Genome-wide CRISPR-Cas9 knockout screening identifies NUDCD2 depletion as sensitizer for bortezomib, carfilzomib and ixazomib in multiple myeloma.

Background/Objectives: The treatment of multiple myeloma (MM) remains a challenge as almost all patients will eventually relapse. Proteasome inhibitors are a cornerstone in the management of MM. Unfortunately, validated biomarkers predict-ing drug response are largely missing. Therefore, we aimed to identify genes associated with drug resistance or sensitization to proteasome inhibitors. Methods: We per-formed genome-wide CRISPR-Cas9 knockout (KO) screens in human KMS-28-BM my-eloma cells to identify genetic determinants associated with resistance or sensitization to proteasome inhibitors. Results: We show that KO of KLF13 and PSMC4 induces drug resistance, while NUDCD2, OSER1 and HERC1 KO cause drug sensitization. Sub-sequently, we focused on top sensitization hit, NUDCD2, which acts as a co-chaperone of Hsp90 to regulate the LIS1/dynein complex. RNA sequencing showed downregula-tion of genes involved in the ERAD pathway and in ER-associated ubiqui-tin-dependent protein catabolic processes in both untreated and carfilzomib-treated NUDCD2 KO cells, suggesting that NUDCD2 depletion alters protein degradation. Furthermore, bortezomib-treated NUDCD2 KO cells showed a decreased expression of genes that have a function in oxidative phosphorylation and the mitochondrial mem-brane, such as Carnitine Palmitoyltransferase 1A (CPT1A). CPT1A catalyzes the up-take of long chain fatty acids into mitochondria. Mitochondrial lipid metabolism has recently been reported as a possible therapeutic target for MM drug sensitivity. Con-clusions: These results contribute to the search of therapeutic targets that can sensitize MM patients to proteasome inhibitors. RNA-sequencing of unreated, bortezomib-treated and carfilzomib-treated NUDCD2 KO myeloma cells.