LAUSR

RUNX1 is a master haematopoietic transcription factor with cell-type dependent functions and thus RUNX1 mutations are seen in a range of haematological disorders. To understand the molecular basis of how different types of RUNX1 mutations send hematopoietic precursors on the path to disease we generated ESCs expressing inducible human RUNX1 mutants. We studied the fusion proteins RUNX1-ETO and RUNX1-EVI1, the truncated RUNX1-R177X protein that consists of the DNA binding domain only and RUNX1-R174Q which has a point mutation in the DNA binding domain. These are all associated with haematological disorders, including MDS, FPD and AML. To examine the immediate effect of oncogene induction on the blood progenitor gene regulatory network, we differentiated transgenic ESCs towards blood progenitors, induced the oncogene and performed systems-wide analysis shortly after induction. All induced progenitors demonstrated disrupted colony forming capacity, in a disease-driver specific fashion. RNA-seq and ATAC-seq analyses of induced cells showed mutation specific changes in gene expression and the chromatin landscape. The chromatin changes had unique motif patterns suggesting perturbed transcription factor interactions. The impact upon the binding of endogenous RUNX1 was varied – both RUNX1-ETO and RUNX1-EVI1 displaced RUNX1 from its binding sites, but induction of RUNX1-EVI1 also shifted RUNX1 binding to new sites. R174Q did not bind to the genome itself but reduced normal RUNX1 binding via decreased interaction with CBFβ as shown by proximity ligation assays. R177X caused only limited changes to RUNX1. Our data show that differential interactions of each RUNX1 mutant protein with the endogenous RUNX1 transcription factor hub cause specific epigenetic changes thus leading to the development of unique gene regulatory networks driving different types of malignancies.