Targeting specificity of APOBEC-based cytosine base editor in human iPSCs determined by whole genome sequencing

McGrath, Erica; Shin, Hyunsu; Zhang, Linyi; Phue, Je-Nie; Wu, Wells W.; Shen, Rong-Fong; Jang, Yoon-Young; Revollo, Javier; Ye, Zhaohui

doi:10.1038/s41467-019-13342-8

Targeting specificity of APOBEC-based cytosine base editor in human iPSCs determined by whole genome sequencing

Journal Article · Mon Nov 25 00:00:00 EST 2019 · Nature Communications

DOI:https://doi.org/10.1038/s41467-019-13342-8· OSTI ID:1624218

McGrath, Erica ^[1]; Shin, Hyunsu ^[2]; Zhang, Linyi ^[2]; ^[3]; Wu, Wells W. ^[3]; Shen, Rong-Fong ^[3]; ^[4]; Revollo, Javier ^[5]; ^[2]

U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States). Div. of Cellular and Gene Therapies, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research; DOE/OSTI
U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States). Div. of Cellular and Gene Therapies, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research
U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States). Facility for Biotechnology Resources, Center for Biologics Evaluation and Research
Johns Hopkins Univ., Baltimore, MD (United States). Dept. of Oncology
U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States). Division of Genetic and Molecular Toxicology, National Center for Toxicology Research

DNA base editors have enabled genome editing without generating DNA double strand breaks. The applications of this technology have been reported in a variety of animal and plant systems, however, their editing specificity in human stem cells has not been studied by unbiased genome-wide analysis. Here we investigate the fidelity of cytidine deaminase-mediated base editing in human induced pluripotent stem cells (iPSCs) by whole genome sequencing after sustained or transient base editor expression. While base-edited iPSC clones without significant off-target modifications are identified, this study also reveals the potential of APOBEC-based base editors in inducing unintended point mutations outside of likely in silico-predicted CRISPR-Cas9 off-targets. The majority of the off-target mutations are C:G->T:A transitions or C:G->G:C transversions enriched for the APOBEC mutagenesis signature. These results demonstrate that cytosine base editor-mediated editing may result in unintended genetic modifications with distinct patterns from that of the conventional CRISPR-Cas nucleases.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)

Sponsoring Organization:: FDA; NIH; USDOE

Grant/Contract Number:: SC0014664

OSTI ID:: 1624218

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 10; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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