SF3B1-mutant mis-splicing ofUBA1confers a targetable therapeutic vulnerability through UBA1 inhibition

Abstract

AbstractSF3B1mutation-driven myelodysplastic syndromes (MDS-SF3B1) arise due to somatic mutation in the splicing factorSF3B1gene.SF3B1mutations induce RNA mis-splicing and loss of expression of critical genes for erythropoiesis, leading to erythroid dysplasia and ultimately refractory anemia. The development of precision medicine approaches for MDS-SF3B1is hampered by the complexity of the mis-splicing landscape and its evaluation in disease-accurate model systems. To identify novel RNA mis-splicing events, isogenicSF3B1K700EandSF3B1WTiPSC lines from an MDS-SF3B1patient were differentiated into hematopoietic cellsin vitroand subjected to unsupervised splicing event analysis using full-length RNA sequencing data. This revealedSF3B1K700E-specific mis-splicing of ubiquitin-like modifier activating enzyme 1 (UBA1) transcripts, which encode the essential E1 protein at the apex of the ubiquitination cascade.UBA1mis-splicing (UBA1ms) preservedUBA1msmRNA but not protein expression. Consequently,UBA1msdiminished the pool of functional UBA1, sensitizingSF3B1K700Ecell lines to the small-molecule UBA1 inhibitor TAK-243. Finally, analysis of CD34+RNA sequencing data from an MDS patient cohort confirmed unique and ubiquitousUBA1msin MDS-SF3B1patients, without detection in other splicing factor-mutated MDS patients, or in healthy individuals. TAK-243 selectively targeted MDS-SF3B1primary CD34+cells and reduced mutant cell number in colony-forming unit studies. In contrast, normal hematopoietic progenitor cells were unaffected. Altogether, we here defineUBA1msas a novel therapeutic vulnerability inSF3B1-mutant cells, introducing UBA1 inhibition as a potential avenue for future MDS-SF3B1treatments.