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Breast Cancer Research and Treatment

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Open Access 01-06-2019 | Mastectomy | Preclinical study

Comparison of protein expression between formalin-fixed core-cut biopsies and surgical excision specimens using a novel multiplex approach

Authors: Mariana Ferreira Leal, Ben P. Haynes, Fiona A. MacNeill, Andrew Dodson, Mitch Dowsett

Published in: Breast Cancer Research and Treatment | Issue 2/2019

Abstract

Purpose

We evaluated whether multiplex protein quantification using antibody bar-coding with photocleavable oligonucleotides (NanoString) can be applied to evaluate protein expression in breast cancer FFPE specimens. We also assessed whether diagnostic core-cuts fixed immediately at time of procedures and surgical excision sections from routinely fixed breast cancers are affected by the same fixation related differences noted using immunohistochemistry (IHC).

Methods

The expression of 26 proteins was analysed using NanoString technology in 16 pairs of FFPE breast cancer core-cuts and surgical excisions. The measurements yielded were compared with those by IHC on Ki67, PgR and HER2 biomarkers and pAKT and pERK1/2 phosphorylated proteins.

Results

When considered irrespective of sample type, expression measured by the two methods was strongly correlated for all markers (p < 0.001; ρ = 0.69–0.88). When core-cuts and excisions were evaluated separately, the correlations between NanoString and IHC were weaker but significant except for pAKT in excisions. Surgical excisions showed lower levels of 8/12 phosphoproteins and higher levels of 4/13 non-phosphorylated proteins in comparison to core-cuts (p < 0.01). Reduced p4EBP1, pAMPKa, pRPS6 and pRAF1 immunogenicity in excisions was correlated with tumour size and mastectomy specimens showed lower p4EBP1 and pRPS6 expression than lumpectomy (p < 0.05).

Conclusions

Our study supports the validity of the new multiplex approach to protein analysis but indicates that, as with IHC, caution is necessary for the analysis in excisions particularly of phosphoproteins. The specimen type, tumour size and surgery type may lead to biases in the quantitative analysis of many proteins of biologic and clinical interest in excision specimens.

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Title: Comparison of protein expression between formalin-fixed core-cut biopsies and surgical excision specimens using a novel multiplex approach
Authors: Mariana Ferreira Leal
Ben P. Haynes
Fiona A. MacNeill
Andrew Dodson
Mitch Dowsett
Publication date: 01-06-2019
Publisher: Springer US
Keywords: Mastectomy
Breast Cancer
Breast Cancer
Published in: Breast Cancer Research and Treatment / Issue 2/2019
Print ISSN: 0167-6806
Electronic ISSN: 1573-7217
DOI: https://doi.org/10.1007/s10549-019-05163-6

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Abstract

Purpose

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Conclusions

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