title: High-Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML.
abstract: Bromodomain and extra-terminal domain (BET) family inhibitors offer an approach to treating hematological malignancies. We used precision nuclear run-on transcription sequencing (PRO-seq) to create high-resolution maps of active RNA polymerases across the genome in t(8;21) acute myeloid leukemia (AML), as these polymerases are exceptionally sensitive to BET inhibitors. PRO-seq identified over 1,400 genes showing impaired release of promoter-proximal paused RNA polymerases, including the stem cell factor receptor tyrosine kinase KIT that is mutated in t(8;21) AML. PRO-seq also identified an enhancer 3' to KIT. Chromosome conformation capture confirmed contacts between this enhancer and the KIT promoter, while CRISPRi-mediated repression of this enhancer impaired cell growth. PRO-seq also identified microRNAs, including MIR29C and MIR29B2, that target the anti-apoptotic factor MCL1 and were repressed by BET inhibitors. MCL1 protein was upregulated, and inhibition of BET proteins sensitized t(8:21)-containing cells to MCL1 inhibition, suggesting a potential mechanism of resistance to BET-inhibitor-induced cell death.
authors: Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors: Yue
authors: Y
authors: Zhao
authors: Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors: Qi
authors: Q
authors: Liu
authors: Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors: Pankaj
authors: P
authors: Acharya
authors: Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors: Kristy R
authors: KR
authors: Stengel
authors: Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors: Quanhu
authors: Q
authors: Sheng
authors: Department of Biological Sciences, Vanderbilt University, Nashville, TN 37212, USA.
authors: Xiaofan
authors: X
authors: Zhou
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors: Hojoong
authors: H
authors: Kwak
authors: Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors: Melissa A
authors: MA
authors: Fischer
authors: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
authors: James E
authors: JE
authors: Bradner
authors: Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors: Stephen A
authors: SA
authors: Strickland
authors: Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors: Sanjay R
authors: SR
authors: Mohan
authors: Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors: Michael R
authors: MR
authors: Savona
authors: Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors: Bryan J
authors: BJ
authors: Venters
authors: Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
authors: Ming-Ming
authors: MM
authors: Zhou
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors: John T
authors: JT
authors: Lis
authors: Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Electronic address: scott.hiebert@vanderbilt.edu.
authors: Scott W
authors: SW
authors: Hiebert
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D001381:Azepines / Q000494:pharmacology; D045744:Cell Line, Tumor; D002891:Chromosomes, Human, Pair 21; D002898:Chromosomes, Human, Pair 8; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism; D019008:Drug Resistance, Neoplasm / Q000187:drug effects / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D015973:Gene Expression Regulation, Leukemic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000188:drug therapy / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D005810:Multigene Family; D064549:Myeloid Cell Leukemia Sequence 1 Protein / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D020033:Protein Isoforms / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D011506:Proteins / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism; D019009:Proto-Oncogene Proteins c-kit / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic; D014178:Translocation, Genetic; D014230:Triazoles / Q000494:pharmacology; D000092468:Bromodomain Containing Proteins
chemical_list: D000970:Antineoplastic Agents; D001381:Azepines; D012321:DNA-Directed RNA Polymerases; D035683:MicroRNAs; D064549:Myeloid Cell Leukemia Sequence 1 Protein; D020033:Protein Isoforms; D011506:Proteins; D019009:Proto-Oncogene Proteins c-kit; D014230:Triazoles; C561695:(+)-JQ1 compound; C579095:MCL1 protein, human; C532045:MIRN29a microRNA, human; C000624329:bromodomain and extra-terminal domain protein, human; D000092468:Bromodomain Containing Proteins