Small-molecule compounds boost genome-editing efficiency of cytosine base editor.

Abstract

Cytosine base editor (CBE) enables targeted C-to-T conversions at single base-pair resolution and thus has potential therapeutic applications in humans. However, the low efficiency of the system limits practical use of this approach. We reported a high-throughput human cells-based reporter system that can be harnessed for quickly measuring editing activity of CBE. Screening of 1813 small-molecule compounds resulted in the identification of Ricolinostat (an HDAC6 inhibitor) that can enhance the efficiency of BE3 in human cells (2.45- to 9.21-fold improvement). Nexturastat A, another HDAC6 inhibitor, could also increase BE3-mediated gene editing by 2.18- to 9.95-fold. Ricolinostat and Nexturastat A also boost base editing activity of the other CBE variants (BE4max, YE1-BE4max, evoAPOBEC1-BE4max and SpRY-CBE4max, up to 8.32-fold). Meanwhile, combined application of BE3 and Ricolinostat led to >3-fold higher efficiency of correcting a pathogenic mutation in ABCA4 gene related to Stargardt disease in human cells. Moreover, we demonstrated that our strategy could be applied for efficient generation of mouse models through direct zygote injection and base editing in primary human T cells. Our study provides a new strategy to improve the activity and specificity of CBE in human cells. Ricolinostat and Nexturastat A augment the effectiveness and applicability of CBE.

• Authors: Tianyuan Zhao, Qing Li, Chenchen Zhou, Xiujuan Lv, Hongyan Liu, Tianxiang Tu, Na Tang, Yanbo Cheng, Xiaoyu Liu, Changbao Liu, Junzhao Zhao, Zongming Song, Haoyi Wang, Jinsong Li, Feng Gu
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 49 Issue 15 Pg. 8974-8986 (09 07 2021) ISSN: 1362-4962 [Electronic] England
• PMID: 34329468 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chemical References

• 4-((1-butyl-3-phenylureido)methyl)-N-hydroxybenzamide
• ABCA4 protein, human
• ATP-Binding Cassette Transporters
• Abca4 protein, mouse
• Hydroxamic Acids
• Phenylurea Compounds
• Pyrimidines
• Small Molecule Libraries
• Cytosine
• HDAC6 protein, human
• Histone Deacetylase 6
• ricolinostat

Topics

• ATP-Binding Cassette Transporters (genetics)
• Animals
• CRISPR-Cas Systems (genetics)
• Cytosine (metabolism)
• Gene Editing (trends)
• HEK293 Cells
• Histone Deacetylase 6 (antagonists & inhibitors, genetics)
• Humans
• Hydroxamic Acids (pharmacology)
• Mice
• Mutation (drug effects)
• Phenylurea Compounds (pharmacology)
• Pyrimidines (pharmacology)
• Small Molecule Libraries (pharmacology)
• Stargardt Disease (drug therapy, genetics, pathology)
• T-Lymphocytes (drug effects)
• Zygote (drug effects)