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Yang H, Tian Z. Analysis of mutation-originated gain-of-glycosylation using mass spectrometry-based N-glycoproteomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9838. [PMID: 38924612 DOI: 10.1002/rcm.9838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024]
Abstract
RATIONALE A general N-glycoproteomics analysis pipeline has been established for characterization of mutation-related gain-of-glycosylation (GoG) at intact N-glycopeptide molecular level, generating comprehensive site and structure information of N-glycosylation. METHODS This study focused on mutation-originated GoG using a mass spectrometry-based N-glycoproteomics analysis workflow. In brief, GoG intact N-glycopeptide databases were built, consisting of 2701 proteins (potential GoG N-glycosites and amino acids derived from MUTAGEN, VARIANT and VAR_SEQ in UniProt) and 6709 human N-glycans (≤50 sequence isomers per monosaccharide composition). We employed the site- and structure-specific N-glycoproteomics workflow utilizing intact N-glycopeptides search engine GPSeeker to identify GoG intact N-glycopeptides from parental breast cancer stem cells (MCF-7 CSCs) and adriamycin-resistant breast cancer stem cells (MCF-7/ADR CSCs). RESULTS With the criteria of spectrum-level false discovery rate control of ≤1%, we identified 87 and 94 GoG intact N-glycopeptides corresponding to 37 and 35 intact N-glycoproteins from MCF-7 CSCs and MCF-7/ADR CSCs, respectively. Micro-heterogeneity and macro-heterogeneity of N-glycosylation from GoG intact N-glycoproteins with VAR_SEQ and VARIANT were found in both MCF-7 CSCs and MCF-7/ADR CSCs systems. CONCLUSIONS The integration of site- and structure-specific N-glycoproteomics approach, conjugating with GoG characterization, provides a universal workflow for revealing comprehensive N-glycosite and N-glycan structure information of GoG. The analysis of mutation-originated GoG can be extended to GoG characterization of other N-glycoproteome systems including complex clinical tissues and body fluids.
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Affiliation(s)
- Hailun Yang
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China
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Bi M, Tian Z. Mass spectrometry-based structure-specific N-glycoproteomics and biomedical applications. Acta Biochim Biophys Sin (Shanghai) 2024; 56:1172-1183. [PMID: 39118567 DOI: 10.3724/abbs.2024133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
N-linked glycosylation is a common posttranslational modification of proteins that results in macroheterogeneity of the modification site. However, unlike simpler modifications, N-glycosylation introduces an additional layer of complexity with tens of thousands of possible structures arising from various dimensions, including different monosaccharide compositions, sequence structures, linking structures, isomerism, and three-dimensional conformations. This results in additional microheterogeneity of the modification site of N-glycosylation, i.e., the same N-glycosylation site can be modified with different glycans with a certain stoichiometric ratio. N-glycosylation regulates the structure and function of N-glycoproteins in a site- and structure-specific manner, and differential expression of N-glycosylation under disease conditions needs to be characterized through site- and structure-specific quantitative analysis. Numerous advanced methods ranging from sample preparation to mass spectrum analysis have been developed to distinguish N-glycan structures. Chemical derivatization of monosaccharides, online liquid chromatography separation and ion mobility spectrometry enable the physical differentiation of samples. Tandem mass spectrometry further analyzes the macro/microheterogeneity of intact N-glycopeptides through the analysis of fragment ions. Moreover, the development of search engines and AI-based software has enhanced our understanding of the dissociation patterns of intact N-glycopeptides and the clinical significance of differentially expressed intact N-glycopeptides. With the help of these modern methods, structure-specific N-glycoproteomics has become an important tool with extensive applications in the biomedical field.
