SF3B1^K700E rewires splicing of cell cycle regulators

Abstract

Pre-mRNA splicing plays a crucial role in maintaining cellular homeostasis, with strict regulation required for processes such as cell cycle progression. SF3B1, a core component of the spliceosome, has emerged as a key player in alternative splicing regulation and is frequently mutated in cancer. Among these mutations, SF3B1^K700E disrupts normal splicing patterns and deregulates cell cycle control. Here we profiled K562 erythroleukemia cells expressing either wild type or SF3B1^K700E by RNA-seq and uncovered 763 high-confidence splicing alterations enriched for G₂/M regulators, including ARPP19, ENSA, STAG2, and ECT2. Notably, increased inclusion of ARPP19 exon 2 produces the ARPP19-long isoform, which sustains PP2A-B55 inhibition and promotes mitotic progression. A core subset of the K700E-linked splicing changes reappeared after siRNA-mediated SF3B1 depletion in HeLa cells, underscoring a mutation-dependent spliceosomal signature that transcends cell type. Pharmacological inhibition of DYRK1A or broad serine/threonine phosphatases shifted ARPP19 exon 2 inclusion in the same direction as SF3B1^K700E, pointing to a kinase–phosphatase signaling axis that influences these splice events. Functionally, ectopic expression of ARPP19-long accelerated mitotic exit, and high ARPP19-long abundance is associated with poorer overall survival in the TCGA–AML cohort. Our findings highlight a connection between SF3B1-dependent splicing, cell cycle progression, and tumorigenesis, offering new insights into the molecular mechanisms underlying cancer-associated splicing dysregulation.