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Zhao Z, Sun X, Cao L, Zhu C, He K, Hu X, Liu C, Feng Q, Qin Y. Salivary Proteome and Intact N-Glycopeptides Analysis Reveal Specific Signatures in Periodontitis. J Proteome Res 2024; 23:25-39. [PMID: 38088868 DOI: 10.1021/acs.jproteome.3c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Periodontitis is a prevalent oral inflammatory disease that can result in tooth loss and is closely linked to type 2 diabetes (T2D). In this study, we analyzed the salivary proteome and intact N-glycopeptides (IGPs) of individuals with mild-moderate, severe, aggressive periodontitis, and periodontitis with T2D, including those treated with antidiabetic drugs, to identify specific signatures associated with the disease. Our results revealed that salivary proteins and glycoproteins were altered in all periodontitis groups (PRIDE ID: 1-20230612-72345), with fucose- and sialic acid-containing N-glycans showing the greatest increase. Additionally, differentially expressed proteins were classified into 9 clusters, including those that were increased in all periodontitis groups and those that were only altered in certain types of periodontitis. Interestingly, treatment with antidiabetic drugs reversed many of the changes observed in the salivary proteome and IGPs in T2D-related periodontitis, suggesting a potential therapeutic approach for managing periodontitis in patients with T2D. Consistent with MS/MS results, the expression of salivary IGHA2 and Fucα1-3/6GlcNAc (AAL) was significantly increased in MP. These findings provide new insights into the pathogenesis of periodontitis and highlight the potential of salivary biomarkers for diagnosis, prognosis, and monitoring of disease progression and treatment response.
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Affiliation(s)
- Zhirong Zhao
- Department of Cell Biology and Genetics and Department of Pathogenic Microbiology & Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
- Xi'an Dian Medical Laboratory Co., Ltd., Xi'an, Shaanxi 710000, China
| | - Xiaoyu Sun
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Periodontology, Stomatologic Hospital & College, Anhui Medical University, Hefei 230032, China
| | - Li Cao
- Department of Cell Biology and Genetics and Department of Pathogenic Microbiology & Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Chunhui Zhu
- Department of Periodontology, College of Stomatology, Xi'an Jiaotong University, Xi'an 710069, China
| | - Kang He
- Department of Periodontology, College of Stomatology, Xi'an Jiaotong University, Xi'an 710069, China
| | - Xiaoyi Hu
- Department of Periodontology, College of Stomatology, Xi'an Jiaotong University, Xi'an 710069, China
| | - Chengcheng Liu
- Department of Cell Biology and Genetics and Department of Pathogenic Microbiology & Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Qiang Feng
- Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Department of Human Microbiome, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yannan Qin
- Department of Cell Biology and Genetics and Department of Pathogenic Microbiology & Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
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Wang Y, Tian Z. New Energy Setup Strategy for Intact N-Glycopeptides Characterization Using Higher-Energy Collisional Dissociation. J Am Soc Mass Spectrom 2020; 31:651-657. [PMID: 31967800 DOI: 10.1021/jasms.9b00089] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
With the optional setting of multiple stepped collisional energies (NCEs), higher-energy collisional dissociation (HCD) as available on Orbitrap instruments is a widely adopted dissociation method for intact N-glycopeptides characterization, where peptide backbones and N-glycan moieties are selectively fragmented at high and low NCEs, respectively. Initially, a dependent setting of a central value plus minus a variation is available to the users to set up NCEs, and the combination of 30 ± 10% to give the energies 20%/30%/40% has been mostly adopted in the literature. With the recent availability of an independent NCEs setup, we found that the combination of 20%/30%/30% is better than 20%/30%/40%; in the analysis of complex intact N-glycopeptides enriched from gastric cancer tissues, total IDs with spectrum-level FDR ≤ 1%, site-specific IDs with site-determining fragment ions, and structure-specific IDs with structure-diagnostic fragment ions were increased by 42% (4,767 → 6,746), 57% (599 → 942), and 97% (1771 → 3495), respectively. This finding will benefit all the coming N-glycoproteomics studies using HCD as the dissociation method.
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Affiliation(s)
- Yue Wang
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
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