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Series GSE42948 Query DataSets for GSE42948
Status Public on Nov 21, 2013
Title Two New Stromal Signatures Stratify Breast Cancers with Different Prognosis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Multiple studies from last decades have shown that the microenvironment of carcinomas plays an important role in the initiation, progression and metastasis of cancer. Our group has previously identified novel cancer stroma gene expression signatures associated with outcome differences in breast cancer by gene expression profiling of two tumors of fibroblasts as surrogates for physiologic stromal expression patterns. The aim of this study is to find additional new types of tumor stroma gene expression patterns.
Results: 53 tumors were sequenced by 3SEQ with an average of 29 million reads per sample. Both the elastofibroma (EF) and fibroma of tendon sheath (FOTS) gene signatures demonstrated robust outcome results for survival in the four breast cancer datasets. The EF signature positive breast cancers (20-33% of the cohort) demonstrated significantly better outcome for survival. In contrast, the FOTS signature positive breast cancers (11-35% of the cohort) had a worse outcome. The combined stromal signatures of EF, FOTS, and our previously identified DTF, and CSF1 signatures characterize, in part, the stromal expression profile for the tumor microenvironment for between 74%-90% of all breast cancers.
Conclusions: We defined and validated two new stromal signatures in breast cancer (EF and FOTS), which are significantly associated with prognosis.
 
Overall design Gene expression profiling by 3SEQ was performed on 8 additional types of fibrous tumors, to identify different fibrous tumor specific gene expression signatures. We then determined the significance of the fibrous tumor gene signatures in four publically available breast cancer datasets (GSE1456, GSE4922, GSE3494, NKI Dataset).
 
Contributor(s) Guo X, Zhu SX, Brunner AL, van de Rijn M, West RB
Citation(s) 24342436
Submission date Dec 16, 2012
Last update date May 15, 2019
Contact name Xiangqian Guo
E-mail(s) xqguo@stanford.edu
Phone 650 725 7742
Organization name Stanford University
Department Department of Pathology
Lab vanderijn-west Lab
Street address 300 Pasteur Dr.
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (53)
GSM1053748 desmoid type fibromatosis (STT5629_DTF)
GSM1053749 desmoid type fibromatosis (STT5634_DTF)
GSM1053750 desmoid type fibromatosis (STT5764_DTF)
Relations
BioProject PRJNA183925
SRA SRP017575

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
GSE42948_10groups.fibrous.tumor.transcriptome_RPM_round.txt.gz 2.9 Mb (ftp)(http) TXT
GSE42948_summary_of_outcome_for_ten_fibrous_tumor_signatures.xlsx.gz 11.9 Kb (ftp)(http) XLSX
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Processed data are available on Series record

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