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Anal Chem. 2018 May 15;90(10):6307-6313. doi: 10.1021/acs.analchem.8b01090. Epub 2018 Apr 23.

Analytical Pipeline for Discovery and Verification of Glycoproteins from Plasma-Derived Extracellular Vesicles as Breast Cancer Biomarkers.

Author information

1
Department of Biochemistry , Purdue University , West Lafayette , Indiana 47907 , United States.
2
Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States.
3
Department of Medicinal Chemistry & Molecular Pharmacology , Purdue University , West Lafayette , Indiana 47907 , United States.
4
Purdue Center for Cancer Research , Purdue University , West Lafayette , Indiana 47907 , United States.
5
Tymora Analytical Operations , West Lafayette , Indiana 47906 , United States.
6
Shanghai Cancer Center and Institutes of Biomedical Sciences , Fudan University , Shanghai 200032 , China.

Abstract

Glycoproteins comprise more than half of current FDA-approved protein cancer markers, but the development of new glycoproteins as disease biomarkers has been stagnant. Here we present a pipeline to develop glycoproteins from extracellular vesicles (EVs) through integrating quantitative glycoproteomics with a novel reverse phase glycoprotein array and then apply it to identify novel biomarkers for breast cancer. EV glycoproteomics show promise in circumventing the problems plaguing current serum/plasma glycoproteomics and allowed us to identify hundreds of glycoproteins that have not been identified in blood. We identified 1,453 unique glycopeptides representing 556 glycoproteins in EVs, among which 20 were verified significantly higher in individual breast cancer patients. We further applied a novel glyco-specific reverse phase protein array to quantify a subset of the candidates. Together, this study demonstrates the great potential of this integrated pipeline for biomarker discovery.

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