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Series GSE54379 Query DataSets for GSE54379
Status Public on Mar 01, 2014
Title Genome-wide chromatin maps of T-cell acute lymphoblastic leukemia (T-ALL) [ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Here we modeled T-ALL resistance to Notch inhibition, identifying ‘persister’ cells that readily expand in the presence of gamma secretase inhibitor (GSI) and the absence of Notch signaling. Rare persister cells are already present in naïve T-ALL populations, and the reversibility of the phenotype is suggestive of an epigenetic mechanism. Relative to GSI-sensitive cells, persisters activate distinct signaling and gene expression programs, and exhibit global chromatin compaction. A shRNA screen identified chromatin regulators whose depletion preferentially impairs persister cell viability, including BRD4, an acetyl-histone reader. BRD4 is up-regulated in the persisters and binds enhancers near genes with critical functions in T-ALL, including MYC and BCL2. Treatment of persisters with the BRD4 inhibitor JQ1 down-regulates these targets and induces growth arrest and apoptosis, at doses well tolerated by GSI-sensitive cells. Prompted by these findings, we examined and established the efficacy of GSI – JQ1 combination therapy against primary human leukemias in vivo. Our findings establish a role for epigenetic heterogeneity in leukemia drug resistance and suggest the potential of combination therapies that include epigenetic modulators to prevent and treat resistant disease.
Overall design Examination of 5 different histone modifications and BRD4 in the T cell leukemia cell lines DND-41 and KOPT-K1 after chronic treatment with gamma Secretase inhibitor (Compound E, 1 uM, EMD4 Bioscience; persister) or vehicle (naïve).
Contributor(s) Knoechel B, Zhu J, Bernstein BE
Citation(s) 24584072
Submission date Jan 24, 2014
Last update date May 15, 2019
Contact name Jiang Zhu
Organization name Massachusetts General Hospital, Harvard Medical School and Broad Institute
Lab Bradley Bernstein Lab
Street address 185 Cambridge Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (28)
GSM1314121 BRD4 ChIP-seq in KOPT-K1
GSM1314122 H3K27ac ChIP-seq in KOPT-K1
GSM1314123 H3K27me3 ChIP-seq in KOPT-K1
This SubSeries is part of SuperSeries:
GSE54380 Genome-wide chromatin maps of T-cell acute lymphoblastic leukemia (T-ALL)
SRA SRP035662
BioProject PRJNA236555

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Supplementary file Size Download File type/resource
GSE54379_RAW.tar 1.6 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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