Venkatasubramanian, M.; Schwartz, L.; Ramachandra, N.; Bennett, J.; Subramanian, K. R.; Gordon-Mitchell, S.; Fromowitz, A.; Pradhan, K.; Shechter, D.; Sahu, S.; Heiser, D.; Scherle, P.; Chen, X.; Chetal, C.; Kulkarni, A.; Myers, K. C.; Weirauch, M. T.; Grimes, H. L.; Starczynowski, D. T.; Verma, A.; Salomonis, N. G.

The role of splicing dysregulation in cancer is underscored by splicing factor mutations; however, its impact in the absence of such rare mutations is poorly understood. To reveal complex patient subtypes and putative regulators of pathogenic splicing in Acute Myeloid Leukemia (AML), we developed a new approach called OncoSplice. Among diverse new subtypes, OncoSplice identified a biphasic poor prognosis signature that partially phenocopies U2AF1-mutant splicing, impacting thousands of genes in over 40% of adult and pediatric AML cases. U2AF1-like splicing co-opted a healthy circadian splicing program, was stable over time and induced a leukemia stem cell (LSC) program. Pharmacological inhibition of the implicated U2AF1-like splicing regulator, PRMT5, rescued leukemia mis-splicing and inhibited leukemic cell growth. Genetic deletion of IRAK4, a common target of U2AF1-like and PRMT5 treated cells, blocked leukemia development in xenograft models and induced differentiation. These analyses reveal a new prognostic alternative-splicing mechanism in malignancy, independent of splicing-factor mutations.