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Pham NT, Zhang Y, Rakkiyappan R, Manavalan B. HOTGpred: Enhancing human O-linked threonine glycosylation prediction using integrated pretrained protein language model-based features and multi-stage feature selection approach. Comput Biol Med 2024; 179:108859. [PMID: 39029431 DOI: 10.1016/j.compbiomed.2024.108859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/19/2024] [Accepted: 07/06/2024] [Indexed: 07/21/2024]
Abstract
O-linked glycosylation is a complex post-translational modification (PTM) in human proteins that plays a critical role in regulating various cellular metabolic and signaling pathways. In contrast to N-linked glycosylation, O-linked glycosylation lacks specific sequence features and maintains an unstable core structure. Identifying O-linked threonine glycosylation sites (OTGs) remains challenging, requiring extensive experimental tests. While bioinformatics tools have emerged for predicting OTGs, their reliance on limited conventional features and absence of well-defined feature selection strategies limit their effectiveness. To address these limitations, we introduced HOTGpred (Human O-linked Threonine Glycosylation predictor), employing a multi-stage feature selection process to identify the optimal feature set for accurately identifying OTGs. Initially, we assessed 25 different feature sets derived from various pretrained protein language model (PLM)-based embeddings and conventional feature descriptors using nine classifiers. Subsequently, we integrated the top five embeddings linearly and determined the most effective scoring function for ranking hybrid features, identifying the optimal feature set through a process of sequential forward search. Among the classifiers, the extreme gradient boosting (XGBT)-based model, using the optimal feature set (HOTGpred), achieved 92.03 % accuracy on the training dataset and 88.25 % on the balanced independent dataset. Notably, HOTGpred significantly outperformed the current state-of-the-art methods on both the balanced and imbalanced independent datasets, demonstrating its superior prediction capabilities. Additionally, SHapley Additive exPlanations (SHAP) and ablation analyses were conducted to identify the features contributing most significantly to HOTGpred. Finally, we developed an easy-to-navigate web server, accessible at https://balalab-skku.org/HOTGpred/, to support glycobiologists in their research on glycosylation structure and function.
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Affiliation(s)
- Nhat Truong Pham
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Gyeonggi-do, Republic of Korea
| | - Ying Zhang
- Beidahuang Industry Group General Hospital, Harbin, China
| | - Rajan Rakkiyappan
- Department of Mathematics, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India.
| | - Balachandran Manavalan
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Gyeonggi-do, Republic of Korea.
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Atashi M, Jiang P, Nwaiwu J, Gutierrez Reyes CD, Nguyen HMT, Li Y, Ahmadi P, Purba WT, Mechref Y. 15N metabolic labeling-TMT multiplexing approach to facilitate the quantitation of glycopeptides derived from cell lines. Anal Bioanal Chem 2024; 416:4071-4082. [PMID: 38958703 DOI: 10.1007/s00216-024-05352-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 07/04/2024]
Abstract
The study of glycoproteomics presents a set of unique challenges, primarily due to the low abundance of glycopeptides and their intricate heterogeneity, which is specific to each site. Glycoproteins play a crucial role in numerous biological functions, including cell signaling, adhesion, and intercellular communication, and are increasingly recognized as vital markers in the diagnosis and study of various diseases. Consequently, a quantitative approach to glycopeptide research is essential. One effective strategy to address this need is the use of multiplex glycopeptide labeling. By harnessing the synergies of 15N metabolic labeling via the isotopic detection of amino sugars with glutamine (IDAWG) technique for glycan parts and tandem mass tag (TMT)pro labeling for peptide backbones, we have developed a method that allows for the accurate quantification and comparison of multiple samples simultaneously. The adoption of the liquid chromatography-synchronous precursor selection (LC-SPS-MS3) technique minimizes fragmentation interference, enhancing data reliability, as shown by a 97% TMT labeling efficiency. This method allows for detailed, high-throughput analysis of 32 diverse samples from 231BR cell lines, using both 14N and 15N glycopeptides at a 1:1 ratio. A key component of our methodology was the precise correction for isotope and TMTpro distortions, significantly improving quantification accuracy to less than 5% distortion. This breakthrough enhances the efficiency and accuracy of glycoproteomic studies, increasing our understanding of glycoproteins in health and disease. Its applicability to various cancer cell types sets a new standard in quantitative glycoproteomics, enabling deeper investigation into glycopeptide profiles.
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Affiliation(s)
- Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Judith Nwaiwu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | | | - Hanh Minh Thu Nguyen
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Yunxiang Li
- Division of Chemistry and Biochemistry, Texas Woman's University, Denton, TX, 76204, USA
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Waziha Tasnim Purba
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA.
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3
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Tian Y, Ma S, Wen L. Towards chemoenzymatic labeling strategies for profiling protein glycosylation. Curr Opin Chem Biol 2024; 80:102460. [PMID: 38678979 DOI: 10.1016/j.cbpa.2024.102460] [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: 12/26/2023] [Revised: 03/31/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024]
Abstract
Protein glycosylation is one of the most common and important post-translational modifications of proteins involved in regulating glycoprotein functions. The chemoenzymatic glycan labeling strategy allows rapid, efficient, and selective interrogation of glycoproteins. Glycoproteomics identifies protein glycosylation events at a large scale, providing information such as peptide sequences, glycan structures, and glycosylated sites. This review discusses the recent development of chemoenzymatic labeling strategies for glycoprotein analysis, mainly including glycoprotein and glycosite profiling. Furthermore, we highlight the chemoenzymatic enrichment approaches in mass spectrometry analysis for three classes of glycan modifications, including N-glycosylation, O-GlcNAcylation, and mucin-type O-glycosylation. Finally, we highlight the emerging trends in new tools and cutting-edge technologies available for glycoproteomic research.
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Affiliation(s)
- Yinping Tian
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shengzhou Ma
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Liuqing Wen
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China.
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4
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Balbisi M, Sugár S, Turiák L. Protein glycosylation in lung cancer from a mass spectrometry perspective. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38576136 DOI: 10.1002/mas.21882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/27/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024]
Abstract
Lung cancer is a severe disease for which better diagnostic and therapeutic approaches are urgently needed. Increasing evidence implies that aberrant protein glycosylation plays a crucial role in the pathogenesis and progression of lung cancer. Differences in glycosylation patterns have been previously observed between healthy and cancerous samples as well as between different lung cancer subtypes, which suggests untapped diagnostic potential. In addition, understanding the changes mediated by glycosylation may shed light on possible novel therapeutic targets and personalized treatment strategies for lung cancer patients. Mass spectrometry based glycomics and glycoproteomics have emerged as powerful tools for in-depth characterization of changes in protein glycosylation, providing valuable insights into the molecular basis of lung cancer. This paper reviews the literature on the analysis of protein glycosylation in lung cancer using mass spectrometry, which is dominated by manuscripts published over the past 5 years. Studies analyzing N-glycosylation, O-glycosylation, and glycosaminoglycan patterns in tissue, serum, plasma, and rare biological samples of lung cancer patients are highlighted. The current knowledge on the potential utility of glycan and glycoprotein biomarkers is also discussed.
