GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE83660 Query DataSets for GSE83660
Status Public on Jul 15, 2016
Title High Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Bromodomain and extra-terminal domain (BET) family inhibitors offer a new 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) that are exceptionally sensitive to BET inhibitors. PRO-seq identified over 1400 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 and 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 up-regulated, 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.
Overall design Kasumi-1 cells were treated with DMSO, 250 nM JQ1, and 125 nM MS417 for 1 and 3 hours, and PRO-seq was performed to study transcriptional changes.
Kasumi-1 cells were treated with 250 nM JQ1 for 0, 15, and 30 minutes, and PRO-seq was performed. Two biological replicates were included for each time point.
Primary AML patient cells were treated with DMSO and 250 nM JQ1 for 1 hour, and PRO-seq was performed to confirm trancriptional effects of BET inhibitors.
Contributor(s) Zhao Y, Acharya P, Hiebert SW
Citation(s) 27498870
Submission date Jun 23, 2016
Last update date May 15, 2019
Contact name Scott W Hiebert
Phone 615-936-3582
Organization name Vanderbilt University
Department Biochemistry
Lab Hiebert Lab
Street address 2220 Pierce Ave
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (22)
GSM2212033 DMSO-1hr (PRO-seq)
GSM2212034 JQ1-1hr (PRO-seq)
GSM2212035 MS417-1hr (PRO-seq)
BioProject PRJNA326664
SRA SRP077005

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83660_RAW.tar 2.4 Gb (http)(custom) TAR (of BEDGRAPH, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap