Potential biomarkers and drug targets in glycoproteome of MCF-7 breast cancer cells based on proteomics and bioinformatics strategies Running title: Protein drug targets in MCF-7 cell line

Abstract

Identifying differentially expressed glycoproteins (DEGs) during cancer progression is an excellent approach to discovering novel biomarkers. The current study investigated detected DEGs in the breast cancer MCF-7 cell line due to finding candidate drug targets and biomarkers. DEGs, using DAVID and Gene Ontology databases, are categorized into three main classes of proteins involved in cancer progression, including receptor proteins, proteins involved in endocytosis, and metastasis. UALCAN database was used for validation and analyze the expression levels of the identified proteins in breast cancer tissue. The protein-protein interaction (PPI) network of DEGs was constructed using the STRING database and analyzed using Cytoscape software. Four up-regulated receptor proteins in the MCF-7 cell line were enriched as follows: CD239, CD55, CD47, and CD112. Gal-3BP and vitronectin proteins involved in endocytosis also showed upregulation in the MCF-7 cell line. CTSD and DPPII were determined as overexpressed proteases in the MCF-7 cell line, which are involved in breast cancer metastasis. Ten glycoproteins were identified only in MCF-7 cells, including APOD, BCAM, CLU, IFI30, GRN, LYPD3, NAAA, PODXL, SEZ6L2, and VTN. Among them, the APOD is expressed at much higher levels (191-fold) in MCF-7 cells versus normal cells. PPI network analysis also demonstrated FN1 and ITGB1 as hub proteins. Our analysis of DEGs in the MCF-7 cells, integrated with data from the UALCAN database, highlighted glycoproteins that can be considered as diagnostic or prognostic biomarkers or potential therapeutic molecular targets.