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Affiliation(s)
- Mirjam Balbisi
- MTA-TTK Lendület (Momentum) Glycan Biomarker Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Semmelweis University Doctoral School, Budapest, Hungary
| | - Simon Sugár
- MTA-TTK Lendület (Momentum) Glycan Biomarker Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Lilla Turiák
- MTA-TTK Lendület (Momentum) Glycan Biomarker Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
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5
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Pascoal C, Francisco R, Mexia P, Pereira BL, Granjo P, Coelho H, Barbosa M, dos Reis Ferreira V, Videira PA. Revisiting the immunopathology of congenital disorders of glycosylation: an updated review. Front Immunol 2024; 15:1350101. [PMID: 38550576 PMCID: PMC10972870 DOI: 10.3389/fimmu.2024.1350101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/26/2024] [Indexed: 04/02/2024] Open
Abstract
Glycosylation is a critical post-translational modification that plays a pivotal role in several biological processes, such as the immune response. Alterations in glycosylation can modulate the course of various pathologies, such as the case of congenital disorders of glycosylation (CDG), a group of more than 160 rare and complex genetic diseases. Although the link between glycosylation and immune dysfunction has already been recognized, the immune involvement in most CDG remains largely unexplored and poorly understood. In this study, we provide an update on the immune dysfunction and clinical manifestations of the 12 CDG with major immune involvement, organized into 6 categories of inborn errors of immunity according to the International Union of Immunological Societies (IUIS). The immune involvement in phosphomannomutase 2 (PMM2)-CDG - the most frequent CDG - was comprehensively reviewed, highlighting a higher prevalence of immune issues during infancy and childhood and in R141H-bearing genotypes. Finally, using PMM2-CDG as a model, we point to links between abnormal glycosylation patterns in host cells and possibly favored interactions with microorganisms that may explain the higher susceptibility to infection. Further characterizing immunopathology and unusual host-pathogen adhesion in CDG can not only improve immunological standards of care but also pave the way for innovative preventive measures and targeted glycan-based therapies that may improve quality of life for people living with CDG.
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Affiliation(s)
- Carlota Pascoal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Rita Francisco
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Patrícia Mexia
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Beatriz Luís Pereira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Pedro Granjo
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Helena Coelho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Mariana Barbosa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Vanessa dos Reis Ferreira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
| | - Paula Alexandra Videira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO– Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- CDG & Allies-Professionals and Patient Associations International Network, Caparica, Portugal
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Gan Q, Fan C. Orthogonal Translation for Site-Specific Installation of Post-translational Modifications. Chem Rev 2024; 124:2805-2838. [PMID: 38373737 PMCID: PMC11230630 DOI: 10.1021/acs.chemrev.3c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
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7
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Zou Y, Pronker MF, Damen JMA, Heck AJR, Reiding KR. Genotype-dependent N-glycosylation and newly exposed O-glycosylation affect plasmin-induced cleavage of histidine-rich glycoprotein (HRG). J Biol Chem 2024; 300:105683. [PMID: 38272220 PMCID: PMC10882129 DOI: 10.1016/j.jbc.2024.105683] [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: 09/06/2023] [Revised: 01/02/2024] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Histidine-rich glycoprotein (HRG) is an abundant plasma protein harboring at least three N-glycosylation sites. HRG integrates many biological processes, such as coagulation, antiangiogenic activity, and pathogen clearance. Importantly, HRG is known to exhibit five genetic variants with minor allele frequencies of more than 10%. Among them, Pro204Ser can induce a fourth N-glycosylation site (Asn202). Considerable efforts have been made to reveal the biological function of HRG, whereas data on HRG glycosylation are scarcer. To close this knowledge gap, we used C18-based LC-MS/MS to study the glycosylation characteristics of six HRG samples from different sources. We used endogenous HRG purified from human plasma and compared its glycosylation to that of the recombinant HRG produced in Chinese hamster ovary cells or human embryonic kidney 293 cells, targeting distinct genotypic isoforms. In endogenous plasma HRG, every N-glycosylation site was occupied predominantly with a sialylated diantennary complex-type glycan. In contrast, in the recombinant HRGs, all glycans showed different antennarities, sialylation, and core fucosylation, as well as the presence of oligomannose glycans, LacdiNAcs, and antennary fucosylation. Furthermore, we observed two previously unreported O-glycosylation sites in HRG on residues Thr273 and Thr274. These sites together showed more than 90% glycan occupancy in all HRG samples studied. To investigate the potential relevance of HRG glycosylation, we assessed the plasmin-induced cleavage of HRG under various conditions. These analyses revealed that the sialylation of the N- and O-glycans as well as the genotype-dependent N-glycosylation significantly influenced the kinetics and specificity of plasmin-induced cleavage of HRG.
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Affiliation(s)
- Yang Zou
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Matti F Pronker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - J Mirjam A Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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8
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Sanji AS, J M, Gurav MJ, Batra SK, Chachadi VB. Cancer snap-shots: Biochemistry and glycopathology of O-glycans: A review. Int J Biol Macromol 2024; 260:129318. [PMID: 38232866 DOI: 10.1016/j.ijbiomac.2024.129318] [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: 11/09/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/19/2024]
Abstract
Cancer pathogenesis is strongly linked to the qualitative and quantitative alteration of the cell surface glycans, that are glycosidically linked to proteins and lipids. Glycans that are covalently linked to the polypeptide backbone of a protein through nitrogen or oxygen, are known as N-glycans or O-glycans, respectively. Although the role of glycans in the expression, physiology, and communication of cells is well documented, the function of these glycans in tumor biology is not fully elucidated. In this context, current review summarizes biosynthesis, modifications and pathological implications of O-glycans The review also highlights illustrative examples of cancer types modulated by aberrant O-glycosylation. Related O-glycans like Thomsen-nouveau (Tn), Thomsen-Friedenreich (TF), Lewisa/x, Lewisb/y, sialyl Lewisa/x and some other O-glycans are discussed in detail. Since, the overexpression of O-glycans are attributed to the aggressiveness and metastatic behavior of cancer cells, the current review attempts to understand the relation between metastasis and O-glycans.
