State Key Laboratory of Common Mechanism Research for Major Diseases; Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
Commun Biol. 2024 Oct 25;7(1):1389. doi: 10.1038/s42003-024-07078-5.
Base editors enable the direct conversion of target bases without inducing double-strand breaks, showing great potential for disease modeling and gene therapy. Yet, their applicability has been constrained by the necessity for specific protospacer adjacent motif (PAM). We generate four versions of near-PAMless base editors and systematically evaluate their editing patterns and efficiencies using an sgRNA-target library of 45,747 sequences. Near-PAMless base editors significantly expanded the targeting scope, with both PAM and target flanking sequences as determinants for editing outcomes. We develop BEguider, a deep learning model, to accurately predict editing results for near-PAMless base editors. We also provide experimentally measured editing outcomes of 20,541 ClinVar sites, demonstrating that variants previously inaccessible by NGG PAM base editors can now be precisely generated or corrected. We make our predictive tool and data available online to facilitate development and application of near-PAMless base editors in both research and clinical settings.
碱基编辑器能够在不诱导双链断裂的情况下直接转换靶碱基，在疾病建模和基因治疗方面显示出巨大的潜力。然而，它们的适用性受到特定的前导间隔基序 (PAM) 的限制。我们生成了四个版本的近无 PAM 碱基编辑器，并使用 45747 个序列的 sgRNA 靶标文库系统地评估了它们的编辑模式和效率。近无 PAM 碱基编辑器显著扩大了靶向范围，PAM 和靶标侧翼序列都是编辑结果的决定因素。我们开发了一种深度学习模型 BEguider，能够准确预测近无 PAM 碱基编辑器的编辑结果。我们还提供了 20541 个 ClinVar 位点的实验测量编辑结果，表明以前无法通过 NGG PAM 碱基编辑器进行编辑的变体现在可以精确生成或纠正。我们提供了我们的预测工具和数据在线，以促进近无 PAM 碱基编辑器在研究和临床环境中的开发和应用。
