Functional diversity of inhibitors tackling the differentiation arrest of MLL-rearranged leukemia

Purpose: The chromosomal rearrangements of the mixed-lineage leukemia (MLL) gene have been extensively characterized as a potent oncogenic driver on the molecular and mechanistic level in acute lymphoblastic (ALL) and acute myeloid (AML) leukemia. For its oncogenic function the MLL fusion protein is hijacking the the multi enzyme super elongation complex (SEC) leading to elevated expression of MLL target genes (e.g. HOXA9 and MEIS). High expression of MLL target genes is overwriting the normal hematopoietic differentiation gene expression program, resulting in undifferentiated blasts cells having a more “stem-cell like” cancer-promoting phenotype. Although extensive resources have been devoted to a better understanding of therapeutic targets for the MLL fusion to overcome the de-differentiation, the inter-dependencies of those targets for the pathophysiology of MLL is still barely understood. Here we report a comparative mode of action analysis of different inhibitors potentially interfering with MLL fusion induced differentiation blockade. We used RNA-seq for transcriptomic profiling in 14 AML and ALL cell lines treated with DMSO control or one of the 5 studied inhibitors (EPZ-5676, Brequinar, BAY-155, BAY-1251152 and OTX015).Methods: We used RNA-seq for transcriptomic profiling in 14 AML and ALL cell lines treated with DMSO control or one of the 5 studied inhibitors (EPZ-5676, Brequinar, BAY-155, BAY-1251152 and OTX015).Results: We discovered significant differences between compounds in their ability to induce differentiation and interfere with MLL target genes expression. We observed that Menin and DOT1L inhibition act very specifically on MLL fused leukemia cell lines, whereas inhibition of BET, DHODH and P-TEFb have strong effects beyond the MLL fusion .Conclusions: These results show a substantial diversity in the molecular activities of those inhibitors and provide valuable insights into the further developmental potential as single agents or in combinations in MLL fused leukemias.