Sousa Alexander A, Hemez Colin, Lei Lei, Traore Soumba, Kulhankova Katarina, Newby Gregory A, Doman Jordan L, Oye Keyede, Pandey Smriti, Karp Philip H, McCray Paul B, Liu David R
Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
Nat Biomed Eng. 2025 Jan;9(1):7-21. doi: 10.1038/s41551-024-01233-3. Epub 2024 Jul 10.
Prime editing (PE) enables precise and versatile genome editing without requiring double-stranded DNA breaks. Here we describe the systematic optimization of PE systems to efficiently correct human cystic fibrosis (CF) transmembrane conductance regulator (CFTR) F508del, a three-nucleotide deletion that is the predominant cause of CF. By combining six efficiency optimizations for PE-engineered PE guide RNAs, the PEmax architecture, the transient expression of a dominant-negative mismatch repair protein, strategic silent edits, PE6 variants and proximal 'dead' single-guide RNAs-we increased correction efficiencies for CFTR F508del from less than 0.5% in HEK293T cells to 58% in immortalized bronchial epithelial cells (a 140-fold improvement) and to 25% in patient-derived airway epithelial cells. The optimizations also resulted in minimal off-target editing, in edit-to-indel ratios 3.5-fold greater than those achieved by nuclease-mediated homology-directed repair, and in the functional restoration of CFTR ion channels to over 50% of wild-type levels (similar to those achieved via combination treatment with elexacaftor, tezacaftor and ivacaftor) in primary airway cells. Our findings support the feasibility of a durable one-time treatment for CF.
碱基编辑(PE)能够实现精确且通用的基因组编辑,而无需双链DNA断裂。在此,我们描述了对PE系统的系统性优化,以有效校正人类囊性纤维化(CF)跨膜电导调节因子(CFTR)F508del,这是一种三核苷酸缺失,是CF的主要病因。通过结合针对PE工程化PE引导RNA的六种效率优化、PEmax结构、显性负性错配修复蛋白的瞬时表达、策略性沉默编辑、PE6变体和近端“失活”单向导RNA,我们将CFTR F508del在HEK293T细胞中的校正效率从低于0.5%提高到永生化支气管上皮细胞中的58%(提高了140倍),以及患者来源的气道上皮细胞中的25%。这些优化还导致了最小的脱靶编辑,编辑与插入缺失的比率比核酸酶介导的同源定向修复所达到的比率高3.5倍,并且在原代气道细胞中CFTR离子通道的功能恢复到超过野生型水平的50%(类似于通过与依列卡福、替扎卡福和依伐卡福联合治疗所达到的水平)。我们的研究结果支持了对CF进行持久一次性治疗的可行性。