Philipp Rathert, Mareike Roth, Tobias Neumann, Felix Muerdter, Jae-Seok Roe et al.
Following the discovery of BRD4 as a non-oncogene addiction target in acute myeloid leukemia (AML), BET inhibitors are being explored as promising therapeutic avenue in numerous cancers. While clinical trials have reported single-agent activity in advanced hematologic malignancies, 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 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.
Philipp Rathert, Mareike Roth, Tobias Neumann, Felix Muerdter, Jae-Seok Roe, Matthias Muhar, Sumit Deswal, Sabine Cerny-Reiterer, Barbara Peter, Julian Jude, Thomas Hoffmann, Łukasz M. Boryń, Elin Axelsson, Norbert Schweifer, Ulrike Tontsch-Grunt, Lukas E. Dow, Davide Gianni, Mark Pearson, Peter Valent, Alexander Stark, Norbert Kraut, Christopher R. Vakoc, Johannes Zuber. Transcriptional plasticity promotes primary and acquired resistance to BET inhibition. 2015-09-14. https://doi.org/10.1038/nature14898
A BAC-fragment library covering approximately 91% of the surrounding 3.1 Mb MYC region, together with 25 genic control BACs, was cloned into an episomal STARR-seq vector with a minimal MYC promoter. The library was electroporated into K-562 cells and assayed after 24 h in DMSO vehicle or 250 nM JQ1.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 10 files (ZIP)GSE63782_filelist.txtGSE63782_series.geo.txtGSM1652928.geo.txtGSM1652928_STARRseq_24h_DMSO.bwGSM1652929.geo.txtGSM1652929_STARRseq_24h_JQ1.bwGSM1652930.geo.txtGSM1652930_STARRseq_input.bwnature14898_supplementary_tables.xlsxSTARR-seq_BACs.tsv