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

Oncotarget
Ivana JovčevskaRadovan Komel

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 i...Continue Reading

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Citations

Mar 25, 2018·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Zhiqiang ChenXuehao Wang
Jan 10, 2019·International Journal of Molecular Sciences·Jun-Hua NieJia Liu
Aug 12, 2020·The FEBS Journal·Serge Muyldermans
Sep 24, 2019·Antibodies·Kasandra BélangerDanica Stanimirovic
Aug 31, 2017·Journal of Biomedical Science·Patrycja CzerwińskaMaciej Wiznerowicz
Apr 5, 2020·Cancers·Zhen Dong, Hongjuan Cui
Mar 10, 2018·Frontiers in Immunology·María Elena IezziGabriela Alicia Canziani
Nov 26, 2020·Annual Review of Animal Biosciences·Serge Muyldermans
Nov 15, 2020·International Journal of Molecular Sciences·Alja ZottelRadovan Komel
Mar 13, 2021·Frontiers in Immunology·Liangyu ChenJie Li

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Methods Mentioned

BETA
surgical resection
ELISA
pull-down
protein folding
size-exclusion chromatography
PCR

Software Mentioned

MASCOT
GraphPad
GraphPad Prism
DeSeq2
Multi Gauge
Firehose
NormFinder
OncoFinder

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