Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes
Abstract Background Gene expression profiling of rare cancers has proven challenging due to limited access to patient materials and requirement of intact, non-degraded RNA for next-generation sequencing. We customized a gene expression panel compatible with degraded RNA from formalin-fixed, paraffin...
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doaj-720e568173dd4f7c802d654c588977a32020-11-25T01:56:48ZengBMCBMC Cancer1471-24072019-09-0119111410.1186/s12885-019-6052-zPathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypesJasmine A. McQuerry0David F. Jenkins1Susan E. Yost2Yuqing Zhang3Daniel Schmolze4W. Evan Johnson5Yuan Yuan6Andrea H. Bild7Department of Oncological Sciences, School of Medicine, University of UtahDivision of Computational Biomedicine, School of Medicine, Boston UniversityDepartment of Medical Oncology and Therapeutics, City of HopeDivision of Computational Biomedicine, School of Medicine, Boston UniversityDepartment of Pathology, City of HopeDivision of Computational Biomedicine, School of Medicine, Boston UniversityDepartment of Medical Oncology and Therapeutics, City of HopeDepartment of Medical Oncology and Therapeutics Research, City of HopeAbstract Background Gene expression profiling of rare cancers has proven challenging due to limited access to patient materials and requirement of intact, non-degraded RNA for next-generation sequencing. We customized a gene expression panel compatible with degraded RNA from formalin-fixed, paraffin-embedded (FFPE) patient cancer samples and investigated its utility in pathway activity profiling in patients with metaplastic breast cancer (MpBC). Methods Activity of various biological pathways was profiled in samples from nineteen patients with MpBC and 8 patients with invasive ductal carcinoma with triple negative breast cancer (TNBC) phenotype using a custom gene expression-based assay of 345 genes. Results MpBC samples of mesenchymal (chondroid and/or osteoid) histology demonstrated increased SNAI1 and BCL2L11 pathway activity compared to samples with non-mesenchymal histology. Additionally, late cornified envelope and keratinization genes were downregulated in MpBC compared to TNBC, and epithelial-to-mesenchymal transition (EMT) and collagen genes were upregulated in MpBC. Patients with high activity of an invasiveness gene expression signature, as well as high expression of the mesenchymal marker and extracellular matrix glycoprotein gene SPARC, experienced worse outcomes than those with low invasiveness activity and low SPARC expression. Conclusions This study demonstrates the utility of gene expression profiling of metaplastic breast cancer FFPE samples with a custom counts-based assay. Gene expression patterns identified by this assay suggest that, although often histologically triple negative, patients with MpBC have distinct pathway activation compared to patients with invasive ductal TNBC. Incorporation of targeted therapies may lead to improved outcome for MpBC patients, especially in those patients expressing increased activity of invasiveness pathways.http://link.springer.com/article/10.1186/s12885-019-6052-zMetaplastic breast cancerGene expression profilingSurvivalInvasivenessNanoString |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jasmine A. McQuerry David F. Jenkins Susan E. Yost Yuqing Zhang Daniel Schmolze W. Evan Johnson Yuan Yuan Andrea H. Bild |
spellingShingle |
Jasmine A. McQuerry David F. Jenkins Susan E. Yost Yuqing Zhang Daniel Schmolze W. Evan Johnson Yuan Yuan Andrea H. Bild Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes BMC Cancer Metaplastic breast cancer Gene expression profiling Survival Invasiveness NanoString |
author_facet |
Jasmine A. McQuerry David F. Jenkins Susan E. Yost Yuqing Zhang Daniel Schmolze W. Evan Johnson Yuan Yuan Andrea H. Bild |
author_sort |
Jasmine A. McQuerry |
title |
Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes |
title_short |
Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes |
title_full |
Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes |
title_fullStr |
Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes |
title_full_unstemmed |
Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes |
title_sort |
pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes |
publisher |
BMC |
series |
BMC Cancer |
issn |
1471-2407 |
publishDate |
2019-09-01 |
description |
Abstract Background Gene expression profiling of rare cancers has proven challenging due to limited access to patient materials and requirement of intact, non-degraded RNA for next-generation sequencing. We customized a gene expression panel compatible with degraded RNA from formalin-fixed, paraffin-embedded (FFPE) patient cancer samples and investigated its utility in pathway activity profiling in patients with metaplastic breast cancer (MpBC). Methods Activity of various biological pathways was profiled in samples from nineteen patients with MpBC and 8 patients with invasive ductal carcinoma with triple negative breast cancer (TNBC) phenotype using a custom gene expression-based assay of 345 genes. Results MpBC samples of mesenchymal (chondroid and/or osteoid) histology demonstrated increased SNAI1 and BCL2L11 pathway activity compared to samples with non-mesenchymal histology. Additionally, late cornified envelope and keratinization genes were downregulated in MpBC compared to TNBC, and epithelial-to-mesenchymal transition (EMT) and collagen genes were upregulated in MpBC. Patients with high activity of an invasiveness gene expression signature, as well as high expression of the mesenchymal marker and extracellular matrix glycoprotein gene SPARC, experienced worse outcomes than those with low invasiveness activity and low SPARC expression. Conclusions This study demonstrates the utility of gene expression profiling of metaplastic breast cancer FFPE samples with a custom counts-based assay. Gene expression patterns identified by this assay suggest that, although often histologically triple negative, patients with MpBC have distinct pathway activation compared to patients with invasive ductal TNBC. Incorporation of targeted therapies may lead to improved outcome for MpBC patients, especially in those patients expressing increased activity of invasiveness pathways. |
topic |
Metaplastic breast cancer Gene expression profiling Survival Invasiveness NanoString |
url |
http://link.springer.com/article/10.1186/s12885-019-6052-z |
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