Functional Consequences of Spliceosome Mutations

Mutations in key factors of the spliceosome occur in over 50% of patients with myelodysplastic syndromes (MDS) and thus splicing represents the most frequently affected pathway in MDS. The vast majority of mutations cluster in four genes: SF3B1, SRSF2, U2AF1, and ZRSR2. Mutations occur in a mutually exclusive manner suggesting a common mechanism by which they cause disease, and yet they segregate to specific subtypes of myeloid malignancies suggesting unique, mutation-specific functions. With the exclusion of ZRSR2, mutations occur at highly restricted residues and are strictly heterozygous, suggestive of gain of function mutations. We and others have shown that mutations affect RNA binding affinity and specificity, and can lead to a variety of outcomes including exon inclusion or skipping, alternative splice site selection, intron retention, and most recently alternative polyadenylation. Overall, these splice changes are subtle: only a small subset of all splice events is affected by these mutations and changes in isoform usage are < 10% for most alternative splice events identified. Furthermore, a direct connection between alternatively spliced transcripts and differentially expressed genes is often not seen. However, these alternative splice events affect genes critical to cellular function and hematopoiesis. Examples include EZH2, ABCB7, macroH2A1, and ATG7. Mutations in SRSF2 result in inclusion of a poison exon in EZH2 resulting in reduced protein levels of this critical epigenetic regulator. Mutations in SF3B1 cause alternative splicing of ABCB7 slating its RNA for non-sense mediated decay. Intriguingly, mutations in U2AF1 promote usage of a distal polyadenylation site in an essential autophagy factor, ATG7, resulting in inefficient translation and decreased protein levels. As a consequence, autophagy is impaired, which can promote cellular transformation, providing a possible explanation for the clonal advantage of cells with splicing factor mutations. Additional research is critical to further determine how alternative splicing contributes to the MDS phenotype with impaired hematopoietic differentiation and cellular function and eventual malignant transformation. Latest findings will be presented here with a focus on mechanistic, functional, and biologic effects of splicing factor mutations.