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-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-tomesenchymal 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.

A comprehensive overview of metaplastic breast cancer: clinical features and molecular aberrations

“…A genomics profiling study performed by McQuerry and colleagues found that MpBC samples with mesenchymal (osteoid or chondroid) histology had increased Snail, BCL-2-like-1 protein, and Akt1 pathway activity in comparison to non-mesenchymal MpBC tumors [ 16 ]. When comparing the gene expression profiles of MpBC to TNBC tumors, MpBC tumors had more upregulation of epithelial-to-mesenchymal transition (EMT) and collagen genes, but downregulation of late cornified envelope and keratinization genes.…”

Molecular Features of Metaplastic Breast Carcinoma: An Infrequent Subtype of Triple Negative Breast Carcinoma

“…The acquisition of a mesenchymal phenotype in MBC is associated with a switching of cadherins (from E-cadherin to N-cadherin and cadherin 11) and the downregulation of epithelial markers including not only E-cadherin ( CDH1 ), but also occludens zone 1 ( ZO1 ), desmoplakin, keratin 7, keratin 18, and keratin 19, among others [ 43 ]. In contrast, genes related to the mesenchymal phenotype, motility, migration, and formation of extracellular matrix, such as vimentin, SPARC, or different collagen types, are upregulated in MBC [ 31 , 43 , 50 , 51 , 52 ].…”

“…EMT in MBC allows cells to acquire different phenotypes due to secondary trans-differentiation. Accordingly, different expression patterns have been reported in SpCC, SqCC, and MBCHMD with chondroid differentiation [ 5 , 52 ]. Thus, SpCC showed the downregulation of epithelial genes, such as CDH1, EPCAM, CLDN3, and CLDN8 .…”

A 9-kDa matricellular SPARC fragment released by cathepsin D exhibits pro-tumor activity in the triple-negative breast cancer microenvironment

“…More recently, it was found that co-expression of cath-D and androgen receptor defines a TNBC subgroup with poorer overall survival (6). SPARC protein and mRNA are also overexpressed in TNBC (31,33,54), and this has been associated with poor prognosis in patients with TNBC (30,31,33). Here, we showed that high mRNA expression of CTSD and SPARC tended to be associated with shorter recurrence-free survival in a cohort of 255 patients with TNBC using an on line survival tool (39).…”

“…In different cancer types, SPARC plays an oncogenic or a tumor-suppressive role (26,27). For instance, in BC, SPARC has a pro-tumorigenic role and has been associated with worse prognosis (24,(28)(29)(30)(31)(32)(33); however, other studies reported anti-tumorigenic functions (34)(35)(36). SPARC includes three different structural and functional modules: the N-terminal acidic domain, followed by the follistatin-like domain, and the C-terminal extracellular Ca 2+ binding domain (21).…”