Deciphering the molecular mechanisms related to proteasome inhibitor resistance in multiple myeloma

Multiple myeloma (MM) is the second most common blood cancer, with 50000 new cases diagnosed annually in Europe. The median survival of patients is about 5 years, ranging from six months to ten years. Proteasome inhibitors (PI) such as Bortezomib (BTZ) and Carfilzomib (CFZ) are commonly used as first-line therapies. Unfortunately, patients inevitably develop resistance to these treatments.
Aberrant RNA splicing is known to be a crucial mechanism in the emergence of cancer resistance to chimiotherapy. To understand the molecular basis of MM resistance, we performed an RNA-seq experiment using BTZ-resistant and CFZ-resistant AMO1 cells compared to sensitive AMO1 cells and analyzed differentially expressed genes as well as altered splicing events.
Among thousands of dysregulated genes, we are interested in downregulation of three Pseudouridine Synthase (PUS) family proteins: PUS1, PUS3 and PUS7. Indeed, PUS proteins are known to isomerize uridine into pseudouridine mainly on tRNAs but also on mRNAs and U snRNAs. Modifications in tRNA pseudouridylation could lead to changes in the translatome of resistant MM cells.
Regarding splicing alteration, we found that exon skipping is the main affected event. Interestingly, we found that transcripts encoding for the core proteins - BRE, BRCC36 and MERIT40 - of the two multi-subunit deubiquitination complexes BRISC and BRCA1 are alternatively spliced in PI-resistant cells. These isoforms could alter the assembly and/or function of the BRISC and BRCA1 complexes, thus limiting their abilities to deubiquitinate K63-polyubiquitin chains of their substrates and therefore impacting their functions in key signaling pathways such as DNA repair or inflammatory processes.