Proteomic and N-glycoproteomic analyses of total subchondral bone protein in patients with primary knee osteoarthritis

N-glycosylation is an important post-translational modification necessary to maintain the structural and functional properties of proteins. Impaired N-glycosylation has been observed in several diseases. It is significantly modified by the state of cells and is used as a diagnostic or prognostic indicator for multiple human diseases, including cancer and osteoarthritis (OA). Aim of the study was to explore the N-glycosylation levels of subchondral bone proteins in patients with primary knee OA (KOA) and screen for potential biological markers for the diagnosis and treatment of primary KOA. A comparative analysis of total protein N-glycosylation under the cartilage was performed in medial subchondral bone (MSB, N  = 5) and lateral subchondral bone (LSB, N = 5) specimens from female patients with primary KOA. To analyse the N-glycosylation sites of the proteins, non-labelled quantitative proteomic and N-glycoproteomic analyses were performed based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) data. Parallel reaction monitoring (PRM) validation experiments were carried out on differential N-glycosylation sites of proteins in selected specimens, including MSB ( N  = 5) and LSB (N = 5), from patients with primary KOA. In total, 1149 proteins with 1369 unique N-chain glycopeptides were detected, and 1215 N-glycosylation sites were found, in which ptmRS scores for 1163 N-glycosylation sites were ≥ 0.9. In addition, N-glycosylation of the total protein in MSB compared to that in LSB was identified, in which 295 N-glycosylation sites were significantly different, including 75 upregulated and 220 downregulated N-glycosylation sites in MSB samples. Importantly, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses of proteins with differential N-glycosylation sites showed that they were primarily associated with metabolic pathways including ECM-receptor interactions, focal adhesion, protein digestion and absorption, amoebiasis, and complement and coagulation cascades. Finally, PRM experiments confirmed the N-glycosylation sites of collagen type VI, alpha 3 (COL6A3, VAVVQHAPSESVDN[+3]ASMPPVK), aggrecan core protein (ACAN, FTFQEAAN[+3]EC[+57]R, TVYVHAN[+3]QTGYPDPSSR), laminin subunit gamma-1 (LAMC1, IPAIN[+3]QTITEANEK), matrix-remodelling-associated protein 5 (MXRA5, ITLHEN[+3]R), cDNA, FLJ92775, highly similar to Homo sapiens melanoma cell adhesion molecule (MCAM), mRNA(B2R642, C[+57]VASVPSIPGLN[+3]R), and aminopeptidase fragment (Q59E93, AEFN[+3]ITLIHPK) in the array data of the top 20 N-glycosylation sites. These abnormal N-glycosylation patterns provide reliable insights for the development of diagnostic and therapeutic methods for primary KOA.