Synthetic lethal targeting of PSMC2-dependent p97-adapted proteasome complexes that confer chemoresistance in multiple myeloma

Abstract Introduction. Multiple myeloma (MM) is the second most common hematological malignancy. The emergence of novel agents has significantly extended patient survival, however, those with certain cytogenetic and clinical features are at risk of poor outcome. While proteasome inhibitors (PIs), e.g., bortezomib (Btz), have transformed MM care, many patients do not respond to therapy, and drug resistance inevitably emerges through molecular mechanisms that remain incompletely characterized. Here, we hypothesized that the expression of proteasome genes in patient tumor cells could inform responses to Btz and identify novel, actionable therapeutic targets to improve patient outcome. Methods. Thephase III APEX trial randomized MM patients that had consented to genomic analyses of tumor samples obtained prior to treatment to receive either Btz or high-dose dexamethasone (Dex). We compared the expression of proteasome genes in Btz responders (Btz-Rs) to non-responders (Btz-NRs) and identified 13 genes significantly overexpressed in Btz-NRs. To corroborate the APEX study results, we analyzed the CoMMpass dataset; a longitudinal study that collects tissue, genetic information, and clinical outcomes from 1,100 NDMM patients. To identify drugs that specifically targeted PSMC2-overexpressing cells, a high throughout screen (HTS) was performed using drugs that targeted ER-dependent protein degradation. Drugs that selectively induced synthetic lethality in PSMC2-overexpressing were identified. The effect of CB-5339, an orally available inhibitor of the chaperone p97's ATPase activity, was evaluated, alone and combined with Btz, against tumor cells isolated from Btz-refractory MM patients and in vivo using xenotransplants in murine models. Results. Cox proportional hazard analysis revealed an even broader impact of the 12 proteasome genes on patient OS. Analysis of the APEX and CoMMpass datasets revealed that greater expression of PSMC2 correlated with inferior OS following Btz treatment. PSMC2 expression was also greater in tumor cells from Btz-NRs relative to Btz-Rs. PSMC2 is a AAA-ATPase responsible for unfolding and translocating substrates through the RP into the 20S CP. We show that expression of the proteasome AAA-ATPase PSMC2 was increased in bortezomib-resistant patients. HTS revealed that CB-5339, an ATP-competitive inhibitor of p97/VCP that chaperones ubiquitinated substrates to proteasomes, was synthetic lethal with PSMC2-overexpression. CB-5339/Btz co-treatment synergistically targeted bortezomib-resistant myeloma cells and improved survival in mice, particularly in PSMC2-overexpressing myeloma xenografts. PSMC2 enhanced p97 complexation with proteasomes and decreased binding of the proteasome inhibitor PSMF1 while PSMC2 KO increased PSMF1 binding. p97-complexed proteasomes exhibited greater catalytic activity and bortezomib-resistance. Discussion. One strategy to target cancers is to attack genes that are not oncogenes but rather genes that cancer cells require to accommodate cancer-specific stresses. Even though proteins within these pathways may be essential, genetic alterations induce a state in which reliance on these pathways creates a therapeutic window and promote clinically actionable synthetic lethality. Here, we identified cancer-specific vulnerabilities in myeloma patient tumor cells through an integrated analysis of expression profiles, genome-scale copy number data and clinical outcome datasets. Using this pipeline, we discovered that PSMC2 overexpressing cells were highly sensitive to CB-5339; an p97/VCP inhibitor well-tolerated in vivo. Taken together, we establish a data-driven platform to leverage cancer genomics using precision oncology to identify and exploit proteasomal adaptations that confer chemoresistance.