MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia [ChIP-seq]

The transcription factor MECOM, located at 3q26, is essential for hematopoietic stem cells (HSCs) in healthy individuals. Enhancer translocations, due to 3q26 rearrangements, drive out-of-context MECOM expression in an aggressive subtype of acute myeloid leukemia (AML). Aberrantly expressed MECOM is essential for the survival and immature phenotype of these leukemia cells. Direct depletion of MECOM using an endogenous auxin-inducible degron immediately upregulates expression of myeloid differentiation factor CEBPA. MECOM depletion is also accompanied by a severe loss of CD34 expression and gain of mature myeloid cell surface marker CD15. MECOM exerts its inhibitory effect on differentiation by binding to the +42kb CEBPA enhancer, which is required for neutrophil development. This is partially dependent on the interaction between MECOM and its essential co-repressor CTBP2, a potential target in this type of AML. We demonstrate that CEBPA overexpression can bypass the MECOM-mediated block of differentiation. In addition, AML patients with MECOM overexpression through enhancer hijacking show significantly reduced CEBPA. Our study provides insight into the mechanism by which MECOM maintains the stem cell state in AML. Furthermore, CEBPA levels are an important read-out for successful targeting of MECOM in 3q26-rearranged AML. Overall design: We introduced an auxin-inducible degron (AID) (V5-AID-T2A-eGFP) 3' of MECOM in inv(3) cell line MUTZ3. Next, chromatin immunoprecipitation followed by sequencing (ChIP-Seq) for EVI1, CTBP2, various transcription factors (p300, RUNX1) and histone modifications (H3K27ac, H3K27me3, H3k9me3) was performed in this cell line, either after auxin-induced MECOM degradation or in the absence of treatment.