Novel mechanisms of gene regulation driving aggressive leukemias

Abstract

Acute myeloid leukemias (AMLs) have an overall poor prognosis with many high-risk cases coopting 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, I engineered and applied targeted protein degradation with functional genomic readouts to demonstrate that MECOM promotes malignant stem cell-like states by directly repressing prodifferentiation gene regulatory programs. Remarkably and unexpectedly, a single node in this network, a MECOM-bound cis-regulatory element located 42 kb downstream of the myeloid differentiation regulator CEBPA, is both necessary and sufficient for maintaining MECOM-driven leukemias. Importantly, targeted activation of this regulatory element promotes differentiation of these aggressive AMLs and reduces leukemia burden in vivo. In an effort to translate these biological insights into a therapeutic strategy, this work also explored the use of heterobifunctional small molecules and chemically induced proximity to rewire MECOM transcriptional activity. While efficacy was limited, this portion of the study revealed key principles to consider when aiming to therapeutically engineer and reprogram transcription in this manner. In sum, these findings suggest a broadly applicable approach for functionally dissecting oncogenic gene regulatory networks to inform improved therapeutic strategies.