Molecular principles of CRISPR-Cas13b design for selective silencing of oncogenic fusion transcripts

Here, we establish CRISPR-PspCas13b as a personalisable platform for systematic silencing of various fusion transcripts. We reveal that recognition and cleavage of the breakpoint sequence by PspCas13b disrupts the fusion transcript, resulting in efficient protein depletion.

Short and long-read RNA sequencing reveal that PspCas13b cleavage produces aberrant, translation-incompetent RNA species with preserved 5’/3’ ends and internal deletions proximal to the cleavage site. Importantly, we demonstrate that targeting the BCR::ABL1 breakpoint sequence efficiently degrades both canonical and drug-resistant BCR::ABL1 mutants, which are the primary drivers of tyrosine kinase inhibitor (TKI) resistance and relapse in chronic myeloid leukemia (CML).