SF3B1-mutant models of RNA mis-splicing uncover UBA1 as a therapeutic target in myelodysplastic neoplasms

This is the authors' abstract. We don't add key points for this paper.

Myelodysplastic syndromes with somatic mutations in the splicing factor SF3B1 gene (MDS- SF3B1 ) result in RNA mis-splicing, erythroid dysplasia and ultimately refractory anemia. Precision medicine approaches for MDS- SF3B1 remain challenging due to both the complexity of the mis-splicing landscape and its evaluation in disease-accurate models. To uncover novel RNA mis-splicing events, isogenic SF3B1 K700E and SF3B1 WT iPSC lines from an MDS- SF3B1 patient were differentiated into hematopoietic cells and analyzed via unsupervised splicing event profiling using full-length RNA sequencing. This identified SF3B1 K700E -specific mis-splicing of ubiquitin-like modifier activating enzyme 1 ( UBA1 ), which encodes a key E1 protein at the apex of the ubiquitination cascade. UBA1 mis-splicing ( UBA1 ms ) introduced protein instability and decreased total UBA1 levels, rendering mutated cells susceptible to the small-molecule UBA1 inhibitor TAK-243. Analysis of CD34 + RNA sequencing data from an MDS patient cohort confirmed unique and ubiquitous UBA1 ms in MDS- SF3B1 patients, absent in other splicing factor-mutated MDS cases or healthy controls. TAK-243 selectively targeted MDS- SF3B1 primary CD34 + cells and reduced mutant cell numbers in colony-forming assays. In contrast, normal hematopoietic progenitor cells were unaffected. Altogether, we here define UBA1 ms as a novel therapeutic vulnerability in SF3B1 -mutant cells, introducing UBA1 inhibition as a potential avenue for future MDS- SF3B1 treatments.