Transient ATM inhibition enhances knock-in efficiency in hematopoietic stem cells by attenuating the DNA damage response

Precise genome editing in hematopoietic stem cells (HSCs) holds great potential for treating inherited blood disorders; however, low knock-in (KI) efficiency and loss of functional HSCs after genome editing remain major obstacles. Here, we demonstrate that transient inhibition of Ataxia-Telangiectasia Mutated (ATM) kinase markedly enhanced KI efficiency in mouse HSCs genome-edited with Cas9/ribonucleoprotein (RNP) and AAV donor DNA. Phosphoproteomic and capillary western blot analyses revealed that ATM inhibition suppressed aberrant Cas9-AAV-induced ATM activation and the subsequent DNA damage response, reduced p53-dependent apoptosis, and enhanced survival of KI HSCs. In serial transplantation assays, ATM inhibition preserved long-term engrafting KI HSCs, increasing their frequency from ~0.3 to 40% in secondary recipients, an over 100-fold improvement. Furthermore, in an X-linked severe combined immunodeficient mouse model, ATM inhibition increased KI efficiency and restored T- and B cell differentiation. Comprehensive safety analyses, including long-read nanopore sequencing, amplicon deep sequencing, whole genome sequencing and clonal tracking, did not detect increased genomic alterations, chromosomal abnormalities, or clonal expansion following transient ATM inhibition. Taken together, these findings establish transient ATM inhibition as an effective strategy to enhance KI-mediated genome editing while maintaining the long-term repopulating capacity of HSCs.