An arrayed CRISPR screen identifies knockout combinations improving antibody productivity in HEK293 cells
Mammalian cells are used to express complex biologics such as multispecific antibodies. While multispecifics enable promising new strategies for treating human disease, their production at high expression titer and purity can be challenging. To understand how cells respond to antibody and multispecific expression, five molecules were selected for bulk RNA-seq early after transfection of a HEK293 host. All five molecules shared a differential expression signature of secretory and protein folding stress, but this signature was stronger for molecules with low titer. We then designed an arrayed CRISPR knockout screen of 206 differentially-expressed target genes and 223 literature-motivated targets to identify knockouts that impact antibody productivity. Eight novel knockout targets were identified that increased expression titers by 20 to 80%. Notably, seven of these top eight hits were from the differentially- expressed set of candidate-gene knockouts. The top knockout target, HIST2H3C, showed evidence for additivity with five other hits, including a knockout combination that increased the titer of a difficult-to-express antibody by up to 100%. Findings for both HIST2H3C and INHBE knockout targets generalized to an alternate HEK293 host expressing an additional antibody and a multispecific with no meaningful impact on product purity. Thus, we propose HIST2H3C and INHBE disruption to be a promising and novel strategy for host-cell engineering to improve antibody and multispecific productivity. Overall design: Five different molecules were selected for transfection into HEK293-6E cells, with 4 replicats of each treatment molecule condition. Bulk RNA was extracted two days after transfection to investigate RNA expression changes relative to empty vector control.