BET inhibitor resistance emerges from leukaemia stem cells

Abstract

Bromodomain and extra terminal protein (BET) inhibitors are first-in-class targeted therapies that deliver a new therapeutic opportunity by directly targeting bromodomain proteins that bind acetylated chromatin marks1,2. Early clinical trials have shown promise, especially in acute myeloid leukaemia3, and therefore the evaluation of resistance mechanisms is crucial to optimize the clinical efficacy of these drugs. Here we use primary mouse haematopoietic stem and progenitor cells immortalized with the fusion protein MLL-AF9 to generate several single-cell clones that demonstrate resistance, in vitro and in vivo, to the prototypical BET inhibitor, I-BET. Resistance to I-BET confers cross-resistance to chemically distinct BET inhibitors such as JQ1, as well as resistance to genetic knockdown of BET proteins. Resistance is not mediated through increased drug efflux or metabolism, but is shown to emerge from leukaemia stem cells both ex vivo and in vivo. Chromatin-bound BRD4 is globally reduced in resistant cells, whereas the expression of key target genes such as Myc remains unaltered, highlighting the existence of alternative mechanisms to regulate transcription. We demonstrate that resistance to BET inhibitors, in human and mouse leukaemia cells, is in part a consequence of increased Wnt/β-catenin signalling, and negative regulation of this pathway results in restoration of sensitivity to I-BET in vitro and in vivo. Together, these findings provide new insights into the biology of acute myeloid leukaemia, highlight potential therapeutic limitations of BET inhibitors, and identify strategies that may enhance the clinical utility of these unique targeted therapies.

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

“…S8D) in line with H23 cells undergoing apoptosis and slower cell proliferation rate (Figure 5(b)). The main components of canonical Wnt/β-catenin signaling are reported to be modulated by JQ1 [6,29,30] and in H23 cells, WNT2, WNT5A, and the mediator of Wnt signaling (LEF1 and TCF genes) were downregulated, while β-catenin encoded by CTNNB1 was only slightly affected (Fig. S8B).…”

Loss of TRIM33 causes resistance to BET bromodomain inhibitors through MYC- and TGF-β–dependent mechanisms

“…While our study was underway, several other groups reported alternative mechanisms of BETi resistance in other cancer lines (39)(40)(41)(42)(43). Although the details of the specific adaptive pathways vary across cell types, a common feature of BETi resistance appears to be reactivation of BRD4-dependent target genes.…”

aBETting therapeutic resistance by Wnt signaling

“…GSEA transcriptome analysis by Fong et al [5] revealed upregulation of the Wnt/β-catenin signaling pathway, which has also been implicated in cancer stem cell maintenance [6]. Importantly, they showed that inhibition of the Wnt pathway restored the more mature myeloid phenotype, survival advantage conferred by I-BET in resistant clones, and abrogation of Myc expression.…”

“…The resistant cell lines generated by Fong et al [5] showed a loss of myeloid lineage markers Gr1 and CD11b and an increase in tumor initiating capacity in limiting dilution assays in vivo. This raised the possibility that resistance to I-BET emerges from a leukemic stem cell (LSC) compartment.…”

“…Fong and colleagues [5] generated murine models of BET inhibitorresistant AML by serially passaging MLL-AF9-transduced hematopoietic stem and progenitor cells (HSPCs) in increasing concentrations of I-BET. Resistant clones showed decreased sensitivity to I-BET in proliferation assays, accompanied by reduced apoptosis and limited cell cycle arrest.…”