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Series GSE120957 Query DataSets for GSE120957
Status Public on Aug 22, 2019
Title The EN1 transcription factor drives neural features and brain metastases in triple negative breats cancer (TNBC)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary To define transcriptional dependencies of TNBCs, we identified transcription factors highly and specifically expressed in primary TNBCs and tested their requirement for cell growth in a panel of breast cancer cell lines. We found that EN1 is overexpressed in TNBCs and its downregulation preferentially and significantly reduces cellular viability and tumorigenicity in TNBC cell lines. Based on RNA-seq and ChIPseq we found that EN1 regulates genes involved in angiogenesis, neurogenesis, and axon guidance in breast cancer cells. Higher expression of EN1 correlates with shorter overall survival among TNBC patients and with higher risk of developing brain metastases. Thus, EN1 is a prognostic marker and a therapeutic target in this particularly lethal subset of TNBCs.
 
Overall design Bulk RNA-Seq: Gene expression analysis of SUM149 and SUM159 cell lines with TET-inducible shRNA against EN1 with the following variables: Two different shRNA labeled shEN1-1 and shEN1-2, doxycyclin (plus/treatment) and no doxycyclin (minus/control), 3 days and 5 days after doxycyclin treatment. All conditions were sequenced in biological duplicates (32 samples). For the MCF7 cellline samples, differential gene expression analysis was performed with inducible overexpression of EN1 with the following variables: doxycyclin (plus/treatment) and no doxycyclin (minus/control). All conditions were sequenced in biological duplicates (4 samples). ChIP-Seq: ChIP-Seq for exogenously expressed V5-tagged EN1 in SUM149, SUM159 and MCF7. ChIP-Seq for histone H3 lysine 27 acetyl (H3K27ac) in SUM149 and SUM159. ChIP-Seq for the transcription factor FOXA1 in MCF7 cells of both LacZ condition and EN1-expressing condition. ChIP-Seq for the transcription factor Beta-catenin in MCF7 cells of both LacZ condition and EN1-expressing condition, and in SUM149 with and without EN1 knockdown. ChIP-Seq for TLE3 in MCF7 cells of both LacZ condition and EN1-expressing condition, and in SUM149 and SUM159 with and without EN1 knockdown.
 
Contributor(s) Peluffo G, Subedee A, Harper NW, Kingston N, Jovanovic B, Flores F, Beca F, Trinh A, Chilamakuri CS, Papachristou E, Su Y, Marusyk A, D'Santos C, Beck A, Caldas C, Carroll J, Polyak K
Citation(s) 31239270
NIH grant(s)
Grant ID Grant title Affiliation Name
R35 CA197623 Targeting intratumor heterogeneity in breast cancer DANA-FARBER CANCER INSTITUTE KORNELIA POLYAK
Submission date Oct 09, 2018
Last update date Aug 22, 2019
Contact name Kornelia Polyak
E-mail(s) kornelia_polyak@dfci.harvard.edu
Phone 617-632-2106
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Polyak
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (89)
GSM3422056 SUM149PT_shEN1-1_Day-3_Dox-minus_1
GSM3422057 SUM149PT_shEN1-1_Day-3_Dox-minus_2
GSM3422058 SUM149PT_shEN1-1_Day-3_Dox-plus_1
Relations
BioProject PRJNA495138
SRA SRP164655

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE120957_RAW.tar 15.7 Mb (http)(custom) TAR (of BED)
GSE120957_combined-gene-level-counts.csv.gz 1.1 Mb (ftp)(http) CSV
GSE120957_combined-gene-level-counts_GSM3687053-GSM3687072.csv.gz 661.6 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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