A Unifying Mechanism for Shared Splicing Aberrations in Splicing Factor Mutant Cancers

Abstract

Cancer-associated splicing factor (SF) mutations in SF3B1, U2AF1, and SRSF2 induce distinct changes in alternative splicing (AS). Yet these mutations are strikingly mutually exclusive, pointing to a convergent downstream mechanism. We hypothesized this would be reflected in the AS transcriptome. By analyzing transcriptomes of 395 patients with clonal myeloid disorders and 64 healthy donors, we found most AS alterations to be mutation-specific. However, a robust subset, enriched in the retained intron (RI) program, was shared across mutants. These RI events were bidirectional but highly concordant, and mirrored the effects of SRSF1 loss. SF-mutant states induced hypophosphorylation of RS domains in SRSF1, reducing its function. This arose from an altered AMPK-AKT balance impairing the AKT-SRPK1-SRSF1 axis. A common upstream trigger was activation of DNA damage response (DDR) by transcriptional R-loops, which increased AMPK signaling and reduced AKT activity. Pharmacologic DDR activation recapitulated reduced AKT/SRPK1 activity and SRSF1 hypophosphorylation, while relieving DDR restored SRSF1 phosphorylation and corrected RI defects. Thus, beyond cis-acting, mutation-specific changes, SF-mutant cancers share a trans-acting, stress-driven AS signature wherein DDR signaling rewires SRSF1 activity impacting AS. Our results link replication stress, kinase signaling, and RNA processing across genetically diverse clonal states, highlighting potential therapeutic approaches at these nodes. HighlightsO_LIWhile most splicing changes differ by splicing factor (SF) mutation, certain retained introns are common across subtypes. C_LIO_LIChanges in RI are bidirectional, concordant across mutant groups, and mirrors SRSF1 loss. C_LIO_LISF mutations activate DDR, triggering an AMPK/AKT imbalance that culminates in SRSF1 hypophosphorylation. C_LIO_LIRelieving R-loop induced DDR restores SRSF1 phosphorylation and reverses RI. C_LI