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Patient sample-oriented analysis of gene expression highlights extracellular signatures in breast cancer progression.

Abstract：

:Although a large collection of cancer cell lines are useful surrogates for patient samples, the physiological relevance of observed molecular phenotypes in cell lines remains controversial. Because transcriptome data are a representative set of molecular phenotypes in cancers, we systematically analyzed the discrepancy of global gene expression profiles between patient samples and cell lines in breast cancers. While the majority of genes exhibited general consistency between patient samples and cell lines, the expression of genes in the categories of extracellular matrix, collagen trimers, receptor activity, catalytic activity and transporter activity were significantly up-regulated only in tissue samples. Genes in the extracellular matrix, particularly collagen trimers, showed a wide variation of expression in tissue, but minimal expression and variation in cell lines. Further analysis of tissue samples exclusively revealed that collagen genes exhibited a cancer stage-dependent expressional variation based on their supramolecular structure. Prognostic collagen biomarkers associated with survival rate were also readily predicted from tissue-oriented transcriptome analysis. This study presents the limitations of cell lines and the exclusive features of tissue samples in terms of functional categories of the cancer transcriptome.

journal_name

Biochem Biophys Res Commun

journal_title

Biochemical and biophysical research communications

authors

Hong Y,Kim N,Li C,Jeong E,Yoon S

doi

10.1016/j.bbrc.2017.04.055

subject

Has Abstract

pub_date

2017-05-27 00:00:00

pages

307-312

issue

2

eissn

0006-291X

issn

1090-2104

pii

S0006-291X(17)30721-0

journal_volume

487

pub_type

杂志文章

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