Harnessing Synthetic Lethal Interactions in Hematological Malignancies: Novel Therapeutic Approaches to Overcome Drug Resistance

Proteasome inhibitors (PIs) are commonly used to treat multiple myeloma (MM) and mantle cell lymphoma. However, many patients either relapse or are intrinsically resistant to these drugs. To identify targets that enhance the efficacy of PIs, we conducted a functional drug screening in the presence of the proteasome inhibitor carfilzomib (CFZ). This screening revealed synergistic interactions, with the ATP5F1C inhibitor bedaquiline (BDQ) and FDAapproved drug, and its fumarate form (BDQ-F), standing out as top candidates for further investigation. Our research showed that BDQ increases CFZ effectiveness in both PIsensitive and PI-resistant MM cells, as well as in amyloidosis cells and other B-cell malignancies. Importantly, the combination of BDQ and CFZ demonstrated a favorable cytotoxic profile toward normal human cells, including peripheral blood mononuclear cells (PBMCs), immortalized B-lymphocytes, and stromal cells. To assess the target selectivity of BDQ, we employed both pharmacological and genetic approaches, confirming that BDQ specifically targets the ATP5F1C subunit. To better understand the molecular mechanisms behind this synergy, we utilized RNA sequencing and proteomics analyses. These analyses revealed significant changes in gene and protein regulation compared to single-agent treatments. Key pathways affected included cell cycle regulation, cell migration, autophagy, response to endoplasmic reticulum stress, ATP metabolism, and proteasomal catabolism. Overall, our findings indicate that BDQ-CFZ cotreatment induces extensive transcriptional and proteomic changes that promote proteotoxic stress and apoptosis, contributing to their strong cytotoxic effects. Mechanistically, BDQ specifically enhances the chymotrypsin-like activity inhibition of CFZ on the proteasome, without significantly affecting its other catalytic activities. Furthermore, we demonstrated that BDQ synergizes with other PIs, such as bortezomib (BTZ), ixazomib (IXA), and marizomib (MRZ), in both PI-sensitive and resistant MM cell lines, while having no additional effects when combined with other MM therapies that utilize different mechanisms. All together, these findings suggest a specific effect of BDQ in enhancing PIs activity. Additionally, BDQ-CFZ treatment enhanced MM cell death within the bone marrow environment, exhibited synergy in patient-derived MM cells, and inhibited tumor growth in a zebrafish MM xenograft model. In conclusion, inhibition of the ATP5F1C subunit enhances the therapeutic efficacy of PIs, supporting the use of lower and less toxic doses and expanding the application of PIs to other malignancies.