Oncotarget

Research Papers:

Differentially expressed proteins in glioblastoma multiforme identified with a nanobody-based anti-proteome approach and confirmed by OncoFinder as possible tumor-class predictive biomarker candidates

Ivana Jovčevska, Neja Zupanec, Žiga Urlep, Andrej Vranič, Boštjan Matos, Clara Limbaeck Stokin, Serge Muyldermans, Michael P. Myers, Anton A. Buzdin, Ivan Petrov and Radovan Komel _

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Oncotarget. 2017; 8:44141-44158. https://doi.org/10.18632/oncotarget.17390

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Abstract

Ivana Jovčevska1, Neja Zupanec1, Žiga Urlep2, Andrej Vranič3, Boštjan Matos4, Clara Limbaeck Stokin5, Serge Muyldermans6, Michael P. Myers7, Anton A. Buzdin8,9, Ivan Petrov10,11 and Radovan Komel1

1Medical Center for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia

2Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia

3Department of Neurosurgery, Foundation Rothschild, Paris, France

4Department of Neurosurgery, University Clinical Center, Ljubljana, Slovenia

5Institute of Histopathology, Charing Cross Hospital, London, United Kingdom

6Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium

7International Center for Genetic Engineering and Biotechnology, Trieste, Italy

8First Oncology Research and Advisory Center, Moscow, Russia

9National Research Center 'Kurchatov Institute', Center of Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia

10Center for Biogerontology and Regenerative Medicine, IC Skolkovo, Moscow, Russia

11Moscow Institute of Physics and Technology, Moscow, Russia

Correspondence to:

Radovan Komel, email: [email protected]

Ivana Jovčevska, email: [email protected]

Keywords: glioblastoma multiforme, biomarkers, nanobodies, cancer biology, OncoFinder

Received: September 14, 2016    Accepted: April 10, 2017    Published: April 24, 2017

ABSTRACT

Glioblastoma multiforme is the most frequent primary malignancy of the central nervous system. Despite remarkable progress towards an understanding of tumor biology, there is no efficient treatment and patient outcome remains poor. Here, we present a unique anti-proteomic approach for selection of nanobodies specific for overexpressed glioblastoma proteins. A phage-displayed nanobody library was enriched in protein extracts from NCH644 and NCH421K glioblastoma cell lines. Differential ELISA screenings revealed seven nanobodies that target the following antigens: the ACTB/NUCL complex, VIM, NAP1L1, TUFM, DPYSL2, CRMP1, and ALYREF. Western blots showed highest protein up-regulation for ALYREF, CRMP1, and VIM. Moreover, bioinformatic analysis with the OncoFinder software against the complete “Cancer Genome Atlas” brain tumor gene expression dataset suggests the involvement of different proteins in the WNT and ATM pathways, and in Aurora B, Sem3A, and E-cadherin signaling. We demonstrate the potential use of NAP1L1, NUCL, CRMP1, ACTB, and VIM for differentiation between glioblastoma and lower grade gliomas, with DPYSL2 as a promising “glioma versus reference” biomarker. A small scale validation study confirmed significant changes in mRNA expression levels of VIM, DPYSL2, ACTB and TRIM28. This work helps to fill the information gap in this field by defining novel differences in biochemical profiles between gliomas and reference samples. Thus, selected genes can be used to distinguish glioblastoma from lower grade gliomas, and from reference samples. These findings should be valuable for glioblastoma patients once they are validated on a larger sample size.


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