Intrinsic Nucleotide Preference of Diversifying Base Editors Guides Antibody Ex Vivo Affinity Maturation.

Summary Base editors (BEs) are emerging tools used for precision correction or diversifying mutation. It provides a potential way to recreate somatic hypermutations (SHM) for generating high-affinity antibody, which is usually screened from antigen-challenged animal models or synthetic combinatorial libraries. By comparing somatic mutations in the same genomic context, we screened engineered deaminases and CRISPR-deaminase coupling approaches and updated diversifying base editors (DBEs) to generate SHM. The deaminase used in DBEs retains its intrinsic nucleotide preference and mutates cytidines at its preferred motifs. DBE with AID targets the same hotspots as physiological AID does in vivo , while DBE with other deaminases generates distinct mutation profiles from the same DNA substrate. Downstream DNA repair pathways further diversified the sequence, while Cas9-nickase restricted mutation spreading. Finally, application of DBE in an antibody display system achieved antibody affinity maturation ex vivo. Our findings provide insight of DBE working mechanism and an alternative antibody engineering approach. Graphical Abstract Highlights • We further developed diversifying base editors (DBEs) with more deaminase tools • Engineered deaminase retains its intrinsic nucleotide preference in DBE • Nick-DBE increases mutation and small-deletion efficiencies inside of sgRNA region • DBE-aided antibody affinity maturation is achieved in ex vivo cultured cells Liu et al. developed diversifying base editors (DBEs) with multiple engineered AID/APOBEC deaminases and discovered deaminase's intrinsic nucleotide preference as one key feature of DBEs. With an expanded DBE toolbox, diverse mutation profiles are generated on immunoglobulin transgenes and antibody affinity maturation is achieved in ex vivo cultured cells. [ABSTRACT FROM AUTHOR]