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Comparative Study
. 2006;8(4):R51.
doi: 10.1186/bcr1542.

Comparison of gene expression profiles in core biopsies and corresponding surgical breast cancer samples

Rosanna Zanetti-Dällenbach  1 , Vincent Vuaroqueaux, Edward Wight, Martin Labuhn, Gad Singer, Patrick Urban, Urs Eppenberger, Wolfgang Holzgreve, Serenella Eppenberger-Castori
Affiliations
Comparative Study

Comparison of gene expression profiles in core biopsies and corresponding surgical breast cancer samples

Rosanna Zanetti-Dällenbach et al. Breast Cancer Res. 2006.

Abstract

Introduction: Gene expression profiling has been successfully used to classify breast cancer into clinically distinct subtypes, and to predict the risk of recurrence and treatment response. The aim of this study was to investigate whether the gene expression profile (GEP) detected in a core biopsy (CB) is representative for the entire tumor, since CB is an important tool in breast cancer diagnosis. Moreover, we investigated whether performing CBs prior to the surgical excision could influence the GEP of the respective tumor.

Methods: We quantified the RNA expression of 60 relevant genes by quantitative real-time PCR in paired CBs and surgical specimens from 22 untreated primary breast cancer patients. Subsequently, expression data were compared with independent GEPs obtained from tumors of 317 patients without preceding CB.

Results: In 82% of the cases the GEP detected in the CB correlated very well with the corresponding profile in the surgical sample (rs > or = 0.95, p < 0.001). Gene-by-gene analysis revealed four genes significantly elevated in the surgical sample compared to the CB; these comprised genes mainly involved in inflammation and the wound repair process as well as in tumor invasion and metastasis.

Conclusion: A GEP detected in a CB are representative for the entire tumor and is, therefore, of clinical relevance. The observed alterations of individual genes after performance of CB deserve attention since they might impact the clinical interpretation with respect to prognosis and therapy prediction of the GEP as detected in the surgical specimen following CB performance.

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Figures

Figure 1
Figure 1
Unsupervised hierarchical clustering of paired core biopsy and surgical tumor tissue samples (Spearman correlation, average linkage). Red color indicates high expression levels (low ΔCt) and green vice versa. Patients 6, 11 and 20 had two core biopsies taken that were analyzed separately. In four cases the paired gene expression profiles did not cluster together close to each other.
Figure 2
Figure 2
Correlation between the gene expression profiles (60 genes) of paired core biopsies (CB) and surgical tumor tissue specimens (ST). (a) Specimens from patient 2 (rs = 0.98), as representative for 82% of all cases. (b) Specimens from patient 12, as representative for less correlated paired gene expression profiles (rs = 0.86).
Figure 3
Figure 3
Box plots displaying the changes in the expression of each gene in the surgical specimens (ST) compared to the respective core biopsies (CB).
Figure 4
Figure 4
Notch box plots of the expression levels of plasminogen activator inhibitor (PAI)-1, cyclooxygenase (COX)-2 and HER-2 as detected (a) in 317 independent surgical specimens of primary breast cancer patients who did not undergo previous diagnosis by core biopsy, (b) in the core biopsy of the 21 patients entering this study, and (c) in the corresponding surgical excisions.
See this image and copyright information in PMC

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