Title: Signal translational efficiency between mRNA expression and antibody-based protein expression for breast cancer and its subtypes from cell lines to tissue

Authors: Aida Yazdanparast; Lang Li; Milan Radovich; Lijun Cheng

Addresses: Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th Street, HS 5000, Indianapolis, IN 46202-5122, USA ' Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th Street, HS 5000, Indianapolis, IN 46202-5122, USA ' Department of Surgery, Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indiana University School of Medicine, 410 W. 10th Street, HS 5000, Indianapolis, IN 46202-5122, USA ' Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th Street, HS 5000, Indianapolis, IN 46202-5122, USA

Abstract: Background: Although gene transcripts and protein expression have been utilised to classify breast cancer subtypes, it is not clear whether the observed measurement of gene transcript abundance can predict its protein expression. Herein, we attempt to address gene transcript/protein associations using publically-available data on breast cancer tumour tissues and cell lines. Method: Correlation analysis between mRNAs and Reverse-phase protein arrays (RPPA) among 421 primary breast tumours and 33 breast cancer cell lines was conducted. Highly concordant proteins/genes were further analysed in different breast cancer subtypes. Results: The overall accordance of mRNA/RPPA correlation between cell lines and primary tissue is R² = 0.71. Since most of these genes are well known drug targets, highly concordant gene/RPPA associations not only confirm that these gene transcripts can serve as biomarkers for their protein products in drug target selection, but also imply that breast cancer cell lines can serve as good models for primary breast cancer tumours.

Keywords: breast cancer; reverse-phase protein array; mRNA; cell lines; protein abundance.

DOI: 10.1504/IJCBDD.2018.090833

International Journal of Computational Biology and Drug Design, 2018 Vol.11 No.1/2, pp.67 - 89

Received: 04 Apr 2017
Accepted: 04 Aug 2017
Published online: 28 Mar 2018 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article