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Affiliation(s)
- Ashwini S Sanji
- P. G. Department of Studies in Biochemistry, Karnatak University, Dharwad, Karnataka 580 003, India
| | - Manasa J
- P. G. Department of Studies in Biochemistry, Karnatak University, Dharwad, Karnataka 580 003, India
| | - Maruti J Gurav
- P. G. Department of Studies in Biochemistry, Karnatak University, Dharwad, Karnataka 580 003, India
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Disease, University of Nebraska Medical Center, Omaha, NE, USA
| | - Vishwanath B Chachadi
- P. G. Department of Studies in Biochemistry, Karnatak University, Dharwad, Karnataka 580 003, India.
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Ming A, Zhao J, Liu Y, Wang Y, Wang X, Li J, Zhang L. O-glycosylation in viruses: A sweet tango. MLIFE 2024; 3:57-73. [PMID: 38827513 PMCID: PMC11139210 DOI: 10.1002/mlf2.12105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 06/04/2024]
Abstract
O-glycosylation is an ancient yet underappreciated protein posttranslational modification, on which many bacteria and viruses heavily rely to perform critical biological functions involved in numerous infectious diseases or even cancer. But due to the innate complexity of O-glycosylation, research techniques have been limited to study its exact role in viral attachment and entry, assembly and exit, spreading in the host cells, and the innate and adaptive immunity of the host. Recently, the advent of many newly developed methodologies (e.g., mass spectrometry, chemical biology tools, and molecular dynamics simulations) has renewed and rekindled the interest in viral-related O-glycosylation in both viral proteins and host cells, which is further fueled by the COVID-19 pandemic. In this review, we summarize recent advances in viral-related O-glycosylation, with a particular emphasis on the mucin-type O-linked α-N-acetylgalactosamine (O-GalNAc) on viral proteins and the intracellular O-linked β-N-acetylglucosamine (O-GlcNAc) modifications on host proteins. We hope to provide valuable insights into the development of antiviral reagents or vaccines for better prevention or treatment of infectious diseases.
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Affiliation(s)
- Annan Ming
- Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Jianxin Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life SciencesCapital Normal UniversityBeijingChina
| | - Yihan Liu
- Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Yibo Wang
- Laboratory of Chemical BiologyChangchun Institute of Applied Chemistry, Chinese Academy of SciencesChangchunChina
| | - Xiaohui Wang
- Laboratory of Chemical BiologyChangchun Institute of Applied Chemistry, Chinese Academy of SciencesChangchunChina
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiChina
- Beijing National Laboratory for Molecular SciencesBeijingChina
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life SciencesCapital Normal UniversityBeijingChina
| | - Leiliang Zhang
- Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
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Helms A, Brodbelt JS. Mass Spectrometry Strategies for O-Glycoproteomics. Cells 2024; 13:394. [PMID: 38474358 DOI: 10.3390/cells13050394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Glycoproteomics has accelerated in recent decades owing to numerous innovations in the analytical workflow. In particular, new mass spectrometry strategies have contributed to inroads in O-glycoproteomics, a field that lags behind N-glycoproteomics due to several unique challenges associated with the complexity of O-glycosylation. This review will focus on progress in sample preparation, enrichment strategies, and MS/MS techniques for the identification and characterization of O-glycoproteins.
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Affiliation(s)
- Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
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Huang Y, Pan W, Bao H, Sun X, Xu C, Ma J. HSF1 Increases EOGT-Mediated Glycosylation of Notch1 to Promote IL-1β-Induced Inflammatory Injury of Chondrocytes. Cartilage 2024:19476035241229211. [PMID: 38366389 DOI: 10.1177/19476035241229211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/18/2024] Open
Abstract
OBJECTIVE Osteoarthritis (OA) is the most common arthritic disease in humans. Nevertheless, the pathogenic mechanism of OA remains unclear. This study aimed to explore that heat-shock transcription factor 1 (HSF1) facilitated interleukin-1 beta (IL-1β) chondrocyte injury by increasing Notch1 O-linked N-acetylglucosamine (O-GlcNAc) modification level. DESIGN Human chondrocytes were incubated with 5 ng/ml interleukin-1 beta (IL-1β) for 24 h to establish OA cell model. The messenger RNA (mRNA) or protein expressions were assessed using reverse transcription-quantitative polymerase chain reaction, western blot, or immunofluorescence. Chondrocyte viability was examined by Cell Counting Kit-8 assay. Enzyme-linked immunosorbent assay was employed to detect the secretion levels of interleukin-6 (IL-6) and interleukin-8 (IL-8). Immunoprecipitation was adopted to detect Notch1 O-GlcNAc modification level. The interaction between HSF1 and epidermal growth factor-like (EGF) domain-specific O-GlcNAc transferase (EOGT) promoter was analyzed by dual-luciferase reporter gene and chromatin immunoprecipitation assays. RESULTS Herein, our results demonstrated that HSF1, EOGT, Notch1, and Notch1 intracellular domain (NICD1) expressions in chondrocytes were markedly increased by IL-1β stimulation. EOGT elevated Notch1 expression in IL-1β-treated chondrocytes by increasing Notch1 O-GlcNAc modification level. EOGT silencing reduced IL-1β-induced chondrocyte inflammatory injury. In addition, HSF1 knockdown relieved IL-1β-induced chondrocyte inflammatory injury. Molecular interaction experiment proved that HSF1 transcriptionally activated EOGT expression in IL-1β-treated chondrocytes. CONCLUSIONS HSF1 promoted IL-1β-induced inflammatory injury in chondrocytes by increasing EOGT-mediated glycosylation of Notch1.
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Affiliation(s)
- Yuanchi Huang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Wenjie Pan
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Huanli Bao
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xiangxiang Sun
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Chao Xu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Jianbing Ma
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
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12
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Vázquez‐Arias A, Vázquez‐Iglesias L, Pérez‐Juste I, Pérez‐Juste J, Pastoriza‐Santos I, Bodelon G. Bacterial surface display of human lectins in Escherichia coli. Microb Biotechnol 2024; 17:e14409. [PMID: 38380565 PMCID: PMC10884992 DOI: 10.1111/1751-7915.14409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 01/02/2024] [Indexed: 02/22/2024] Open
Abstract
Lectin-glycan interactions sustain fundamental biological processes involved in development and disease. Owing to their unique sugar-binding properties, lectins have great potential in glycobiology and biomedicine. However, their relatively low affinities and broad specificities pose a significant challenge when used as analytical reagents. New approaches for expression and engineering of lectins are in demand to overcome current limitations. Herein, we report the application of bacterial display for the expression of human galectin-3 and mannose-binding lectin in Escherichia coli. The analysis of the cell surface expression and binding activity of the surface-displayed lectins, including point and deletion mutants, in combination with molecular dynamics simulation, demonstrate the robustness and suitability of this approach. Furthermore, the display of functional mannose-binding lectin in the bacterial surface proved the feasibility of this method for disulfide bond-containing lectins. This work establishes for the first time bacterial display as an efficient means for the expression and engineering of human lectins, thereby increasing the available toolbox for glycobiology research.
