Orthogonal CRISPR systems for targeted integration and multiplex base editing enable nonviral engineering of allogeneic CAR T cells

Multiple genomic modifications, including targeted transgene integrations and knockouts, may be required to develop potent, allogeneic chimeric antigen receptor (CAR) T cell therapies. Conventional CRISPR/Cas systems generate double-strand breaks (DSBs) associated with genomic rearrangements and genotoxicities. DSB-free base editing reduces these risks. Here we facilitate multiplex editing by combining S. aureus Cas9 (SaCas9) mRNA base editors for DSB-free knockout of B2M and REGNASE-1 with S. pyogenes Cas9 (SpCas9) nucleases for targeted integration of an anti-CD19 CAR transgene at the T cell receptor α constant (TRAC) locus. Combined, these edits have been reported to generate safer allogeneic CAR T cells with enhanced activity and persistence. We demonstrate multiplex gene editing in primary human T cells with B2M and REGNASE-1 base editing frequencies reaching 66% and 84%, respectively, while integrating the anti-CD19 CAR transgene in up to 36% or 71% of cells using nonviral ssDNA repair templates or viral vector templates (AAV6), respectively. Importantly, no detrimental effects on CAR T cell function were observed in vitro or in vivo, and knockout by base editing reduced rates of balanced chromosomal translocations by 210-fold. This orthogonal CRISPR/Cas engineering approach represents a novel and safer strategy for nonviral, multiplexed genetic engineering of CAR T cells.