Targeting Caseinolytic Mitochondrial Matrix Peptidase, a Novel Contributor to High-risk Behavior, in Multiple Myeloma

• High expression of CLPP, a mitochondrial CLP endopeptidase component, associates with advanced disease burden and confers a poor prognosis.

• CLP suppression depletes cellular ATP stores, induces apoptosis and mitophagy, overcomes drug resistance, and exerts anti-tumor efficacy.

Plasma cell dyscrasias encompass a spectrum from the precursors monoclonal gammopathy of undetermined significance and smoldering myeloma to symptomatic myeloma, but the genes that enable progression and confer poor prognosis are incompletely understood. Using single cell transcriptomics, we identified the Caseinolytic protease proteolytic subunit (CLPP), a key component of the mitochondrial CLP serine endopeptidase, as being over-expressed in CD138+ neoplastic versus normal, and in symptomatic versus precursor plasma cells. Its high expression was associated with an adverse prognosis across multiple molecularly defined subgroups in the newly diagnosed and relapsed/refractory settings, and with extramedullary disease. Pharmacologic CLPP inhibition and genetic suppression reduced organoid growth, cell viability, and cell cycle progression, while triggering an unfolded protein response and apoptosis. This occurred in association with mitochondrial transmembrane potential loss, and caspase and proteasome activation in a reactive oxygen species-dependent manner. Downstream consequences included autophagy and mitophagy induction, and reductions in oxidative phosphorylation and glycolysis with consequent compromise of mitochondrial and cytoplasmic ATP production. CLP endopeptidase inhibition overcame conventional and novel drug resistance, induced apoptosis in primary samples, showed efficacy in vivo, and could be achieved with the clinically relevant agent inobrodib. Finally, regimens combining a CLPP and proteasome inhibitor showed enhanced efficacy, as did combinations with inhibitors of intermediary metabolism and autophagy. Taken together, our data indicate that CLPP is a key contributor to transformed plasma cells, a novel mediator of high-risk behavior, and a legitimate target for myeloma therapy whose inhibitors could be rationally combined with current therapeutics to improve outcomes.