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Affiliation(s)
- Alba Vázquez‐Arias
- CINBIOUniversidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS‐UVIGOVigoSpain
| | - Lorena Vázquez‐Iglesias
- CINBIOUniversidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS‐UVIGOVigoSpain
| | | | - Jorge Pérez‐Juste
- CINBIOUniversidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS‐UVIGOVigoSpain
- Departamento de Química FísicaUniversidade de VigoVigoSpain
| | - Isabel Pastoriza‐Santos
- CINBIOUniversidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS‐UVIGOVigoSpain
- Departamento de Química FísicaUniversidade de VigoVigoSpain
| | - Gustavo Bodelon
- CINBIOUniversidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS‐UVIGOVigoSpain
- Departamento de Biología Funcional y Ciencias de la SaludUniversidade de VigoVigoSpain
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13
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Goli M, Jiang P, Fowowe M, Hakim MA, Mechref Y. Hydrophilic Interaction Liquid Chromatography (HILIC) Enrichment of Glycopeptides Using PolyHYDROXYETHYL A. Methods Mol Biol 2024; 2762:267-280. [PMID: 38315371 DOI: 10.1007/978-1-0716-3666-4_16] [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: 02/07/2024]
Abstract
Glycosylation of proteins is an important post-translational modification that plays a role in a wide range of biological processes, including immune response, intercellular signaling, inflammation, and host-pathogen interaction. Abnormal protein glycosylation has been correlated with various diseases. However, the study of protein glycosylation remains challenging due to its low abundance, microheterogeneity of glycosylation sites, and low ionization efficiency. During the past decade, several methods for enrichment and for isolation of glycopeptides from biological samples have been developed and successfully employed in glycoproteomics research. In this chapter, we discuss the sample preparation protocol and the strategies for effectively isolating and enriching glycopeptides from biological samples, using PolyHYDROXYETHYL A as a hydrophilic interaction liquid chromatography (HILIC) enrichment technique.
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Affiliation(s)
- Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Mojibola Fowowe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Md Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
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14
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Hale RC, Morais D, Chou J, Stowell SR. The role of glycosylation in clinical allergy and immunology. J Allergy Clin Immunol 2024; 153:55-66. [PMID: 37717626 PMCID: PMC10872775 DOI: 10.1016/j.jaci.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023]
Abstract
While glycans are among the most abundant macromolecules on the cell with widespread functions, their role in immunity has historically been challenging to study. This is in part due to difficulties assimilating glycan analysis into routine approaches used to interrogate immune cell function. Despite this, recent developments have illuminated fundamental roles for glycans in host immunity. The growing field of glycoimmunology continues to leverage new tools and approaches to uncover the function of glycans and glycan-binding proteins in immunity. Here we utilize clinical vignettes to examine key roles of glycosylation in allergy, inborn errors of immunity, and autoimmunity. We will discuss the diverse functions of glycans as epitopes, as modulators of antibody function, and as regulators of immune cell function. Finally, we will highlight immune modulatory therapies that harness the critical role of glycans in the immune system.
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Affiliation(s)
- Rebecca C Hale
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass; Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Dominique Morais
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass.
| | - Sean R Stowell
- Department of Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Harvard Glycomics Center, Harvard Medical School, Boston, Mass.
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15
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Long Y, Li Z, Wang L, Ao X, Zhang Z, Chen Q, Zhu D, Liu X, Liu R, Chen B, Zhu H, Su Y. Highly efficient identification of nucleocytoplasmic O-glycosylation by the TurboID-based proximity labeling method in living cells. Biotechnol J 2024; 19:e2300090. [PMID: 37897200 DOI: 10.1002/biot.202300090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/06/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Glycosylation is a ubiquitous posttranslational modification and plays an important role in many processes, such as protein stability, folding, processing, and trafficking. Among glycosylation types, O-glycosylation is difficult to analyze due to the complex glycan composition, low abundance and lack of glycosidases to remove the O-glycans. Many methods have been applied to analyze the O-glycosylation of membrane glycoproteins and secreted glycoproteins since the synthesis of O-glycosylation occurred in the Golgi apparatus. In recent years, some O-glycosylation has been reported in the nucleus. In this work, we present a proximity labeling strategy based on TurboID by combining core 1 β1-3 galactosyltransferase (C1GalT1), which has been reported in the nucleus, to characterize nucleocytoplasmic O-glycosylation in living HeLa cells. The O-glycosylated protein C1GalT1 was biotinylated by the proximity labeling method in living HeLa cells overexpressing C1GalT1 fused by TurboID and enriched by streptavidin-coated beads. Following digestion with trypsin and mass spectrometry analysis, 68 high-confidence and 298 putative O-glycosylated sites were identified on 366 peptides mapped to 267 proteins. These results indicated that the proximity labeling method is a highly efficient technique to identify O-glycosylation. Furthermore, the finding of abundant O-glycosylation from nucleocytoplasmic proteins indicates a new pathway of O-glycosylation synthesis in cells.
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Affiliation(s)
- Yunfeng Long
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
| | - Zhunjie Li
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, P. R. China
| | - Long Wang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan, Hubei, P. R. China
| | - Xin Ao
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
| | - Zhengrong Zhang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
| | - Qingjie Chen
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
| | - Dan Zhu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
| | - Xinghui Liu
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan, Hubei, P. R. China
| | - Ruolan Liu
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan, Hubei, P. R. China
| | - Banghang Chen
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan, Hubei, P. R. China
| | - He Zhu
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Yanting Su
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan, Hubei, P. R. China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
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16
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González-Domínguez Á, Belmonte T, González-Domínguez R. Childhood obesity, metabolic syndrome, and oxidative stress: microRNAs go on stage. Rev Endocr Metab Disord 2023; 24:1147-1164. [PMID: 37672200 PMCID: PMC10698091 DOI: 10.1007/s11154-023-09834-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 09/07/2023]
Abstract
The incidence of childhood obesity and metabolic syndrome has grown notably in the last years, becoming major public health burdens in developed countries. Nowadays, oxidative stress is well-recognized to be closely associated with the onset and progression of several obesity-related complications within the framework of a complex crosstalk involving other intertwined pathogenic events, such as inflammation, insulin disturbances, and dyslipidemia. Thus, understanding the molecular basis behind these oxidative dysregulations could provide new approaches for the diagnosis, prevention, and treatment of childhood obesity and associated disorders. In this respect, the transcriptomic characterization of miRNAs bares great potential because of their involvement in post-transcriptional modulation of genetic expression. Herein, we provide a comprehensive literature revision gathering state-of-the-art research into the association between childhood obesity, metabolic syndrome, and miRNAs. We put special emphasis on the potential role of miRNAs in modulating obesity-related pathogenic events, with particular focus on oxidative stress.
