CRISPR genome-wide screening identifies dependence on the proteasome subunit PSMC6 for Bortezomib sensitivity in multiple myeloma

Bortezomib (BTZ) is highly effective in the treatment of Multiple Myeloma (MM), however emergent drug resistance is common. Consequently, we employed CRISPR targeting 19,052 human genes to identify unbiased targets that contribute to BTZ resistance. Specifically, we engineered an RPMI8226 MM cell line to express Cas9 and a lentiviral-vector CRISPR library and cultured derived cells in doses of BTZ lethal to parental cells. Sequencing was performed on surviving cells to identify inactivated genes responsible for drug resistance. From two independent whole genome screens, we selected 31 candidate genes and constructed a second CRISPR sgRNA library, specifically targeting each of these 31 genes with four sgRNAs. After secondary screening for BTZ resistance, the top 20 "resistance" genes were selected for individual validation. Of these 20 targets the proteasome regulatory subunit PSMC6 was the only gene validated to reproducibly confer BTZ resistance. We confirmed that inhibition of chymotrypsin-like proteasome activity by BTZ was significantly reduced in cells lacking PSMC6. We individually investigated other members of the PSMC group (PSMC1 to 5) and found that deficiency in each of those subunits also imparts BTZ resistance. We found 36 mutations in 19S proteasome subunits out of 895 patients in the IA10 release of the CoMMapss study (http://ift.tt/2xBOiSL). Our findings demonstrate that the PSMC6 subunit is the most prominent target required for BTZ sensitivity in MM cells and should be examined in drug refractory populations.

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