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Differential analysis of core-fucosylated glycoproteomics enabled by single-step truncation of N-glycans

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Abstract

Alpha-1,6 fucosylation of N-glycans (core fucosylation, CF) represents a unique form of N-glycans and is widely involved in disease progression. In order to accurately identify CF glycoproteins, several approaches have been developed based on sequential cleavage with different glycosidases to truncate the N-glycans. Since multi-step sample treatments may introduce quantitation bias and affect the practicality of these approaches in large-scale applications. Here, we systematically evaluated the performance of the single-step treatment of intact glycopeptides by endoglycosidase F3 for CF glycoproteome. The single-step truncation (SST) strategy demonstrated higher quantitative stability and higher efficiency compared with previous approaches. The strategy was further practiced on both cell lines and serum samples. The dysregulation of CF glycopeptides between preoperative and postoperative serum from patients with pancreatic ductal adenocarcinoma was revealed, and the CF modifications of BCHE_N369, CDH5_N112 and SERPIND1_N49 were found to be potential prognostic markers. This study thus provides an efficient solution for large-scale quantitative analysis of the CF glycoproteome.

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The data in this article will be available on reasonable request to the corresponding author.

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Funding

This work was supported by the National Natural Science Foundation of China (32001048).

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Authors and Affiliations

  1. School of Basic Medical Science, Anhui Medical University, Hefei, 230032, China

    Yao Min & Wantao Ying

  2. Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, 102206, China

    Jianhui Wu, Xiaoya Guan & Chunyi Hao

  3. State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China

    Yao Min, Wenhao Hou, Xiaoyu Li, Xinyuan Zhao, Xiaohong Qian & Wantao Ying

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  1. Yao Min
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Correspondence to Chunyi Hao or Wantao Ying.

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The serum samples used in this study were obtained from the Peking University Cancer Hospital in China, with the approval of the Research Ethics Committee.

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Supplementary Material 1: Table S3. Glycopeptides identified by SST, HEE or HEP methods (XLSX)

Supplementary Material 2: Table S4. The CF glycopeptides differentially expressed between PANC-1 and BxPC-3 (XLSX)

10719_2023_10130_MOESM3_ESM.xlsx

Supplementary Material 3: Table S5. The proteins and site-specific CF glycopeptides differentially expressed between pre- and postoperative serum of patients with PDAC (XLSX)

Supplementary Material 4

Supplementary Material 5

Supplementary Material 6

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Min, Y., Wu, J., Hou, W. et al. Differential analysis of core-fucosylated glycoproteomics enabled by single-step truncation of N-glycans. Glycoconj J 40, 541–549 (2023). https://doi.org/10.1007/s10719-023-10130-x

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  • DOI: https://doi.org/10.1007/s10719-023-10130-x

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