A stress-responsive enhancer induces dynamic drug resistance in acute myeloid leukemia
Mark S. Williams, Fabio M.R. Amaral, Fabrizio Simeoni, Tim C.P. Somervaille
Mark S. Williams, Fabio M.R. Amaral, Fabrizio Simeoni, Tim C.P. Somervaille
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Research Article Hematology Oncology

A stress-responsive enhancer induces dynamic drug resistance in acute myeloid leukemia

Abstract

The drug efflux pump ABCB1 is a key driver of chemoresistance, and high expression predicts treatment failure in acute myeloid leukemia (AML). In this study, we identified and functionally validated the network of enhancers that controls expression of ABCB1. We show that exposure of leukemia cells to daunorubicin activated an integrated stress response–like transcriptional program to induce ABCB1 through remodeling and activation of an ATF4-bound, stress-responsive enhancer. Protracted stress primed enhancers for rapid increases in activity following re-exposure of cells to daunorubicin, providing an epigenetic memory of prior drug treatment. In primary human AML, exposure of fresh blast cells to daunorubicin activated the stress-responsive enhancer and led to dose-dependent induction of ABCB1. Dynamic induction of ABCB1 by diverse stressors, including chemotherapy, facilitated escape of leukemia cells from targeted third-generation ABCB1 inhibition, providing an explanation for the failure of ABCB1 inhibitors in clinical trials. Stress-induced upregulation of ABCB1 was mitigated by combined use of the pharmacologic inhibitors U0126 and ISRIB, which inhibit stress signaling and have potential for use as adjuvants to enhance the activity of ABCB1 inhibitors.

Authors

Mark S. Williams, Fabio M.R. Amaral, Fabrizio Simeoni, Tim C.P. Somervaille

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Figure 3

Regulatory element landscape of ABCB1.

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Regulatory element landscape of ABCB1. (A) ChIP-Seq tracks for H3K27Ac a...
(A) ChIP-Seq tracks for H3K27Ac and H3K4me1 surrounding ABCB1 (chr7:87,495,508–87,626,404; hg38) in the indicated human cells and tissues, including CD34+ hematopoietic stem and progenitor cells. Putative enhancers (E1–E4) are highlighted in blue. Lower track shows a local contact profile generated from 4C sequencing of K562_R1 using a viewpoint centered on the ABCB1 promoter. Regions of contact that do not contain an active enhancer in K562_R1–3 are highlighted in red (C1–C3). (B) Experimental outline (left); and representative flow cytometry plot (right) showing double-positive population (blue; K562_R1 BFP+RFP+) and negative control population (red). FC, flow cytometry. (C) H3K9me3 ChIP-Seq tracks for each sgRNA. Signal from empty vector was subtracted to show only histone methylation resulting from presence of the guide. Red arrows indicate the position of the target sequence. H3K27Ac ChIP-Seq tracks from A are included for reference.