Oncogenic Splicing Factor U2AF35 Mutations Disrupt ATG7 mRNA Processing

Recurrent somatic mutations in splicing factors, including U2AF35, occur in myelodysplastic syndrome (MDS) and in multiple hematologic and solid malignancies. Despite their association with cancer, the mechanisms by which U2AF35 mutations promote transformation remain unknown. Park and colleagues generated cell lines transformed by the oncogenic splicing mutant U2AF35(S34F), and identified abnormally processed pre-mRNAs by RNA sequencing. The most frequently altered mRNA processing event was increased use of a distal cleavage and polyadenylation (CP) site in various pre-mRNAs, including autophagy related factor 7 (ATG7). The cleavage factor lm (CFlm) complex associates with U2AF35 and regulates alternative CP site selection. CFlm25 heterodimerizes with CFlm59 to increase use of proximal CP sites, whereas CFlm25 heterodimerizes with CFlm68 to repress use of proximal CP sites. As expected, knockdown of CFlm59 reduced use of the ATG7 proximal CP site, whereas CFlm68 knockdown increased use of the proximal CP site. In U2AF35(S34F) cells the amount of ATG7 pre-mRNA bound to CFlm59 was lower, and the amount bound to CFlm68 was higher, than in wild-type U2AF35 cells, altogether suggesting that U2AF35(S34F) increased the association of CFlm68 with the ATG7 proximal CP site, thus increasing use of the distal CP site. Increased use of the distal CP site in U2AF35(S34F) cells resulted in a longer 3′ UTR, translational repression, and reduced ATG7 protein levels. Consistent with the role of ATG7 in autophagy, U2AF35(S34F) cells exhibited an autophagy defect, which led to genomic instability predisposing cells to secondary mutations that further promoted transformation. The autophagy defect enhanced U2AF35(S34F) cell sensitivity to cytotoxic agents. Further, in patients with MDS and acute myeloid leukemia, U2AF35(S34F) was associated with increased use of the ATG7 distal CP site. Altogether, these findings reveal a mechanism by which splicing factor mutations can transform cells via disruption of autophagy, and suggest that the autophagy defect in U2AF35(S34F) cells may be therapeutically exploitable.

Park SM, Ou J, Chamberlain L, Simone TM, Yang H, Virbasius C-M, et al. U2AF35(S34F) promotes transformation by directing aberrant ATG7 pre-mRNA 3′ end formation. Mol Cell 2016;62:479–90.