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Cytosine base editors induce off-target mutations and adverse phenotypic effects in transgenic mice

Author

Listed:
  • Nana Yan

    (Chinese Academy of Agricultural Sciences)

  • Hu Feng

    (Chinese Academy of Agricultural Sciences)

  • Yongsen Sun

    (Chinese Academy of Agricultural Sciences)

  • Ying Xin

    (Chinese Academy of Agricultural Sciences
    Huazhong Agricultural University)

  • Haihang Zhang

    (Chinese Academy of Agricultural Sciences)

  • Hongjiang Lu

    (Chinese Academy of Agricultural Sciences
    Huazhong Agricultural University)

  • Jitan Zheng

    (Chinese Academy of Agricultural Sciences
    Guangxi University)

  • Chenfei He

    (Chinese Academy of Agricultural Sciences)

  • Zhenrui Zuo

    (Chinese Academy of Agricultural Sciences)

  • Tanglong Yuan

    (Chinese Academy of Agricultural Sciences)

  • Nana Li

    (Chinese Academy of Agricultural Sciences
    Huazhong Agricultural University)

  • Long Xie

    (Chinese Academy of Agricultural Sciences)

  • Wu Wei

    (University of Chinese Academy of Sciences, Chinese Academy of Sciences
    Lingang Laboratory)

  • Yidi Sun

    (Chinese Academy of Sciences)

  • Erwei Zuo

    (Chinese Academy of Agricultural Sciences)

Abstract

Base editors have been reported to induce off-target mutations in cultured cells, mouse embryos and rice, but their long-term effects in vivo remain unknown. Here, we develop a Systematic evaluation Approach For gene Editing tools by Transgenic mIce (SAFETI), and evaluate the off-target effects of BE3, high fidelity version of CBE (YE1-BE3-FNLS) and ABE (ABE7.10F148A) in ~400 transgenic mice over 15 months. Whole-genome sequence analysis reveals BE3 expression generated de novo mutations in the offspring of transgenic mice. RNA-seq analysis reveals both BE3 and YE1-BE3-FNLS induce transcriptome-wide SNVs, and the numbers of RNA SNVs are positively correlated with CBE expression levels across various tissues. By contrast, ABE7.10F148A shows no detectable off-target DNA or RNA SNVs. Notably, we observe abnormal phenotypes including obesity and developmental delay in mice with permanent genomic BE3 overexpression during long-time monitoring, elucidating a potentially overlooked aspect of side effects of BE3 in vivo.

Suggested Citation

  • Nana Yan & Hu Feng & Yongsen Sun & Ying Xin & Haihang Zhang & Hongjiang Lu & Jitan Zheng & Chenfei He & Zhenrui Zuo & Tanglong Yuan & Nana Li & Long Xie & Wu Wei & Yidi Sun & Erwei Zuo, 2023. "Cytosine base editors induce off-target mutations and adverse phenotypic effects in transgenic mice," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37508-7
    DOI: 10.1038/s41467-023-37508-7
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    References listed on IDEAS

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    Cited by:

    1. Hongzhi Zeng & Qichen Yuan & Fei Peng & Dacheng Ma & Ananya Lingineni & Kelly Chee & Peretz Gilberd & Emmanuel C. Osikpa & Zheng Sun & Xue Gao, 2023. "A split and inducible adenine base editor for precise in vivo base editing," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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