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Affiliation(s)
- Álvaro González-Domínguez
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, 11009, Spain.
| | - Thalía Belmonte
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Raúl González-Domínguez
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, 11009, Spain
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17
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Karmaus PWF, Tata A, Meacham JM, Day F, Thrower D, Tata PR, Fessler MB. Meta-Analysis of COVID-19 BAL Single-Cell RNA Sequencing Reveals Alveolar Epithelial Transitions and Unique Alveolar Epithelial Cell Fates. Am J Respir Cell Mol Biol 2023; 69:623-637. [PMID: 37523502 DOI: 10.1165/rcmb.2023-0077oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) of BAL cells has provided insights into coronavirus disease (COVID-19). However, reports have been limited by small patient cohorts. We performed a meta-analysis of BAL scRNA-seq data from healthy control subjects (n = 13) and patients with COVID-19 (n = 20), sourced from six independent studies (167,280 high-quality cells in total). Consistent with the source reports, increases in infiltrating leukocyte subtypes were noted, several with type I IFN signatures and unique gene expression signatures associated with transcellular chemokine signaling. Noting dramatic reductions of inferred NKX2-1 and NR4A1 activity in alveolar epithelial type II (AT-II) cells, we modeled pseudotemporal AT-II-to-AT-I progression. This revealed changes in inferred AT-II cell metabolic activity, increased transitional cells, and a previously undescribed AT-I state. This cell state was conspicuously marked by the induction of genes of the epidermal differentiation complex, including the cornified envelope protein SPRR3 (small proline-rich protein 3), upregulation of multiple KRT (keratin) genes, inferred mitochondrial dysfunction, and cell death signatures including apoptosis and ferroptosis. Immunohistochemistry of lungs from patients with COVID-19 confirmed upregulation and colocalization of KRT13 and SPRR3 in the distal airspaces. Forced overexpression of SPRR3 in human alveolar epithelial cells ex vivo did not activate caspase-3 or upregulate KRT13, suggesting that SPRR3 marks an AT-I cornification program in COVID-19 but is not sufficient for phenotypic changes.
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Affiliation(s)
| | - Aleksandra Tata
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina
| | | | - Frank Day
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; and
| | - David Thrower
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; and
| | - Purushothama Rao Tata
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina
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18
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Xiao Y, Chang L, Ji H, Sun H, Song S, Feng K, Nuermaimaiti A, Halemubieke S, Mei L, Lu Z, Yan Y, Wang L. Posttranslational modifications of ACE2 protein: Implications for SARS-CoV-2 infection and beyond. J Med Virol 2023; 95:e29304. [PMID: 38063421 DOI: 10.1002/jmv.29304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/21/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023]
Abstract
The present worldwide pandemic of coronavirus disease 2019 (COVID-19) has highlighted the important function of angiotensin-converting enzyme 2 (ACE2) as a receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry. A deeper understanding of ACE2 could offer insights into the mechanisms of SARS-CoV-2 infection. While ACE2 is subject to regulation by various factors in vivo, current research in this area is insufficient to fully elucidate the corresponding pathways of control. Posttranslational modification (PTM) is a powerful tool for broadening the variety of proteins. The PTM study of ACE2 will help us to make up for the deficiency in the regulation of protein synthesis and translation. However, research on PTM-related aspects of ACE2 remains limited, mostly focused on glycosylation. Accordingly, a comprehensive review of ACE2 PTMs could help us better understand the infection process and provide a basis for the treatment of COVID-19 and beyond.
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Affiliation(s)
- Yingzi Xiao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Le Chang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Huimin Ji
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Huizhen Sun
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Shi Song
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Kaihao Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Abudulimutailipu Nuermaimaiti
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Shana Halemubieke
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Ling Mei
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Zhuoqun Lu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Ying Yan
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Lunan Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People's Republic of China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
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19
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Li R, Dong X, Chen S, Tan J, Chen X, Liu J, Wen T, Ru X. Tn antigen promotes breast cancer metastasis via impairment of CASC4. Cell Biol Int 2023; 47:1854-1867. [PMID: 37493437 DOI: 10.1002/cbin.12077] [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: 02/10/2023] [Revised: 07/10/2023] [Accepted: 07/16/2023] [Indexed: 07/27/2023]
Abstract
Breast cancer is one of the most serious and deadly cancers in women worldwide, with distant metastases being the leading cause of death. Tn antigen, a tumor-associated carbohydrate antigen, was frequently detected in breast cancer, but its exact role in breast cancer metastasis has not been well elucidated. Here we investigated the impact of Tn antigen expression on breast cancer metastasis and its underlying mechanisms. The expression of Tn antigen was induced in two breast cancer cell lines by deleting T-synthase or Cosmc, both of which are required for normal O-glycosylation. It showed that Tn-expressing cancer cells promoted epithelial-mesenchymal transition (EMT) and metastatic features as compared to Tn(-) control cells both in vitro and in vivo. Mechanistically, we found that cancer susceptibility candidate 4 (CASC4), a heavily O-glycosylated protein, was significantly downregulated in both Tn(+) cells. Overexpression of CASC4 suppressed Tn-induced activation of EMT and cancer metastasis via inhibition of Cdc42 signaling. Furthermore, we confirmed that O-glycosylation is essential for the functional role of CASC4 because defective O-glycosylated CASC4 (mutant CASC4, which lacks nine O-glycosylation sites) exerted marginal metastatic-suppressing effects in comparison with WT CASC4. Collectively, these data suggest that Tn-mediated aberrant O-glycosylation contributes to breast cancer metastasis via impairment of CASC4 expression and function.
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Affiliation(s)
- Ruijun Li
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Xichen Dong
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Shibin Chen
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Jingyu Tan
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Xiangyu Chen
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Jian Liu
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Tao Wen
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Xiaoli Ru
- Department of Gynecology and Obstetrics, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
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20
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Xu J, Du H, Shi H, Song J, Yu J, Zhou Y. Protein O-glycosylation regulates diverse developmental and defense processes in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6119-6130. [PMID: 37220091 DOI: 10.1093/jxb/erad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/16/2023] [Indexed: 05/25/2023]
Abstract
Post-translational modifications affect protein functions and play key roles in controlling biological processes. Plants have unique types of O-glycosylation that are different from those of animals and prokaryotes, and they play roles in modulating the functions of secretory proteins and nucleocytoplasmic proteins by regulating transcription and mediating localization and degradation. O-glycosylation is complex because of the dozens of different O-glycan types, the widespread existence of hydroxyproline (Hyp), serine (Ser), and threonine (Thr) residues in proteins attached by O-glycans, and the variable modes of linkages connecting the sugars. O-glycosylation specifically affects development and environmental acclimatization by affecting diverse physiological processes. This review describes recent studies on the detection and functioning of protein O-glycosylation in plants, and provides a framework for the O-glycosylation network that underlies plant development and resistance.
