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Series GSE39412 Query DataSets for GSE39412
Status Public on Jun 10, 2015
Title Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [SNP]
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but high degree of heterogeneity in basal-like breast cancers that correlates with clinical outcome. We also found that protein extracts of basal-like cells is sufficient to induce luminal-to-basal phenotypic switch implying a trigger of basal-like autoregulatory circuits. We determined that KDM6A might be required for luminal-basal fusions, and identified EN1, TBX18, and TCF4 as candidate transcriptional regulators of luminal-to-basal switch. Our findings highlight the remarkable epigenetic plasticity of breast cancer cells.
Overall design We investigated the potential contribution of genetic factors to defining cell type-specific gene expression patterns by analyzing allelic inheritance based on Affymetrix SNP6.0 array hybridization of DNA from parental and fusion cells
Contributor(s) Polyak K, Gimelbrant A, Maruyama R
Citation(s) 26051943
Submission date Jul 17, 2012
Last update date Nov 27, 2018
Contact name Kornelia Polyak
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)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (19)
GSM967817 SUM159neo_SNP6
GSM967818 MDA231neo_SNP6
GSM967819 mcf7puro_SNP6
This SubSeries is part of SuperSeries:
GSE38548 Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer
BioProject PRJNA170834

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
GSE39412_RAW.tar 548.3 Mb (http)(custom) TAR (of CEL)
GSE39412_TableS4-SNP-updated_121114.xlsx 1.0 Mb (ftp)(http) XLSX
Processed data included within Sample table
Processed data are available on Series record

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