CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias [ATAC-Seq]

Acute myeloid leukemias (AMLs) have an overall poor prognosis and many high-risk cases co-opt stem cell gene regulatory programs, yet the mechanisms through which this occurs remain poorly understood. Increased expression of the stem cell transcription factor, MECOM, underlies one key driver mechanism in largely incurable AMLs. How MECOM results in such aggressive AML phenotypes remains unknown. To address existing experimental limitations, we engineered and applied targeted protein degradation with functional genomic readouts to demonstrate that MECOM promotes malignant stem cell-like states by directly repressing pro-differentiation gene regulatory programs. Remarkably and unexpectedly, a single node in this network, a MECOM-interacting regulatory element located 42 kb downstream of the myeloid differentiation regulator CEBPA is both necessary and sufficient for MECOM-driven leukemogenesis. Importantly, targeted activation of this regulatory element promotes differentiation of these aggressive AMLs and reduces leukemia burden in vivo, suggesting a broadly applicable differentiation-based approach for improving therapy.