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Affiliation(s)
- Jin Xu
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Hongyu Du
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Huanran Shi
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Jianing Song
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Jingquan Yu
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
- Hainan Institute, Zhejiang University, Sanya, 572025, P.R. China
- Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Yuhangtang Road 866, Hangzhou, 310058, P.R. China
| | - Yanhong Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, P.R. China
- Hainan Institute, Zhejiang University, Sanya, 572025, P.R. China
- Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Yuhangtang Road 866, Hangzhou, 310058, P.R. China
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21
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Hussnaetter KP, Palm P, Pich A, Franzreb M, Rapp E, Elling L. Strategies for Automated Enzymatic Glycan Synthesis (AEGS). Biotechnol Adv 2023; 67:108208. [PMID: 37437855 DOI: 10.1016/j.biotechadv.2023.108208] [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: 12/22/2022] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Glycans are the most abundant biopolymers on earth and are constituents of glycoproteins, glycolipids, and proteoglycans with multiple biological functions. The availability of different complex glycan structures is of major interest in biotechnology and basic research of biological systems. High complexity, establishment of general and ubiquitous synthesis techniques, as well as sophisticated analytics, are major challenges in the development of glycan synthesis strategies. Enzymatic glycan synthesis with Leloir-glycosyltransferases is an attractive alternative to chemical synthesis as it can achieve quantitative regio- and stereoselective glycosylation in a single step. Various strategies for synthesis of a wide variety of different glycan structures has already be established and will exemplarily be discussed in the scope of this review. However, the application of enzymatic glycan synthesis in an automated system has high demands on the equipment, techniques, and methods. Different automation approaches have already been shown. However, while these techniques have been applied for several glycans, only a few strategies are able to conserve the full potential of enzymatic glycan synthesis during the process - economical and enzyme technological recycling of enzymes is still rare. In this review, we show the major challenges towards Automated Enzymatic Glycan Synthesis (AEGS). First, we discuss examples for immobilization of glycans or glycosyltransferases as an important prerequisite for the embedment and implementation in an enzyme reactor. Next, improvement of bioreactors towards automation will be described. Finally, analysis and monitoring of the synthesis process are discussed. Furthermore, automation processes and cycle design are highlighted. Accordingly, the transition of recent approaches towards a universal automated glycan synthesis platform will be projected. To this end, this review aims to describe essential key features for AEGS, evaluate the current state-of-the-art and give thought- encouraging impulses towards future full automated enzymatic glycan synthesis.
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Affiliation(s)
- Kai Philip Hussnaetter
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany
| | - Philip Palm
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany
| | - Andrij Pich
- Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry and DWI Leibniz-Institute for Interactive Materials e.V., RWTH Aachen University, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Matthias Franzreb
- Karlsruher Institute of Technology (KIT), Institute of Functional Interfaces, Hermann v. Helmholtz, Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Erdmann Rapp
- glyXera GmbH, Brenneckestrasse 20 * ZENIT, 39120 Magdeburg, Germany; Max Planck Institute for Dynamics of Complex Technical System, Bioprocess Engineering, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Lothar Elling
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany.
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22
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Zhang X, Chen X, Wang Z, Meng X, Hoffmann-Sommergruber K, Cavallari N, Wu Y, Gao J, Li X, Chen H. Goblet cell-associated antigen passage: A gatekeeper of the intestinal immune system. Immunology 2023; 170:1-12. [PMID: 37067238 DOI: 10.1111/imm.13648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/02/2023] [Indexed: 04/18/2023] Open
Abstract
Effective delivery of luminal antigens to the underlying immune system is the initial step in generating antigen-specific responses in the gut. However, a large body of information regarding the immune response activation process remains unknown. Recently, goblet cells (GCs) have been reported to form goblet cell-associated antigen passages (GAPs). Luminal antigens can be transported inside GAPs and reach subepithelial immune cells to induce antigen-specific immune responses, contributing largely to gut homeostasis and the prevention of some intestinal diseases like allergic enteritis and bacterial translocation. In this article, we summarized recent observations on the formation of intestinal GAPs and their roles in mucosal immunity. We hope that this review can offer a fresh perspective and valuable insights for clinicians and researchers interested in studying the intestinal immune system.
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Affiliation(s)
- Xing Zhang
- State Key Laboratory Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- School of Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, People's Republic of China
| | - Xiao Chen
- State Key Laboratory Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- School of Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, People's Republic of China
| | - Zhongliang Wang
- State Key Laboratory Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- School of Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, People's Republic of China
| | - Xuanyi Meng
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, People's Republic of China
| | | | - Nicola Cavallari
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Yong Wu
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, People's Republic of China
| | - Jinyan Gao
- State Key Laboratory Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- School of Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, People's Republic of China
| | - Xin Li
- State Key Laboratory Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- School of Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, People's Republic of China
| | - Hongbing Chen
- State Key Laboratory Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- School of Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, People's Republic of China
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23
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Li Y, Zhang R, Hei H. Advances in post-translational modifications of proteins and cancer immunotherapy. Front Immunol 2023; 14:1229397. [PMID: 37675097 PMCID: PMC10477431 DOI: 10.3389/fimmu.2023.1229397] [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: 05/26/2023] [Accepted: 07/21/2023] [Indexed: 09/08/2023] Open
Abstract
Protein post-translational modification (PTM) is a regulatory mechanism for protein activity modulation, localization, expression, and interactions with other cellular molecules. It involves the addition or removal of specific chemical groups on the amino acid residues of proteins. Its common forms include phosphorylation, ubiquitylation, methylation, and acetylation. Emerging research has highlighted lactylation, succinylation, and glycosylation. PTMs are involved in vital biological processes. The occurrence and development of diseases depends on protein abundance and is regulated by various PTMs. In addition, advancements in tumor immunotherapy have revealed that protein PTM is also involved in the proliferation, activation, and metabolic reprogramming of immune cells in tumor microenvironment. These PTMs play an important role in tumor immunotherapy. In this review, we comprehensively summarize the role of several types of PTMs in tumor immunotherapy. This review could provide new insights and future research directions for tumor immunotherapy.
