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Series GSE56022 Query DataSets for GSE56022
Status Public on Sep 18, 2015
Title Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Glucocorticoids (GC) have been widely used as coadjuvants in the treatment of solid tumors, but GC treatment may be associated with poor pharmacotherapeutic response and/or prognosis. The genomic action of GC in these tumors is largely unknown. Here we find that dexamethasone (Dex, a synthetic GC) regulated genes in triple-negative breast cancer (TNBC) cells are associated with drug resistance. Importantly, these GC-regulated genes are aberrantly expressed in TNBC patients and associated with unfavorable clinical outcomes. Interestingly, in TNBC cells, Compound A (CpdA, a selective GR modulator) only regulates a small number of genes not involved in carcinogenesis and therapy resistance. Mechanistic studies using a ChIP-exo approach reveal that Dex- but not CpdA-liganded glucocorticoid receptor (GR) binds to a single glucocorticoid response element (GRE), which drives the expression of pro-tumorigenic genes. Our data suggest that development of safe coadjuvant therapy should consider the distinct genomic function between Dex- and CpdA-liganded GR.
Overall design To study GR-regulated genes and define GRE in human genome, RNA-seq and GR ChIP-exo are performed in MDA-MB-231 cells before/after dex and CpdA stimulation. Each experiment includes two replicates.
Contributor(s) Wang Q, Chen Z
Citation(s) 26374485
Submission date Mar 19, 2014
Last update date May 15, 2019
Contact name Xun Lan
Phone 7738345917
Organization name Stanford University
Department Genetics
Lab Pritchard's Lab
Street address 318 Campus Dr. Room S240
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (22)
GSM1350526 GR_Vehicle_1
GSM1350527 GR_Vehicle_2
GSM1350528 GR_Dexamethasone_1
BioProject PRJNA242236
SRA SRP040300

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

Supplementary file Size Download File type/resource
GSE56022_RAW.tar 28.0 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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