Identification of common and distinct epigenetic reprogramming properties of RUNX1 fusion proteins in acute myeloid leukaemia

Abstract

BackgroundRegulation of gene expression by transcription factors such as RUNX1 is crucial for haemopoiesis. The most common RUNX1 translocation resulting in acute myeloid leukaemia is t(8;21), which forms RUNX1–ETO; a second translocation—t(3;21)—results in RUNX1–EVI-1. Although, these two fusion proteins have the same DNA binding domain, the prognoses of patients with these translocations differ greatly. Whether different RUNX1 fusion proteins deregulate the same genes is unknown. We sought to understand the differences in the epigenome that underlie these prognostic differences. MethodsDNase-seq maps regions of open chromatin that represent active gene regulatory elements. By using this technique with RNA-seq, we were able to describe the epigenetic landscape in CD34+ purified, primary material from patients with RUNX1–EVI-1 and RUNX1–ETO leukaemias, and in healthy controls. We used ChIP-seq to map the binding sites of both normal RUNX1 and the fusion proteins. We integrated these analyses to determine transcription factor networks that characterise each type of leukaemia. FindingsRUNX1–EVI-1, but not RUNX1–ETO, directly regulated a unique subset of genes required for stem-cell function. We found that these differences in binding sites of the two fusion proteins were associated with differences in the transcription factor complexes that collaborate with them, and were directly related to the differences in the epigenetic landscape of each leukaemia. RUNX1–EVI-1 knockdown restored differentiation of t(3;21) cells and this finding was associated with upregulation of genes crucial for myeloid differentiation, including C/EBPα. We showed that C/EBPα was necessary and sufficient for the response of t(3;21) cells to RUNX1–EVI-1 knockdown and that C/EBPα was commonly deregulated in both leukaemias. InterpretationThe differences in the clinical outcomes of each RUNX1 mutant leukaemia was reflected by differences in their epigenetic landscape. This finding was driven by differences in the transcription factor networks in each type of leukaemia. Despite these differences, both leukaemias were dependent on downregulating C/EBP, thereby providing a common therapeutic route for both RUNX1–ETO and RUNX1–EVI-1 leukaemia. FundingKay Kendall Leukaemia Fund, Bloodwise.