A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia

Abstract

Acute myeloid leukemia with KMT2A (MLL) rearrangements is characterized by specific patterns of gene expression and enhancer architecture, implying unique core transcriptional regulatory circuitry. Here, we identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. Rapid transcription factor degradation followed by measurements of genome-wide transcription rates and superresolution microscopy revealed that MEF2D and IRF8 form a distinct core regulatory module with a narrow direct transcriptional program that includes activation of the key oncogenes MYC, HOXA9, and BCL2. Our study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes.

Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia

“…Thus, these findings can be complementary to our study and further explain the non-redundant function of MEF2D to IRF8. In line with Harada et al. (2022) highlighting the importance understanding the mechanism by which the IRF8/MEF2D TF circuit is activated, we found that AML carrying certain types of mutations, such as KMT2A -fusion and FLT3 ITD and NPM1c cooperating mutations ( Yun et al., 2021 ), can subsequently activate the MEF2D-IRF8 circuit and consequently require it for AML maintenance.…”

“…Here, we leveraged comprehensive approaches to extensively demonstrate the essential role of MEF2D in AML, functionally characterized a patient-relevant intronic enhancer of MEF2D and uncovered the formation of the MEF2D-IRF8 circuit via binding to mutual enhancer element. To date, recent studies revealed the essential roles and activation of MEF2D in AML carrying KMT2A -r, and different mechanisms underlying AML maintenance by MEF2D were proposed, including inhibition of CEBPE-mediated myeloid differentiation program, and direct regulation of MYC and HOXA9, which is largely redundant with its homolog TF MEF2C ( Harada et al., 2022 ; Zhao et al., 2021 ). Although our model suggests the IRF8-MEF2D circuit and MYC program function in parallel in AML, we cannot entirely rule out the context- and cell type-specific roles of MEF2D.…”

Rapid-kinetics degron benchmarking reveals off-target activities and mixed agonism-antagonism of MYB inhibitors

“…MYB is a critical transcriptional dependency of acute myeloid leukemia (AML) 11,18,28,29 , where it has been a longterm focus of therapeutic efforts [30][31][32][33][34][35][36][37] , making AML a relevant context for functional characterization of MYB inhibitors. We therefore began by engineering a chemical degron model of MYB in AML cells.…”

“…5 Recently, direct gene-regulatory functions of TFs have been established in pre-steady state assays where rapid TF degradation is coupled with measurements of genome-wide transcription rates. [8][9][10][11][12][13] These studies have demonstrated that TFs have narrow direct transcriptional programs and that long-term TF deprivation (e.g. after a CRISPR/Cas9-mediated knockout) leads to significant secondary effects obscuring a direct functional readout.…”

“…after a CRISPR/Cas9-mediated knockout) leads to significant secondary effects obscuring a direct functional readout. 8,11 We reasoned that the specificity and on-target activity of TF inhibitors would be best evaluated in a rapid kinetics system where their immediate transcriptional effects are benchmarked against targeted TF degradation (Figure 1A).…”