一种减少旁观者编辑的简化碱基编辑器工程策略。
A streamlined base editor engineering strategy to reduce bystander editing.
作者信息
Valdez Izabella, O'Connor Ian, Patel Divesh, Gierer Katherine, Harrington Jan, Ellis Ethan, Caponetti Stephen A, Sebra Robert P, Valley Hillary C, Coote Kevin, Mense Martin, Marro Samuele G, Jiang Tingting
机构信息
Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
出版信息
Nat Commun. 2025 Aug 30;16(1):8115. doi: 10.1038/s41467-025-63609-6.
Base editing (BE) can permanently correct over half of known human pathogenic genetic variants without requiring a repair template, thus serving as a promising therapeutic tool to treat a broad spectrum of genetic diseases. However, the broad activity windows of current base editors pose a major challenge to their therapeutic application. Here, we show that integrating a naturally occurring oligonucleotide binding module into the deaminase active center of TadA-8e, a highly active deoxyadenosine deaminase, enhances its editing specificity. When conjugated with a Cas9 nickase or alternative PAM Cas9 variants, the engineered TadA variant-TadA-NW1-consistently achieves robust A-to-G editing efficiencies within an editing window consisting of four nucleotides, substantially narrower than the 10-bp editing window of the TadA-8e-derived ABEs. Moreover, compared to ABE8e, ABE-NW1 shows significantly decreased Cas9-dependent and -independent off-target activity while maintaining similar on-target editing efficiency. Further, TadA-NW1 can be reprogrammed to perform desired cytidine deamination and adenine transversion within a restricted editing window. Finally, in a cystic fibrosis (CF) cell model, ABE-NW1 outperforms existing ABEs in accurately and efficiently correcting the CFTR W1282X variant, one of the most common CF-causing mutations. In all, we engineered a suite of base editors with refined activity windows, enabling more precise base editing. Importantly, this study presents a streamlined genome editor re-engineering strategy to accelerate the development of therapeutic base editing.
碱基编辑(BE)无需修复模板就能永久纠正超过一半已知的人类致病基因变异,因此有望成为治疗多种遗传疾病的有效治疗工具。然而,目前碱基编辑器宽泛的活性窗口对其治疗应用构成了重大挑战。在此,我们表明,将一个天然存在的寡核苷酸结合模块整合到高活性脱氧腺苷脱氨酶TadA-8e的脱氨酶活性中心,可提高其编辑特异性。当与Cas9切口酶或替代PAM的Cas9变体偶联时,工程化的TadA变体TadA-NW1在由四个核苷酸组成的编辑窗口内始终能实现强大的A到G编辑效率,该窗口比源自TadA-8e的ABE的10个碱基对编辑窗口窄得多。此外,与ABE8e相比,ABE-NW1在保持相似的靶向编辑效率的同时,显示出显著降低的依赖Cas9和不依赖Cas9的脱靶活性。此外,TadA-NW1可以重新编程,在受限的编辑窗口内进行所需的胞嘧啶脱氨和腺嘌呤颠换。最后,在囊性纤维化(CF)细胞模型中,ABE-NW1在准确高效地纠正CFTR W1282X变体(最常见的导致CF的突变之一)方面优于现有的ABE。总之,我们设计了一套具有精细活性窗口的碱基编辑器,实现了更精确的碱基编辑。重要的是,本研究提出了一种简化的基因组编辑器重新设计策略,以加速治疗性碱基编辑的开发。