Inducible, split base editors for in vivo cancer functional genomics

Ren, Diqiu, Wang, Shangshang, Yamada, Keisuke, Liu, Yuqiao, Hapke, Robert, Alpsoy, Aktan, Ho, Yugong, Zhang, Canjing, Lan, Yemin, Zhang, Shuo, Milazzo, Joseph P, Lohia, Ruchi, Berríos, Kiara N, Li, Yongjun, Weber, Evan W, Li, Qin, Vakoc, Christopher R, Minn, Andy J, Kohli, Rahul M, Shi, Junwei (April 2026) Inducible, split base editors for in vivo cancer functional genomics. Nature Biotechnology. ISSN 1087-0156 (Public Dataset)

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Abstract

Cancer functional genomics using CRISPR base editors (BEs) holds great promise for molecular characterization and new target discovery. However, traditional BEs, using intact DNA deaminases as mutators, are often constrained by limited control and nonspecific toxicities. Here we developed a small-molecule-controllable system using split-engineered BEs (seBEs). By placing deaminase activity under small-molecule control, seBEs significantly reduced cellular toxicity and enabled robust and inducible in vivo functional genomics screens. High-density seBE genetic screens using ~11,000 single guide RNAs in vitro and ~3,700 single guide RNAs in vivo reveal known and previously unknown loss-of-function and dominant-negative mutations in cancer therapeutic targets. A deeper tiling seBE screen against Adar1, a key mediator in cancer immunotherapy, reveals critical residues within functional domains that show no phenotype in vitro but distinctively elicit non-cell-autonomous cancer dependencies in vivo. Overall, our seBE system offers a generalizable, controllable and highly efficient method to systematically identify key residues in cancer functional genomics.

Item Type: Paper
Subjects: diseases & disorders > cancer
diseases & disorders
CSHL Authors:
Communities: CSHL labs > Vakoc lab
CSHL Post Doctoral Fellows
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 15 April 2026
Date Deposited: 16 Apr 2026 18:05
Last Modified: 16 Apr 2026 18:05
Related URLs:
Dataset ID:
  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE316050
URI: https://repository.cshl.edu/id/eprint/42158

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