Transcriptional plasticity promotes primary and acquired resistance to BET inhibition

Abstract

Summary Following the discovery of BRD4 as a non-oncogene addiction target in acute myeloid leukemia (AML)1,2, BET inhibitors are being explored as promising therapeutic avenue in numerous cancers3–5. While clinical trials have reported single-agent activity in advanced hematologic malignancies6, mechanisms determining the response to BET inhibition remain poorly understood. To identify factors involved in primary and acquired BET resistance in leukemia, we performed a chromatin-focused RNAi screen in a sensitive MLL/AF9; NrasG12D -driven AML model, and investigated dynamic transcriptional profiles in sensitive and resistant murine and human leukemias. Our screen reveals that suppression of the PRC2 complex, contrary to effects in other contexts, promotes BET inhibitor resistance in AML. PRC2 suppression does not directly affect the regulation of Brd4-dependent transcripts, but facilitates the remodeling of regulatory pathways that restore the transcription of key targets such as Myc. Similarly, while BET inhibition triggers acute MYC repression in human leukemias regardless of their sensitivity, resistant leukemias are uniformly characterized by their ability to rapidly restore MYC transcription. This process involves the activation and recruitment of WNT signaling components, which compensate for the loss of BRD4 and drive resistance in various cancer models. Dynamic ChIP- and STARR-seq enhancer profiles reveal that BET-resistant states are characterized by remodeled regulatory landscapes, involving the activation of a focal MYC enhancer that recruits WNT machinery in response to BET inhibition. Together, our results identify and validate WNT signaling as a driver and candidate biomarker of primary and acquired BET resistance in leukemia, and implicate the rewiring of transcriptional programs as an important mechanism promoting resistance to BET inhibitors and, potentially, other chromatin-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).…”

Concepts to Target MYC in Pancreatic Cancer

“…Interestingly, it has been shown that one resistance mechanism was associated with the upregulation of WNT signaling, and this process is needed to restore the expression of important drivers initially downregulated by BET-I, including MYC (51). Consistently, in cell-based PDAC models, activation of the WNT signaling pathway confers resistance, whereas WNT inhibition was synergistic with the JQ1 response (51).…”

“…The context specificity is not only observed between different tumors, but also within a given tumor entity. In line, transcriptome profiles of BET-I-treated cells demonstrated a dramatic heterogeneous response, even in tumors of the same entity (51). Furthermore, in breast cancer models, the regulation of MYC mRNA in response to BET-I does not discriminate between sensitive and insensitive lines, further pointing to the highly context-dependent function of MYC in the response toward these kinds of drugs (52).…”

aBETting therapeutic resistance by Wnt signaling

“…While Rathert et al [7] did not find major differences in gene expression between sensitive and resistant clones upon short-term treatment with JQ1, resistant clones over time displayed divergent gene expression patterns including the restoration of multiple crucial transcripts such as Tifab and Myc. Rebound expression of Myc was also a feature of resistant human AML cell lines versus sensitive lines despite initial loss in both.…”

“…In a separate study that focused on intrinsic resistance, Rathert and colleagues [7] employed a screen against an shRNA library of 626 chromatin modifiers, aiming to identify crucial factors that confer BET inhibitor resistance to the murine MLL-AF9;Nras G12D model of AML. Cells expressing shRNAs targeting Suz12, Psip12, and Dnmt3 showed robust resistance to JQ1 treatment.…”