Overcoming imatinib resistance conferred by the BIM deletion polymorphism in chronic myeloid leukemia with splice-switching antisense oligonucleotides

Abstract

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.

Aberrant RNA Splicing in Cancer and Drug Resistance

“…Exon 4 of BIM encodes a BH3 domain, which is essential for the pro-apoptotic function of BIM. The exon 4-to-exon 3 switch introduces a polyadenylation signal sequence leading to premature translation termination and loss of the BH3 domain [ 129 , 130 ]. Indeed, BCR-ABL-positive CML and EGFR mutation-positive non-small cell lung cancer (NSCLC) cells expressing BIM-γ exhibit resistance to imatinib and gefitinib (EGFR TKI), respectively [ 124 ].…”

“…More recently, a systematic antisense splice-switching oligonucleotide (ASO) ‘walking’ screen identified 67 ASOs that corrected aberrant BIM splicing by preventing the exon 4-to-exon 3 switch. This led to a restoration of TKI sensitivity and re-sensitized leukemic cells to imatinib-induced apoptosis [ 130 ].…”

SRSF1 modulates PTPMT1 alternative splicing to regulate lung cancer cell radioresistance

“…Moreover, SRSF1 regulates the epithelial-to-mesenchymal transition (EMT) through modulating the splicing of Ron proto-oncogene [29], as well as controls the alternative splicing of PRRC2C and MKNK2 to regulate lung cancer progression [28,30]. Most importantly, SRSF1 regulates the splicing of BIM to inhibit imatinib-induced apoptosis, thereby conferring cancer cells resistance to imatinib [31]. In addition, other splicing factors, such as hnRNP A1 and PTB, have been reported to influence pyruvate kinase splicing and cell metabolism to affect tumorigenesis [32], whereas RBM4 controls the alternative splicing of Bcl-x to inhibit lung cancer progression [14].…”

A Novel FGFR3 Splice Variant Preferentially Expressed in African American Prostate Cancer Drives Aggressive Phenotypes and Docetaxel Resistance

“…In melanoma, a 61 kDa isoform encoded by a BRAF splice variant missing exons 4-8 lacks the RAS-binding domain, resulting in constitutive isoform dimerization and kinase activity and resistance to the inhibitor vemurafenib (32). A splice variant of BIM (BIM-g), encoding a protein that lacks the BH3 domain, has been identified as a mechanism for TKI (e.g., imatinib and gefitinib) resistance in chronic myeloid leukemia (33)(34)(35). It should be noted that none of these splicing events occur within the tyrosine kinase domain.…”