Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding

Abstract

The t(8;21) translocation fuses the DNA-binding domain of the hematopoietic master regulator RUNX1 to the ETO protein. The resultant RUNX1/ETO fusion protein is a leukemia-initiating transcription factor that interferes with RUNX1 function. The result of this interference is a block in differentiation and, finally, the development of acute myeloid leukemia (AML). To obtain insights into RUNX1/ETO-dependant alterations of the epigenetic landscape, we measured genome-wide RUNX1- and RUNX1/ETO-bound regions in t(8;21) cells and assessed to what extent the effects of RUNX1/ETO on the epigenome depend on its continued expression in established leukemic cells. To this end, we determined dynamic alterations of histone acetylation, RNA Polymerase II binding and RUNX1 occupancy in the presence or absence of RUNX1/ETO using a knockdown approach. Combined global assessments of chromatin accessibility and kinetic gene expression data show that RUNX1/ETO controls the expression of important regulators of hematopoietic differentiation and self-renewal. We show that selective removal of RUNX1/ETO leads to a widespread reversal of epigenetic reprogramming and a genome-wide redistribution of RUNX1 binding, resulting in the inhibition of leukemic proliferation and self-renewal, and the induction of differentiation. This demonstrates that RUNX1/ETO represents a pivotal therapeutic target in AML.

CBFB–MYH11/RUNX1 together with a compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupies self-renewal genes in inv(16) acute myeloid leukemia

“…Of the 4900 identified proteins, over 40 had highly significant ratios (44) (Figure 2c; Supplementary Table S1) indicating specific binding to the CBFb-MYH11/RUNX1 complex, whereas over 100 additional proteins, including previously identified RUNX1 interactors TAL1, FLI1 and BMI1, 27 had lower ratio's (42) and might represent transient-or context-dependent interactions (Supplementary Table S1). …”

“…In the case of AML, our analysis of PML-RARa and AML1-ETO were among the first to report on the genome-wide actions of oncofusion proteins. 25,26,44 Here, we analyzed the genome-widebinding pattern of CBFb-MYH11 and its interplay with other regulators of hematopoiesis in cell lines and patient primary blasts.…”

Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia

“…In acute myeloid leukemia, binding of the RUNX1-RUNX1T1 fusion results in widespread alterations throughout the epigenome (Ptasinska et al 2012(Ptasinska et al , 2014. A binding site for RUNX1-RUNX1T1 (DuqueAfonso et al 2011b) at intronic region 3 of LAT2, which contains prominent peaks in RUNX1-ChIP assay, was markedly repressed in GRO-seq by the E/R fusion (Fig.…”

Systems Analysis of the NCI-60 Cancer Cell Lines by Alignment of Protein Pathway Activation Modules with “-OMIC” Data Fields and Therapeutic Response Signatures

“…The transcription factor RUNX1T1 (together with RUNX1) is known to be involved in several cancers, above all hematopoietic malignancies, due to its repressor activity that involves histone deacetylases and the ability to undergo chromosomal translocation, where the t8;21 is the most well known, and results in expression of a leukemia-specific chimeric transcription factor (22). On the basis of our analysis, we propose a model of interactions (Fig.…”

“…On the basis of our analysis, we propose a model of interactions (Fig. 4) based on both previous data (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29) and the interactions we found. This example provides evidence that our approach has identified "-omic" linkages that, although new, have basis in biochemical rationale and are supported, in part, by past research (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29).…”