Overcoming Imatinib Resistance Conferred by the Deletion Polymorphism in Chronic Myeloid Leukemia with Splice-switching Antisense Oligonucleotides

Many tyrosine kinase-driven cancers, including chronic myeloid leukemia (CML), are characterized by high response rates to specific tyrosine kinase inhibitors (TKIs) like imatinib. In East Asians, primary imatinib resistance is caused by a deletion polymorphism in Intron 2 of the gene, whose product is required for TKI-induced apoptosis. The deletion biases splicing from exon 4 to exon 3, generating splice isoforms lacking the exon 4-encoded pro-apoptotic BH3 domain, which impairs the ability of TKIs to induce apoptosis. We sought to identify splice-switching antisense oligonucleotides (ASOs) that block exon 3 but enhance exon 4 splicing, and thereby resensitize deletion-containing cancers to imatinib. First, we mapped multiple -acting splicing elements around exon 3 by minigene mutations, and found an exonic splicing enhancer acting via SRSF1. Second, by a systematic ASO walk, we isolated ASOs that corrected the aberrant splicing. Eight of 67 ASOs increased exon 4 levels in deletion-containing cells, and restored imatinib-induced apoptosis and TKI sensitivity. This proof-of-principle study proves that resistant CML cells by deletion polymorphism can be resensitized to imatinib via splice-switching ASOs. Future optimizations might yield a therapeutic ASO as precision-medicine adjuvant treatment for -polymorphism-associated TKI-resistant CML and other cancers.