Tay-Sachs disease is a fatal neurodegenerative disorder caused by HEXA mutations inactivating the metabolic enzyme HexA. The most common mutation is c.1278insTATC, a tandem 4 base pair (bp) duplication disrupting HEXA expression by frameshift. In an engineered cell model, we explore the use of CRISPR/Cas9 for therapeutic editing of c.1278insTATC. Within genomic microduplications, the microhomology-mediated end joining (MMEJ) pathway is favoured to repair double-stranded breaks with collateral deletion of one repeat. Protospacer adjacent motif (PAM) constraints on Cas9 endonuclease activity prevented cleavage at the duplication centre – the optimal position for MMEJ initiation. Rather, cleavage 1 bp from the c.1278insTATC duplication centre spontaneously reconstructed the wildtype sequence at ∼14.7% frequency, with concomitant restoration of normal cellular HexA activity. As an alternative to perfect correction, short insertions/deletions were serially introduced to restore an open reading frame across a 19 bp sequence encompassing c.1278insTATC. Frame-restored variants did not recover significant HexA function, presumably due to structural incompatibility of incurred amino acid insertions. Hence, precise correction of c.1278insTATC is the only therapeutically relevant outcome achieved in this study, with MMEJ highlighted as a potential template-free CRISPR/Cas9 modality to that end.
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