Genotoxic effects of base and prime editing in human hematopoietic stem cells [BARseq_BaseE]

Emerging base and prime editing may provide safer and more precise genetic engineering than nuclease-based approaches bypassing the dependence on DNA double strand breaks (DSBs). However, little is known about cellular responses and genotoxicity. Here, we comparatively assessed state-of-the-art base and prime editors (B/PE) versus Cas9 in human hematopoietic stem/progenitor cells (HSPCs). BE and PE induced detrimental transcriptional responses constraining editing efficiency and/or HSPC repopulation in xenotransplants, albeit to a lesser extent than Cas9. DNA DSBs and their genotoxic byproducts, including deletions and translocations, were less frequent but not abrogated by BE and PE, particularly for cytidine BE due to suboptimal inhibition of base excision repair. Tailoring timing and B/PE expression enabled highly efficient and precise editing of long-term repopulating HSPCs. However, we uncovered a genome-wide effect of BEs on the mutational landscape of HSPCs, raising concerns for a potential genotoxic impact and calling for further investigations and improvements in view of clinical application. BAR-Seq clonal tracking performed on samples from a pool of 6 CB donors, treated with different editing conditions, namely, mock electroporation (mock electro), Cas9, BE4max, and ABE8.20-m, in different organs and lineages.