Comment[ArrayExpressAccession] E-GEOD-80365 MAGE-TAB Version 1.1 Public Release Date 2016-06-01 Investigation Title Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [tumor samples RNA-seq] Comment[Submitted Name] Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [tumor samples RNA-seq] Experiment Description Transcriptomic changes and estrogen and progesterone receptor binding in multiple ER+/PR+ models (eight ER+/PR+ patient tumors, various T47Ds, ZR75) and multiple ER+/PR-negative models (four ER+/PR- patient tuumors, PR-deficient T47D and MCF7 cells) treated with various hormone combinations. Results: In isolation, estrogen and progestin act as genomic agonists by regulating the expression of common target genes in similar directions, but at different levels. Similarly, in isolation, progestin is also a weak phenotypic agonist of estrogen action. However, in the presence of both hormones, progestin behaves as a phenotypic estrogen antagonist. PR remodels nucleosomes to noncompetitively redirect ER genomic binding to distal enhancers enriched for BRCA1 binding motifs and sites that link PR and ER/PR complexes. Importantly, when both hormones are present, progestin modulates estrogen action such that responsive transcriptomes, cellular processes and ER/PR recruitment to genomic sites correlate with those observed with PR alone, but not ER alone. Conclusions: Genomic Agonism and Phenotypic Antagonism between Estrogen and Progesterone Receptors in Breast Cancer. Individual and concerted actions of ER and PR highlight the prognostic and therapeutic value of PR in ER+/PR+ breast cancers. ER+/PR+ and ER+/PR-deficient model systems were deprived of steroids by culturing them in phenol red free RPMI 1640 media that is supplemented with 10% charcoal-stripped fetal bovine serum and 1% penicillin/streptomycin. Subsequently, these steroid-deprived models were treated with either vehicle, 10 nM estradiol, 10 nM progestin R5020 or 10 nM of both the hormones and genomics (ChIP-seq and RNA-seq) was performed. ChIP-seq was done after 45 minutes of hormone treatments. For cell models, RNA-seq was done after 12 hours of hormone treatments. Tumor explants were treated with either 24 or 48 hours. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Singhal Greene Singhal Person First Name Hari Geoffrey Hari Person Email hari_singhal@dfci.harvard.edu Person Affiliation University of Chicago Person Address Ben May Department for Cancer Research, University of Chicago, 929 E 57th St, Chicago, IL, USA Person Roles submitter Protocol Name P-GSE80365-1 P-GSE80365-3 P-GSE80365-2 Protocol Description Steroid-deprived tumor explants were treated with 10 nM estradiol, 10 nM R5020 or 10 nM of both the hormones for 24 or 48 hours. Finer details are provided in materials and methods section (Patient tumor explants) Hormone-treated explant was homogenized and total RNA was extracted using Qiagen RNAeasy kit PolyA tail selection was performed on 250 ng of total RNA. RNA-seq libraries were prepared using NEBNext kit. Details of library preparation strategy are provided in the materials and methods section (RNA expression and RNA-sequencing) of the paper. Tumor explants: Within one hour of surgery, sliced pieces of tumors were incubated on gelatin sponges for 36 hours in charcoal-stripped serum media. Representative pieces of tumors were in parallel fixed in 4% formalin and subsequently immunohistochemistry for ER and PR protein was performed to assess the status of tumors for these receptors. Protocol Type sample treatment protocol nucleic acid library construction protocol growth protocol Experimental Factor Name drug treatment er/pr status tissue type hormone exposure time Experimental Factor Type drug treatment er/pr status tissue type hormone exposure time Comment[SecondaryAccession] GSE80365 Comment[GEOReleaseDate] 2016-06-01 Comment[ArrayExpressSubmissionDate] 2016-04-18 Comment[GEOLastUpdateDate] 2016-06-01 Comment[AEExperimentType] RNA-seq of coding RNA Comment[AdditionalFile:Data1] GSE80365_tumor_N1_RNAseq.csv Comment[AdditionalFile:Data2] GSE80365_tumor_N2_RNAseq.csv Comment[AdditionalFile:Data3] GSE80365_tumor_N3_RNAseq.csv Comment[AdditionalFile:Data4] GSE80365_tumor_N4_RNAseq.csv Comment[AdditionalFile:Data5] GSE80365_tumor_P1_RNAseq.csv Comment[AdditionalFile:Data6] GSE80365_tumor_P2_RNAseq.csv Comment[AdditionalFile:Data7] GSE80365_tumor_P3_RNAseq.csv Comment[AdditionalFile:Data8] GSE80365_tumor_P4_RNAseq.csv Comment[AdditionalFile:Data9] GSE80365_tumor_P5_RNAseq.csv Comment[AdditionalFile:Data10] GSE80365_tumor_P6_RNAseq.csv Comment[AdditionalFile:Data11] GSE80365_tumor_P7_RNAseq.csv Comment[AdditionalFile:Data12] GSE80365_tumor_P8_RNAseq.csv SDRF File E-GEOD-80365.sdrf.txt