Investigating the Role of RNA-Binding Motif Protein 17 (RBM17) in Acute Myeloid Leukemia Stem Cells

Abstract

AML is thought to be sustained by sub-populations of LSCs, which possess the capacity for self-renewal and differentiation and are believed to be responsible for disease initiation, relapse and chemo-resistance. Previous studies demonstrated that aberrant splicing is prevalent in AML patients, in particular within the LSC populations. Dysregulated AS pathway members may represent key therapeutic targets and diagnostic markers for facilitating AML treatments. Here, we demonstrated the splicing factor RBM17 is significantly higher expressed in LSCs and is associated with AML poor prognosis. Gene expression signature of AML patients with higher RBM17 expression is similar to LSC gene signature. Importantly, knockdown of RBM17 in primitive primary AML cells results in myeloid differentiation and the impairment of their stem and progenitor potential. By performing global analysis of the RBM17-RNA interactome and proteome changes downstream of RBM17 knockdown, we show that RBM17 knockdown leads to inclusion of poison exons and production of nonsense-mediated decay (NMD)-sensitive transcripts for pro-leukemic factors such as RBM39 and EZH2, along with the translation initiation factor EIF4A2. We further show that EIF4A2 expression is enriched in LSC populations and inhibition of EIF4A2 impairs colony-forming ability of primary AML. Proteome analysis of AML cells after EIF4A2 knockdown demonstrate that knockdown of EIF4A2 largely recapitulates the biological effect of RBM17 knockdown. These two proteins also share downstream proteins enriched in ribosome biogenesis pathways. By applying a modified dCas9/sgRNA assisted chromatin-protein complex purification method, we identify CDK12 and USP16 as two potential upstream regulators of RBM17 and demonstrate that RBM17 mRNA expression is repressed by CDK12 knockdown but promoted by USP16 knockdown. Altogether, these results provide a rationale to target RBM17 and/or its downstream NMD-sensitive splicing substrates and upstream regulators in primitive leukemic cells for AML treatment.