Clinical utility of reverse phase protein array for molecular classification of breast cancer

Negm, Ola H. and Muftah, Abir A. and Aleskandarany, Mohammed A. and Hamed, Mohamed R. and Ahmad, Dena A.J. and Nolan, Christopher C. and Diez-Rodriguez, Maria and Tighe, Patrick J. and Ellis, Ian O. and Rakha, Emad A. and Green, Andrew R. (2016) Clinical utility of reverse phase protein array for molecular classification of breast cancer. Breast Cancer Research and Treatment, 155 (1). pp. 25-35. ISSN 1573-7217

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Abstract

Reverse Phase Protein Array (RPPA) represents a sensitive and high-throughput technique allowing simultaneous quantitation of protein expression levels in biological samples. This study aimed to confirm the ability of RPPA to classify archival formalin-fixed paraffin-embedded (FFPE) breast cancer tissues into molecular classes used in the Nottingham prognostic index plus (NPI+) determined by immunohistochemistry (IHC). Proteins were extracted from FFPE breast cancer tissues using three extraction protocols: the Q-proteome FFPE Tissue Kit (Qiagen, Hilden, Germany) and two in-house methods using Laemmli buffer with either incubation for 20 min or 2 h at 105 °C. Two preparation methods, full-face sections and macrodissection, were used to assess the yield and quality of protein extracts. Ten biomarkers used for the NPI+ (ER, PgR, HER2, Cytokeratins 5/6 and 7/8, EGFR, HER3, HER4, p53 and Mucin 1) were quantified using RPPA and compared to results determined by IHC. The Q-proteome FFPE Tissue Kit produced significantly higher protein concentration and signal intensities. The intra- and inter-array reproducibility assessment indicated that RPPA using FFPE lysates was a highly reproducible and robust technique. Expression of the biomarkers individually and in combination using RPPA was highly consistent with IHC results. Macrodissection of the invasive tumour component gave more reliable results with the majority of biomarkers determined by IHC, (80 % concordance) compared with full-face sections (60 % concordance). Our results provide evidence for the technical feasibility of RPPA for high-throughput protein expression profiling of FFPE breast cancer tissues. The sensitivity of the technique is related to the quality of extracted protein and purity of tumour tissue. RPPA could provide a quantitative technique alternative to IHC for the biomarkers used in the NPI+.

Item Type: Article
Schools/Departments: University of Nottingham, UK > Faculty of Medicine and Health Sciences > School of Medicine > Division of Medical Sciences and Graduate Entry Medicine
Identification Number: 10.1007/s10549-015-3654-2
Depositing User: Negm, Ola
Date Deposited: 19 Jul 2017 10:31
Last Modified: 19 Jul 2017 10:35
URI: http://eprints.nottingham.ac.uk/id/eprint/44244

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