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Naveed M, Javed K, Aziz T, Abid A, Rehman HM, Alharbi M, Alshammari A, Alasmari AF. Optimizing the resveratrol fragments for novel in silico hepatocellular carcinoma de novo drug design. Sci Rep 2024; 14:17336. [PMID: 39068301 PMCID: PMC11283494 DOI: 10.1038/s41598-024-68403-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024] Open
Abstract
Hepatocellular carcinoma (HCC) incidence varies widely around the world and is impacted by factors such as the prevalence of chronic hepatitis B and C infections, alcohol intake, and access to healthcare. The proteins (BRAF_human, VGFR3_human, EGFR_human and UFO_human) play a vital role in hepatocellular carcinoma prognosis, which involves cell proliferation, cell growth, transmission of extracellular signals to the cell nucleus and consequently regulating many other cellular processes. Fostamatinib has been studied for its possible use in the treatment of hepatocellular cancer because it is a more convenient therapy choice for patients and has minor side effects on the human body. However, resveratrol phytochemical has been investigated for its potential use in the prevention and treatment of a wide range of disorders, including cancer, cardiovascular disease, diabetes, and neurological problems due to its frequently antioxidant, anti-inflammatory, and immune-modulating characteristics, which can aid in the prevention of chronic illnesses. This study developed de novo-based fragment-optimized resveratrol (FOR), enhancing therapeutic potential and lowering toxicity. The docking study was performed with four target proteins, and the findings reveal that the vascular endothelial growth factor receptor 3 protein possessed the highest binding energy values of -7.6 kcal/mol with FOR. Additionally, it completely fulfills the criteria of drug-likeliness rules. Thus, FOR proves to be an efficient drug candidate for future in-vivo studies against hepatocellular carcinoma.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590, Punjab, Pakistan.
| | - Khushbakht Javed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590, Punjab, Pakistan
| | - Tariq Aziz
- Laboratory of Animal Health Hygiene and Quality, University of Ioannina, 47132, Arta, Greece.
| | - Amina Abid
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590, Punjab, Pakistan
| | - Hafiz Muzzammel Rehman
- Department of Biological Sciences, Faculty of Sciences, Superior University, Lahore, 54590, Punjab, Pakistan
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, PO Box 11451, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, PO Box 11451, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, PO Box 11451, Riyadh, Saudi Arabia
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Yang H, Xu F, Chen Y, Tian Z. Structural N-glycoproteomics characterization of cell-surface N-glycosylation of MCF-7/ADR cancer stem cells. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1219:123647. [PMID: 36870092 DOI: 10.1016/j.jchromb.2023.123647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
Breast cancer is responsible for the highest mortality all over the world. Cancer stem cells (CSCs) along with epithelial mesenchymal transition (EMT) are identified as a driver of cancer which are responsible for cancer metastasis and drug resistance. Several signaling pathways are associated with drug resistance. Additionally, glycosyltransferases regulate different types of glycosylation which are involved in drug resistance. To the end, it is urgent to figure out the knowledge on cell-surface altered N-glycosylation and putative markers. Here, differential cell-surface intact N-glycopeptides in adriamycin (ADR)-resistant michigan breast cancer foundation-7 stem cells (MCF-7/ADR CSCs) relative to ADR-sensitive MCF-7 CSCs were analyzed with site- and structure-specific quantitative N-glycoproteomics. The intact N-glycopeptides and differentially expressed intact N-glycopeptides (DEGPs) were determined and quantified via intact N-glycopeptide search engine GPSeeker. Totally, 4777 intact N-glycopeptides were identified and N-glycan sequence structures among 2764 IDs were distinguished from their isomers by structure-diagnostic fragment ions. Among 1717 quantified intact N-glycopeptides, 104 DEGPs were determined (fold change ≥ 1.5 and p value < 0.05). Annotation of protein-protein interaction and biological processes among others of DEGPs were finally carried out; down-regulated intact N-glycopeptide with bisecting GlcNAc from p38-interacting protein and up-regulated intact N-glycopeptide with β1,6-branching N-glycan from integrin beta-5 were found.
