A circular RNA overcomes acquired resistance to BET inhibitors by antagonizing IGF2BP2-mediated c-MYC translation in triple-negative breast cancer

The bromodomain and extra-terminal domain (BET) proteins are promising therapeutic targets to treat refractory solid tumors including triple-negative breast cancer (TNBC); however, acquired resistance remains a major challenge in the clinic. Therefore, elucidation on the mechanism underlying acquired drug resistance is of practical significance. In this study, we found that abnormally upregulated RNA-binding protein IGF2BP2 acts as crucial contributor to triggering acquired BETi resistance in TNBC by facilitating the translational process of c-myc mRNAs. Considering that IGF2BP2 itself are not ideal drug target for small-molecular compounds, we carried out an RIP-seq experiment and identified circRNA-BISC as a potent IGF2BP2 repressor, which was able to repress both c-MYC translation process and acquired BETi resistance. BISC possesses a typical 'CAC-linker-XGGX' motif to specifically bind with IGF2BP2 without interactions with IGF2BP1 and IGF2BP3. The effectiveness and specificity of BISC on IGF2BP2 prompted further evaluation of the BISC-based RNA therapeutics in TNBC. In vitro transcribed and circularized BISC, when combined with OTX-015, achieves impressive tumor remission of the BETi-resistant TNBCs without obvious toxicities. Collectively, our result support BISC as a potent IGF2BP2 repressor and highlight the feasibility of pursuing BISC restoration by circRNA therapeutics to overcome BETi resistance. Overall design: Both MDA-MB-231 parental cells and acquired BETi resistant cells were probed to RIP-seq using anti-IGF2BP2 mAb or normal rabbit IgG. Enrichment of IGF2BP2-associating circRNAs was measured by deducting the circRNA RPMs in IgG. Delta enrichment of IGF2BP2-associating circRNAs were calculated by minusing enrichment in parental cells from acquired BETi resistant cells. Candidates harboring the minus delta enrichments were considered as circRNAs whose association with IGF2BP2 were decreased upon acquired BETi resistance establishment.