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Affiliation(s)
| | | | - Hu Hei
- Department of Thyroid and Neck, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
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24
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Czyrnik ED, Wiesehöfer M, Dankert JT, Wach S, Wagner M, Spahn M, Kruithof de Julio M, Wennemuth G. Stromal-epithelial interaction induces GALNT14 in prostate carcinoma cells. Front Oncol 2023; 13:1212585. [PMID: 37671061 PMCID: PMC10475991 DOI: 10.3389/fonc.2023.1212585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/13/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction Cell-cell communication is an important process in healthy tissue but also gains enhanced attention regarding pathological tissue. To date, the tumor microenvironment is gradually brought into focus when studying tumorigenesis. In the prostate gland, stromal and epithelial cells greatly interact to maintain homeostasis or tissue integrity. This study focuses on an indirect communication via soluble factors. Methods To investigate the cell-cell interaction via soluble factors, the prostate carcinoma cell line LNCaP and the stromal primary cells p21 were co-cultured without direct contact and RNA was isolated at defined time points. Differences in gene expression were finally analyzed by RNA sequencing. Results RNA sequencing revealed a time-depending differential expression profile. Selected factors were subsequently characterized at molecular level and analyzed in human prostate tissue of different developmental stages as well as pathology. GALNT14 was one of the highest induced co-culture-specific genes in LNCaP cells. Detection in healthy tissue and BPH revealed an age-dependent decrease in GALNT14 expression. Moreover, in prostate carcinoma, GALNT14 expression heavily varied independent of the Gleason score. Conclusion Overall, this work provides a basis for further studies related to paracrine stromal-epithelial interaction in prostate carcinoma and highlights the importance of GALNT14.
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Affiliation(s)
- Elena D. Czyrnik
- University Hospital Essen, Department of Anatomy, Essen, Germany
| | - Marc Wiesehöfer
- University Hospital Essen, Department of Anatomy, Essen, Germany
| | | | - Sven Wach
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Erlangen, Germany
| | - Mathias Wagner
- University Hospital Saarland, Department of General and Special Pathology, Homburg, Germany
| | - Martin Spahn
- Lindenhofspital Bern, Department of Urology, Bern, Switzerland
- University Hospital Essen, Department of Urology, Essen, Germany
| | - Marianna Kruithof de Julio
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, Bern, Switzerland
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25
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Harduin-Lepers A. The vertebrate sialylation machinery: structure-function and molecular evolution of GT-29 sialyltransferases. Glycoconj J 2023; 40:473-492. [PMID: 37247156 PMCID: PMC10225777 DOI: 10.1007/s10719-023-10123-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/09/2023] [Accepted: 05/10/2023] [Indexed: 05/30/2023]
Abstract
Every eukaryotic cell is covered with a thick layer of complex carbohydrates with essential roles in their social life. In Deuterostoma, sialic acids present at the outermost positions of glycans of glycoconjugates are known to be key players in cellular interactions including host-pathogen interactions. Their negative charge and hydrophilic properties enable their roles in various normal and pathological states and their expression is altered in many diseases including cancers. Sialylation of glycoproteins and glycolipids is orchestrated by the regulated expression of twenty sialyltransferases in human tissues with distinct enzymatic characteristics and preferences for substrates and linkages formed. However, still very little is known on the functional organization of sialyltransferases in the Golgi apparatus and how the sialylation machinery is finely regulated to provide the ad hoc sialome to the cell. This review summarizes current knowledge on sialyltransferases, their structure-function relationships, molecular evolution, and their implications in human biology.
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Affiliation(s)
- Anne Harduin-Lepers
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.
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26
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Martins ÁM, Lopes TM, Diniz F, Pires J, Osório H, Pinto F, Freitas D, Reis CA. Differential Protein and Glycan Packaging into Extracellular Vesicles in Response to 3D Gastric Cancer Cellular Organization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300588. [PMID: 37340602 PMCID: PMC10460857 DOI: 10.1002/advs.202300588] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/26/2023] [Indexed: 06/22/2023]
Abstract
Alterations of the glycosylation machinery are common events in cancer, leading to the synthesis of aberrant glycan structures by tumor cells. Extracellular vesicles (EVs) play a modulatory role in cancer communication and progression, and interestingly, several tumor-associated glycans have already been identified in cancer EVs. Nevertheless, the impact of 3D tumor architecture in the selective packaging of cellular glycans into EVs has never been addressed. In this work, the capacity of gastric cancer cell lines with differential glycosylation is evaluated in producing and releasing EVs when cultured under conventional 2D monolayer or in 3D culture conditions. Furthermore, the proteomic content is identified and specific glycans are studied in the EVs produced by these cells, upon differential spatial organization. Here, it is observed that although the proteome of the analyzed EVs is mostly conserved, an EV differential packaging of specific proteins and glycans is found. In addition, protein-protein interaction and pathway analysis reveal individual signatures on the EVs released by 2D- and 3D-cultured cells, suggesting distinct biological functions. These protein signatures also show a correlation with clinical data. Overall, this data highlight the importance of tumor cellular architecture when assessing the cancer-EV cargo and its biological role.
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Affiliation(s)
- Álvaro M. Martins
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS)University of PortoR. Jorge de Viterbo FerreiraPorto4050-313Portugal
| | - Tânia M. Lopes
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
| | - Francisca Diniz
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS)University of PortoR. Jorge de Viterbo FerreiraPorto4050-313Portugal
| | - José Pires
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
- Faculty of Medicine of the University of PortoAlameda Prof. Hernâni MonteiroPorto4200-319Portugal
| | - Hugo Osório
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
- Faculty of Medicine of the University of PortoAlameda Prof. Hernâni MonteiroPorto4200-319Portugal
| | - Filipe Pinto
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
| | - Daniela Freitas
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
| | - Celso A. Reis
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS)University of PortoR. Jorge de Viterbo FerreiraPorto4050-313Portugal
- Faculty of Medicine of the University of PortoAlameda Prof. Hernâni MonteiroPorto4200-319Portugal
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27
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Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
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28
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Tang H, Tang Q, Zhang Q, Feng P. O-GlyThr: Prediction of human O-linked threonine glycosites using multi-feature fusion. Int J Biol Macromol 2023; 242:124761. [PMID: 37156312 DOI: 10.1016/j.ijbiomac.2023.124761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023]
Abstract
O-linked glycosylation is one of the most complex post-translational modifications (PTM) of human proteins modulating various cellular metabolic and signaling pathways. Unlike N-glycosylation, the O-glycosylation has nonspecific sequence features and nonstable glycan core structure, which makes identification of O-glycosites more challenging either by experimental or computational methods. Biochemical experiments to identify O-glycosites in batches are technically and economically demanding. Therefore, development of computation-based methods is greatly warranted. This study constructed a prediction model based on feature fusion for O-glycosites linked to the threonine residues in Homo sapiens. In the training model, we collected and sorted out high-quality human protein data with O-linked threonine glycosites. Seven feature coding methods were fused to represent the sample sequence. By comparison of different algorithms, random forest was selected as the final classifier to construct the classification model. Through 5-fold cross-validation, the proposed model, namely O-GlyThr, performed satisfactorily on both training set (AUC: 0.9308) and independent validation dataset (AUC: 0.9323). Compared with previously published predictors, O-GlyThr achieved the highest ACC of 0.8475 on the independent test dataset. These results demonstrated the high competency of our predictor in identifying O-glycosites on threonine residues. Furthermore, a user-friendly webserver named O-GlyThr (http://cbcb.cdutcm.edu.cn/O-GlyThr/) was developed to assist glycobiologists in the research associated with glycosylation structure and function.
