Different mutant RUNX1 oncoprotein classes program alternate hematopoietic differentiation trajectories [ChIP-Seq]

Mutations of the hematopoietic master regulator RUNX1 cause acute myeloid leukaemia, familial platelet disorder and other haematological malignancies whose phenotypes and prognoses depend on the class of RUNX1 mutation. The biochemical behavior of these oncoproteins and their ability to cause unique diseases has been well studied but the genomic basis of their differential action is unknown. To address this question we compared integrated phenotypic, transcriptomic and genomic data from cells expressing four types of RUNX1 oncoproteins in an inducible fashion during blood development from embryonic stem cells. We show that each class of RUNX1 mutation rapidly deregulates endogenous RUNX1 function by different mechanisms, leading to specific alterations in developmentally controlled transcription factor binding and chromatin programming. The result are distinct perturbations in the trajectories of gene regulatory network changes underlying blood cell development that are consistent with the nature of the final disease phenotype. The development of novel treatments for RUNX1-driven diseases will therefore require consideration beyond RUNX1 haploinsufficiency. Overall design: ChIP-Seq targeting RUNX1 and H3K27ac in mouse hematopietic progenitor cells expressing a doxycyclin inducible Runx1 oncoprotein construct. Samples include cells with and without doxycycline treatment.