Chromatin state changes induced by targeted degradation of MLL-AF9 are phenocopied by combined DOT1L and MENIN inhibition. [RNA-Seq]

Using RNA-seq we examined the transcriptional changes following MLL-AF9 degradation in MLL-AF9-HA-FKPB12 transformed murine (BM2222) and human (HCB1) cells. We also examined transcriptional changes in human MLL-AF9-HA-FKBP12 transformed cells (HCB1) and MOLM13 cells in response to DOT1L inhibition, Menin-MLL inhibition, and the combination of DOT1L and Menin-MLL inhibition. Lastly we assessed gene expression in murine neutrophils isolated directly from mice. Gene expression changes were assessed in MLL-AF9-HA-FKBP12 transformed murine (BM2222) and human cells (HCB1) following MLL-AF9 degradation. Specifically, murine MLL-AF9-HA-FKBP12 cells (BM2222) were treated with 500nM dTAG-13 for 3 hours, 24 hours, and 5 days and gene expression was compared to DMSO control. Similarly, human MLL-AF9-HA-FKBP12 cells (HCB1) were treated with 500nM dTAG-VHL for 3 hours, 24 hours, and 5 days and gene expressoin was compared to DMSO control. Gene expression changes were also assessed in the human MLL-AF9-HA-FKBP12 cells (HCB1) and MOLM13 cells following drug treatment with EPZ-5676, VTP-50469 and the drug combination at the indicated timepoints. Lastly, murine neutrophils were isolated from murine bone marrow to assess gene expression in neutrophils.