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

Area of Science:

• Molecular Biology
• Cancer Genomics
• RNA Splicing

Background:

• Mutations in splicing factors (SFs) like SF3B1, U2AF1, and SRSF2 drive distinct alternative splicing (AS) changes in cancer.
• Despite mutation-specific AS alterations, the mutual exclusivity of these SF mutations suggests a convergent downstream mechanism.

Purpose of the Study:

• To investigate the shared AS transcriptome alterations in myeloid disorders with SF mutations.
• To identify the common molecular mechanisms underlying AS changes induced by different SF mutations.

Main Methods:

• Analysis of transcriptomes from 395 patients with clonal myeloid disorders and 64 healthy donors.
• Investigated the impact of SF mutations on kinase signaling pathways (AMPKα, AKT, SRPK1) and SRSF1 phosphorylation.
• Utilized pharmacologic activation and relief of DNA damage response (DDR) to assess its role in AS regulation.

Main Results:

• Most AS alterations were mutation-specific, but a subset involving retained introns (RI) was common across SF mutants.
• SF mutations led to SRSF1 hypophosphorylation, impairing its function via an altered AMPKα-AKT balance.
• Transcriptional R-loops activated DDR, increasing AMPKα and reducing AKT activity, which contributed to SRSF1 hypophosphorylation and the RI program.

Conclusions:

• SF-mutant cancers share a trans-acting, stress-driven AS signature characterized by a retained intron program.
• DNA damage response signaling acts as a common upstream trigger, rewiring SRSF1 activity and impacting AS.
• Targeting the nodes linking replication stress, kinase signaling, and RNA processing may offer therapeutic strategies for SF-mutant cancers.