Deep Proteomic and Phosphoproteomic Profiling in Proteasome Inhibitor-Resistant Multiple Myeloma

ABSTRACT: Proteasome inhibitors (PIs) are frontline therapies for multiple myeloma (MM). Although MM patients initially respond to PIs, resistance frequently emerges. While clinical PIs primarily target the same proteasomal catalytic subunit (PSMB5), the extent to which resistance mechanisms are shared among different PIs remains poorly understood. To elucidate these resistance mechanisms, we performed deep proteomic and phosphoproteomic profiling of 12 MM cell line models, comprising four parental lineages (AMO-1, ARH77, L363, and RPMI8226) and their paired derivatives with acquired resistance to bortezomib (BTZ) and carfilzomib (CFZ). We quantified over 7,000 proteins and up to 10,000 phosphopeptides per cell line, enabling a systematic comparative analysis of shared and cell line-specific resistance signatures. Crucially, we discovered that acquired PI resistance is primarily driven by massive, stable reprogramming of the global proteome, while the phosphoproteome remains surprisingly constrained. Alongside known adaptations such as the overexpression of the PI target PSMB5 and the drug efflux transporter ABCB1, we identified the antioxidant flavoenzymes NQO1 and NQO2 as significantly upregulated proteins under chronic proteotoxic stress. Importantly, our functional validation revealed that protein abundance does not strictly dictate essentiality; even in contexts with lower basal expression, NQO2 serves as a critical vulnerability. Co-inhibiting NQO1 alongside the established ABCB1 efflux pump effectively restored PI sensitivity. Collectively, our dataset provides a rich resource for MM research and reveals pan-NQO inhibition as a highly effective, actionable strategy to overcome PI resistance.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Bone Marrow

DISEASE(S): Multiple Myeloma

SUBMITTER: Chien-Yun Lee  

LAB HEAD: Bernhard Kuster

PROVIDER: PXD077254 | Pride | 2026-07-15

REPOSITORIES: Pride