The nuclear oncoprotein SET is necessary for MLL/KMT2A mediated transcriptional activation

The nuclear oncoprotein SET (patient "SE" translocation) has been implicated in the etiology of MLL (KMT2A) induced leukemia. Here we examine the details of this dependency in murine, primary hematopoietic cells. ChIP, RNAseq and immunoprecipitations demonstrated Set as downstream target of HoxA9 and confirmed a direct interaction with Mll. Set and Mll globally co-localized to promoter regions. Impairing Set expression phenocopied a knockdown of select Mll fusion targets with Set driving a pro-proliferative gene expression program that contained features indicative for Mll involvement. Molecularly, Set depletion caused dissociation of Mll from chromatin accompanied by a selective loss of RNA PolymeraseII Ser2-P. Concomitant with a function of Set as inhibitor of protein phosphatase 2A (PP2A), specific recruitment of PP2A to the Meis1 promoter, a known Mll target, inhibited transcription in reporter assays and in the natural chromatin environment. We identified Mitogen and stress induced kinase 1 (Msk1) as potential substrate protected by Set from dephosphorylation. Phosphorylated Msk1-P colocalized with Mll and disappeared from chromatin upon Set depletion. Biochemically, Msk-1 bound directly to Mll as well as to menin, a known Mll tethering factor. Loss of Set/Mll/Msk1 selectively affected H3K14 acetylation at promoters and this could be partially attributed to the reduced presence of the histone acetyltransferase Moz (Kat6a). Finally, we show that kinase inhibitors augment menin inhibitor activity in MLL leukemia cells, indicating a connection between cellular signaling and MLL-function.