GSE124963
Suppression of oncogenic super enhancers in MYC-dependent AMLs by NR4A Nuclear Receptors
NR4A nuclear receptors are tumor suppressors of acute myeloid leukemia (AML) that are silenced in AML at the level of transcription elongation. Using RNA-Seq, we show that NR4As inhibit leukemic cell growth largely through suppression of MYC pathway genes. MYC is highly expressed in AML and contributes to AML progression and therapeutic resistance. MYC expression in AML is driven by a super enhancer cluster 1.8Mbp downstream of the MYC locus, which is highly sensitive to therapeutic intervention, including treatment with BET inhibitors. We recently identified dihydroergotamine (DHE) as an FDA-approved drug that strongly induces NR4A transcription in AML cells and operates effectively as an antileukemic therapy. RNA-Seq in MOLM-14 identified MYC as the most statistically repressed target of DHE. Using ChIP-Seq for MED1 as a readout for Mediator occupancy, we identified super enhancers in MOLM-14 cells and show that treatment with DHE significantly suppresses MED1 signal across a subset of super enhancers, including the MYC super enhancer. Finally, we demonstrate that NR4As are broadly associated with global super enhancers, including sites where super enhancer activity is retained, reduced, or gained. Overall design: For this study, we performed total RNA-Seq in MOLM-14 human AML cells electroporated with in vitro-transcribed RNA expression of GFP or NR4A1, followed by 6 hour incubation. Duplicate samples for each treatment condition (ie. GFP1, GFP2, NR4A1-1, NR4A1-2) are included. We also performed RNA-Seq in MOLM-14 treated with vehicle (DMSO) or 10uM dihydroergotamine (DHE), followed by 6 hour incubation. Duplicate samples for each treatment condition (ie. Veh1, Veh2, DHE1, DHE2) are included. Additionally, we performed ChIP-Seq for MED1 in MOLM-14 cells treated with vehicle (DMSO) or 10uM DHE for 4 hours. Duplicate samples for each treatment condition (ie. MED1 Veh1, Veh2, DHE1, DHE2) are included. Finally, we performed ChIP-Seq for NR4A in MOLM-14 cells treated with 10uM DHE for 4 hours, which is included as a single replicate.