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Affiliation(s)
- Hailun Yang
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, 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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Yang W, Jiang Y, Guo Q, Tian Z, Cheng Z. Aberrant N-glycolylneuraminic acid in breast MCF-7 cancer cells and cancer stem cells. Front Mol Biosci 2022; 9:1047672. [DOI: 10.3389/fmolb.2022.1047672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022] Open
Abstract
N-Glycolylneuraminic acid (Neu5Gc) is not normally detected in humans because humans lack the hydroxylase enzyme that converts cytidine-5′-monophosphate-N-acetylneuraminic acid (CMP-Neu5Ac) to CMP-Neu5Gc; thus, any Neu5Gc appearing in the human body is aberrant. Neu5Gc has been observed in human cancer cells and tissues. Moreover, antibodies against Neu5Gc have been detected in healthy humans, which are obstacles to clinical xenotransplantation and stem cell therapies. Thus, the study of Neu5Gc in humans has important pathological and clinical relevance. Here, we report the N-glycoproteomics characterization of aberrant Neu5Gc in breast MCF-7 cancer cells and cancer stem cells (CSCs) at the molecular level of intact N-glycopeptides, including comprehensive information (peptide backbones, N-glycosites, N-glycan monosaccharide compositions, and linkage structures) based on a target-decoy theoretical database search strategy and a spectrum-level false discovery rate (FDR) control ≤1%. The existence of Neu5Gc on N-glycan moieties was further confirmed according to its characteristic oxonium fragment ions in the MS/MS spectra of either m/z 308.09816 (Neu5Gc) or 290.08759 (Neu5Gc-H2O). The results are an important addition to previously reported Neu5Ac data and can be further validated with targeted MS methods such as multiple and parallel reaction monitoring and biochemical methods such as immunoassays. This MS-based N-glycoproteomics method can be extended to the discovery and characterization of putative aberrant Neu5Gc in other biological and clinical systems.
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Qin S, Qin S, Tian Z. Comprehensive site- and structure-specific characterization of N-glycosylation in model plant Arabidopsis using mass-spectrometry-based N-glycoproteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1198:123234. [DOI: 10.1016/j.jchromb.2022.123234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/12/2022] [Accepted: 03/28/2022] [Indexed: 02/05/2023]
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Su P, Li M, Li X, Yuan X, Gong Z, Wu L, Song J, Yang Y. Glutathione functionalized magnetic covalent organic frameworks with dual-hydrophilicity for highly efficient and selective enrichment of glycopeptides. J Chromatogr A 2022; 1667:462869. [DOI: 10.1016/j.chroma.2022.462869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/19/2022] [Accepted: 01/31/2022] [Indexed: 12/31/2022]
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Fang P, Ji Y, Oellerich T, Urlaub H, Pan KT. Strategies for Proteome-Wide Quantification of Glycosylation Macro- and Micro-Heterogeneity. Int J Mol Sci 2022; 23:ijms23031609. [PMID: 35163546 PMCID: PMC8835892 DOI: 10.3390/ijms23031609] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/03/2022] Open
Abstract
Protein glycosylation governs key physiological and pathological processes in human cells. Aberrant glycosylation is thus closely associated with disease progression. Mass spectrometry (MS)-based glycoproteomics has emerged as an indispensable tool for investigating glycosylation changes in biological samples with high sensitivity. Following rapid improvements in methodologies for reliable intact glycopeptide identification, site-specific quantification of glycopeptide macro- and micro-heterogeneity at the proteome scale has become an urgent need for exploring glycosylation regulations. Here, we summarize recent advances in N- and O-linked glycoproteomic quantification strategies and discuss their limitations. We further describe a strategy to propagate MS data for multilayered glycopeptide quantification, enabling a more comprehensive examination of global and site-specific glycosylation changes. Altogether, we show how quantitative glycoproteomics methods explore glycosylation regulation in human diseases and promote the discovery of biomarkers and therapeutic targets.
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Affiliation(s)
- Pan Fang
- Department of Biochemistry and Molecular Biology, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China;
| | - Yanlong Ji
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
| | - Thomas Oellerich
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (H.U.); (K.-T.P.)
| | - Kuan-Ting Pan
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
- Correspondence: (H.U.); (K.-T.P.)
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