Comparative glycoproteomics study on the surface of SKOV3 versus IOSE80 cell lines

Abstract

Objective: Site- and structure-specific quantitative N-glycoproteomics study of differential cell-surface N-glycosylation of ovarian cancer SKOV3 cells with the non-cancerous ovarian epithelial IOSE80 cells as the control.Methods: C18-RPLC-MS/MS (HCD with stepped normalized collision energies) was used to analyze the 1: 1 mixture of labeled intact N-glycopeptides from SKOV3 and IOSE80 cells, and the site- and structure-specific intact N-glycopeptide search engine GPSeeker was used to conduct qualitative and quantitative search on the obtained raw datasets.Results: With the control of the spectrum-level false discovery rate ≤1%, 13,822 glycopeptide spectral matches coming from 2,918 N-glycoproteins with comprehensive N-glycosite and N-glycan structure information were identified; 3,733 N-glycosites and 3,754 N-glycan sequence structures were confirmed by site-determining and structure-diagnostic fragment ions, respectively. With the control of no less than two observations among the three technical replicates, fold change ≥1.5, and p-value ≤ 0.05, 746 DEPGs in SKOV3 cells relative to IOSE80 cells were quantified, where 421 were upregulated and 325 downregulated.Conclusion: Differential cell-surface N-glycosylation of ovarian cancer SKOV3 cells were quantitatively analyzed by isotopic labeling and site- and structure-specific N-glycoproteomics. This discovery study provides putative N-glycoprotein biomarker candidates for future validation study using multiple reaction monitoring and biochemical methods.

Dual-Aptamer Recognition of DNA Logic Gate Sensor-Based Specific Exosomal Proteins for Ovarian Cancer Diagnosis

“…To verify the specificity of the DNA ternary polymer for ovarian cancer exosome recognition, we evaluated its response to exosomes from diverse sources. Human normal ovarian cells (IOSE80) that expressed no EpCAM or CD24, 42 human cervical cancer cells (Hela) that expressed CD24 only, 43 and mouse breast cancer cells (4T1) that expressed EpCAM only 44 were selected as control groups. As shown in Figure S9, the polymer yielded significantly lower CL signals for exosomes secreted by IOSE, HeLa, or 4T1 compared to SKOV3 exosomes.…”