Targeted gene editing of PCCA pseudoexon using CRISPR-Cas12a for potential therapy in propionic acidemia

Deep-intronic variants activating pseudoexons (PEs) are a common cause for monogenic diseases. Removal of the PE region predictably corrects the splicing defect, offering a potential therapeutic strategy. Previous studies, including our own, have identified an 84-bp PE in intron 14 of the gene PCCA that is included in the mature mRNA at relatively high basal levels across all tissues. When activated by the c.1285-1416A>G variant, this PE becomes fully included, ultimately causing the potentially lethal neurometabolic disorder propionic acidemia due to the deficiency of propionyl-CoA carboxylase (PCC) enzyme. In this study, we explored, through a CRISPR-Cas12-assisted non-homologous end joining (NHEJ)-mediated approach, whether PE removal or abrogation of the splice enhancer strengthened by the variant could efficiently restore normal transcript and functional PCCA protein. Both in wild-type hepatoma cells and in an edited cellular model homozygous for the activating variant, we show that the CRISPR-Cas12a approach increases PCC activity, with the highest values obtained with a guide RNA (gRNA) targeting the enhancer region in the PEs. The results provide proof-of-concept of its therapeutic potential for patients with PE activation and those with hypomorphic missense variants in whom residual activity levels may be effectively raised.