Next generation sequencing-based expression profiling identifies signatures from benign stromal proliferations that define stromal components of breast cancer

Breast Cancer Research : BCR
Xiangqian GuoRobert B West

Abstract

Multiple studies have shown that the tumor microenvironment (TME) of carcinomas can play an important role in the initiation, progression, and metastasis of cancer. Here we test the hypothesis that specific benign fibrous soft tissue tumor gene expression profiles may represent distinct stromal fibroblastic reaction types that occur in different breast cancers. The discovered stromal profiles could classify breast cancer based on the type of stromal reaction patterns in the TME. Next generation sequencing-based gene expression profiling (3SEQ) was performed on formalin fixed, paraffin embedded (FFPE) samples of 10 types of fibrous soft tissue tumors. We determined the extent to which these signatures could identify distinct subsets of breast cancers in four publicly available breast cancer datasets. A total of 53 fibrous tumors were sequenced by 3SEQ with an average of 29 million reads per sample. Both the gene signatures derived from elastofibroma (EF) and fibroma of tendon sheath (FOTS) demonstrated robust outcome results for survival in the four breast cancer datasets. The breast cancers positive for the EF signature (20-33% of the cohort) demonstrated significantly better outcome for survival. In contrast, the FOTS signatur...Continue Reading

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Citations

Feb 25, 2014·Seminars in Cancer Biology·Janna Paulsson, Patrick Micke
Aug 5, 2015·Genomics Data·Xiangqian GuoMatt van de Rijn
Apr 28, 2018·Journal of Neuro-oncology·Caroline ApraMarc Sanson
Mar 18, 2020·Journal of Clinical Medicine·Patricia Fernández-NogueiraNeus Carbó
Jul 16, 2020·Breast Cancer Research : BCR·Claire BonneauFatima Mechta-Grigoriou
Apr 22, 2015·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Xiangqian GuoMatt van de Rijn

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Datasets Mentioned

BETA
GSE42948
GSE1456
GSE3494
GSE4922

Methods Mentioned

BETA
RNA-Seq

Software Mentioned

SOAP2
3seq
Path
GraphPad
fastx
GraphPad Prism5
R
Cluster
TreeView
SAM

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