Lei Lei, Masako M. Kaufmann, Jessica Lao, Gudrun Thoulass, Sandra Ammann, Hui Xiao, Manuel Rhiel, Viviane Dettmer‐Monaco, Julian Grünewald, Geoffroy Andrieux, Jamal Alzubi, Bret R. Miller, Kristoffer Weißert, Linda Gräßel, Christoph Schell, Anna L. Illert, J. Keith Joung, Melanie Boerries, Tatjana I. Cornu, Stephan Ehl, Miriam Erlacher, Peter Aichele, Toni Cathomen
Base editors enable precise correction of point mutations without requiring DNA double-strand breaks, yet platform- and cell type-specific genotoxicities remain incompletely characterized. Here, we applied cytosine base editing (CBE) to disrupt a cryptic splice-site mutation in the Unc13d locus of Jinx mice, a model of familial hemophagocytic lymphohistiocytosis type 3 (FHL3). Efficient editing (62%-89%) in fibroblasts, T cells, and hematopoietic stem cells (HSCs) restored Unc13d splicing, reconstituted cytotoxic T cell function, and protected mice from virus-triggered hyperinflammation after transplantation of edited HSCs. Comparative genotoxicity profiling revealed distinct platform- and cell type-specific patterns: hyperactive CBE induced broader off-target activity and more structural variants than CRISPR-Cas9. Although off-target sequence edits persisted, the stability of CBE-induced chromosomal translocations differed between cell types. These findings establish base editing as a therapeutic strategy for a genetically predisposed hyperinflammatory syndrome and underscore the importance of context-specific safety profiling to guide the clinical translation of genome editors.