan Jerabek, Chanju Jung, Michelle Kappy, Qiaojin Zhao, Julie Sung, Ning Wang, Euihyun Kim, Jimin Kim, Marcos Iuri Roos Kulmann, Madeleine Bliss King, Mitchell John McAndrew, Meng Li, Sakshi Bhatele, Melisa Isado, Hong-Su Jang, Michal Dolezal, Robert Prosser, Shuangyi Xu, Gue-Ho Hwang, Iva Pichova, Jia Xu, Diego Marin, Jae-Sung Woo, Sangsu Bae, Nathan Treff, Audrone Lapinaite, Dieter Egli
Cas9-based tools enable programmable DNA lesions for studying repair outcomes, gene function, and genome correction. In human embryos, Cas9-induced DNA double-strand breaks are genotoxic, causing frequent aneuploidy and large deletions1,2. Here, we evaluate DNA repair outcomes at nicks and mismatches introduced by base editors at the PCSK9 and HBG loci in human embryos. Delivering ABE8e-V106W as a protein at fertilization achieved editing at all PCSK9 alleles, supporting development to the blastocyst stage and the derivation of homozygous edited stem cell lines. No insertions or deletions were detected, although rare on-target chromosome breakage and chromosomal abnormalities occurred. Nevertheless, editing at bystander and off-target sites was mosaic, and the introduction of the editor as mRNA caused frequent embryo arrest due to guide-independent deaminase activity. Thus, unlike Cas9-induced DNA breaks, base editor-induced lesions are efficiently repaired. However, undesirable consequences for the genome and development can occur, currently precluding clinical use in reproduction.