Overcoming imatinib resistance conferred by the BIM 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 Bim gene, whose product is required for TKI-induced Apoptosis. The deletion biases Bim 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 Bim deletion-containing cancers to imatinib. First, we mapped multiple cis-acting splicing elements around Bim 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 Bim splicing. Eight of 67 ASOs increased exon 4 levels in Bim deletion-containing cells, and restored imatinib-induced Apoptosis and TKI sensitivity. This proof-of-principle study proves that resistant CML cells by Bim deletion polymorphism can be resensitized to imatinib via splice-switching Bim ASOs. Future optimizations might yield a therapeutic ASO as precision-medicine Adjuvant treatment for Bim-polymorphism-associated TKI-resistant CML and Other cancers.