title: Transcriptional plasticity promotes primary and acquired resistance to BET inhibition.
abstract: Following the discovery of BRD4 as a non-oncogene addiction target in acute myeloid leukaemia (AML), bromodomain and extra terminal protein (BET) inhibitors are being explored as a promising therapeutic avenue in numerous cancers. While clinical trials have reported single-agent activity in advanced haematological malignancies, mechanisms determining the response to BET inhibition remain poorly understood. To identify factors involved in primary and acquired BET resistance in leukaemia, here we perform a chromatin-focused RNAi screen in a sensitive MLL-AF9;Nras(G12D)-driven AML mouse model, and investigate dynamic transcriptional profiles in sensitive and resistant mouse and human leukaemias. Our screen shows 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 remodelling of regulatory pathways that restore the transcription of key targets such as Myc. Similarly, while BET inhibition triggers acute MYC repression in human leukaemias regardless of their sensitivity, resistant leukaemias are uniformly characterized by their ability to rapidly restore MYC transcription. This process involves the activation and recruitment of WNT signalling components, which compensate for the loss of BRD4 and drive resistance in various cancer models. Dynamic chromatin immunoprecipitation sequencing and self-transcribing active regulatory region sequencing of enhancer profiles reveal that BET-resistant states are characterized by remodelled 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 signalling as a driver and candidate biomarker of primary and acquired BET resistance in leukaemia, and implicate the rewiring of transcriptional programs as an important mechanism promoting resistance to BET inhibitors and, potentially, other chromatin-targeted therapies.
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Philipp
authors.initials: P
authors.lastname: Rathert
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Mareike
authors.initials: M
authors.lastname: Roth
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Tobias
authors.initials: T
authors.lastname: Neumann
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Felix
authors.initials: F
authors.lastname: Muerdter
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Jae-Seok
authors.initials: JS
authors.lastname: Roe
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Matthias
authors.initials: M
authors.lastname: Muhar
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Sumit
authors.initials: S
authors.lastname: Deswal
authors.affiliation: Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.|Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, 1090 Vienna, Austria.
authors.forename: Sabine
authors.initials: S
authors.lastname: Cerny-Reiterer
authors.affiliation: Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.|Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, 1090 Vienna, Austria.
authors.forename: Barbara
authors.initials: B
authors.lastname: Peter
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Julian
authors.initials: J
authors.lastname: Jude
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Hoffmann
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Łukasz M
authors.initials: ŁM
authors.lastname: Boryń
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Elin
authors.initials: E
authors.lastname: Axelsson
authors.affiliation: Boehringer Ingelheim - Regional Center Vienna GmbH, 1121 Vienna, Austria.
authors.forename: Norbert
authors.initials: N
authors.lastname: Schweifer
authors.affiliation: Boehringer Ingelheim - Regional Center Vienna GmbH, 1121 Vienna, Austria.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Tontsch-Grunt
authors.affiliation: Department of Medicine, Hematology & Medical Oncology, Weill Cornell Medical College, New York 10065, USA.
authors.forename: Lukas E
authors.initials: LE
authors.lastname: Dow
authors.affiliation: Boehringer Ingelheim - Regional Center Vienna GmbH, 1121 Vienna, Austria.
authors.forename: Davide
authors.initials: D
authors.lastname: Gianni
authors.affiliation: Boehringer Ingelheim - Regional Center Vienna GmbH, 1121 Vienna, Austria.
authors.forename: Mark
authors.initials: M
authors.lastname: Pearson
authors.affiliation: Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.|Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, 1090 Vienna, Austria.
authors.forename: Peter
authors.initials: P
authors.lastname: Valent
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Alexander
authors.initials: A
authors.lastname: Stark
authors.affiliation: Boehringer Ingelheim - Regional Center Vienna GmbH, 1121 Vienna, Austria.
authors.forename: Norbert
authors.initials: N
authors.lastname: Kraut
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Vakoc
authors.affiliation: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors.forename: Johannes
authors.initials: J
authors.lastname: Zuber
mesh_terms: D000818:Animals; D001381:Azepines / Q000494:pharmacology*; D018797:Cell Cycle Proteins; D045744:Cell Line, Tumor; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D019008:Drug Resistance, Neoplasm / Q000187:drug effects* / Q000235:genetics*; D004742:Enhancer Elements, Genetic / Q000235:genetics; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects* / Q000235:genetics; D016259:Genes, myc / Q000235:genetics; D015470:Leukemia, Myeloid, Acute / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D008297:Male; D051379:Mice; D009687:Nuclear Proteins / Q000037:antagonists & inhibitors* / Q000378:metabolism; D014157:Transcription Factors / Q000037:antagonists & inhibitors* / Q000378:metabolism; D014158:Transcription, Genetic / Q000187:drug effects* / Q000235:genetics; D014230:Triazoles / Q000494:pharmacology*; D060449:Wnt Signaling Pathway / Q000187:drug effects; D000092468:Bromodomain Containing Proteins
chemical_list: D001381:Azepines; D018797:Cell Cycle Proteins; D002843:Chromatin; D009687:Nuclear Proteins; D014157:Transcription Factors; D014230:Triazoles; C561695:(+)-JQ1 compound; C441289:BRD4 protein, human; D000092468:Bromodomain Containing Proteins