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Affiliation(s)
- Hua Tang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Qiang Tang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qian Zhang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Pengmian Feng
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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29
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Li J, Qiu Y, Zhang C, Wang H, Bi R, Wei Y, Li Y, Hu B. The role of protein glycosylation in the occurrence and outcome of acute ischemic stroke. Pharmacol Res 2023; 191:106726. [PMID: 36907285 DOI: 10.1016/j.phrs.2023.106726] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
Acute ischemic stroke (AIS) is a serious and life-threatening disease worldwide. Despite thrombolysis or endovascular thrombectomy, a sizeable fraction of patients with AIS have adverse clinical outcomes. In addition, existing secondary prevention strategies with antiplatelet and anticoagulant drugs therapy are not able to adequately decrease the risk of ischemic stroke recurrence. Thus, exploring novel mechanisms for doing so represents an urgent need for the prevention and treatment of AIS. Recent studies have discovered that protein glycosylation plays a critical role in the occurrence and outcome of AIS. As a common co- and post-translational modification, protein glycosylation participates in a wide variety of physiological and pathological processes by regulating the activity and function of proteins or enzymes. Protein glycosylation is involved in two causes of cerebral emboli in ischemic stroke: atherosclerosis and atrial fibrillation. Following ischemic stroke, the level of brain protein glycosylation becomes dynamically regulated, which significantly affects stroke outcome through influencing inflammatory response, excitotoxicity, neuronal apoptosis, and blood-brain barrier disruption. Drugs targeting glycosylation in the occurrence and progression of stroke may represent a novel therapeutic idea. In this review, we focus on possible perspectives about how glycosylation affects the occurrence and outcome of AIS. We then propose the potential of glycosylation as a therapeutic drug target and prognostic marker for AIS patients in the future.
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Affiliation(s)
- Jianzhuang Li
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanmei Qiu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunlin Zhang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hailing Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rentang Bi
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanhao Wei
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanan Li
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Bo Hu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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30
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Yue Z, Yu Y, Gao B, Wang D, Sun H, Feng Y, Ma Z, Xie X. Advances in protein glycosylation and its role in tissue repair and regeneration. Glycoconj J 2023; 40:355-373. [PMID: 37097318 DOI: 10.1007/s10719-023-10117-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 04/10/2023] [Accepted: 04/16/2023] [Indexed: 04/26/2023]
Abstract
After tissue damage, a series of molecular and cellular events are initiated to promote tissue repair and regeneration to restore its original structure and function. These events include inter-cell communication, cell proliferation, cell migration, extracellular matrix differentiation, and other critical biological processes. Glycosylation is the crucial conservative and universal post-translational modification in all eukaryotic cells [1], with influential roles in intercellular recognition, regulation, signaling, immune response, cellular transformation, and disease development. Studies have shown that abnormally glycosylation of proteins is a well-recognized feature of cancer cells, and specific glycan structures are considered markers of tumor development. There are many studies on gene expression and regulation during tissue repair and regeneration. Still, there needs to be more knowledge of complex carbohydrates' effects on tissue repair and regeneration, such as glycosylation. Here, we present a review of studies investigating protein glycosylation in the tissue repair and regeneration process.
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Affiliation(s)
- Zhongyu Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Yajie Yu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Boyuan Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Du Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Hongxiao Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Yue Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Zihan Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Xin Xie
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China.
- GeWu Medical Research Institute (GMRI), Xi'an, China.
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31
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Vergoten G, Bailly C. N-glycosylation reinforces interaction of immune checkpoint TIM-3 with a small molecule ligand. Comput Biol Chem 2023; 104:107852. [PMID: 36965447 DOI: 10.1016/j.compbiolchem.2023.107852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/27/2023]
Abstract
N-glycosylation of eukaryotic proteins plays roles in protein folding, trafficking, and signal transduction. The biological influence of the process is well understood, whereas the pharmacological impact of protein N-glycosylation is not well under discerned. The role of N-glycosylation on drug binding to protein has been rarely studied. We have modeled the influence of a bi-antennary N-glycan introduced at position N78 on the immune checkpoint TIM-3 (T cell immunoglobulin domain and mucin domain-containing molecule 3) on the interaction with a selective drug antagonist. The bulky N-glycan introduced at the consensus sequence Asn-Val-Thr has no influence on drug binding when the glycan adopts an extended conformation. But in a folded conformation, the glycan can interact directly with the triazoloquinazolinone derivative so as to further stabilize the drug-TIM-3 complex. The non-fucosylated glycan at position N78 markedly consolidates the drug interaction, via an additional H-bond interaction with the α3-mannose residue. It provides a gain of empirical potential energy of interaction (ΔE) of about 30 %. The presence of a more rigid fucosylated N-glycan is a little less favorable, with a gain of ΔE of about 20 %. The folded N-glycan appears to protect the ligand bound to the protein cavity, with the tricyclic core of the heterocyclic molecule sandwiched between two indole rings of tryptophan residues. Similar results were obtained when using a biantennary disialyl N-glycan with a bisecting GlcNAc residue and a tetra-antennary N-glycan. The molecular models illustrate the drug-stabilizing capacity of a bulky N-glycan positioned at a validated glycosylation site (N78 corresponding to N100 for the full-length protein). The modeling approach is useful to delineate further the role of the N-glycan of the immune checkpoint TIM-3 in interaction with small molecule ligands, and to guide the design of more potent compounds. The approach is transposable to other proteins to better comprehend the influence of N-glycans on drug-receptor interactions.
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Affiliation(s)
- Gérard Vergoten
- University of Lille, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, 3 rue du Professeur Laguesse, F-59006 Lille, France
| | - Christian Bailly
- University of Lille, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, 3 rue du Professeur Laguesse, F-59006 Lille, France; University of Lille, CNRS, Inserm, CHU Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, 59000 Lille, France; OncoWitan, Lille (Wasquehal), 59290, France.
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Yin H, Zhu J. Methods for quantification of glycopeptides by liquid separation and mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:887-917. [PMID: 35099083 PMCID: PMC9339036 DOI: 10.1002/mas.21771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/14/2021] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
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Affiliation(s)
- Haidi Yin
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
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Vrablova V, Blsakova A, Lorencova L, Kollar J, Vikartovska A, Kasak P, Tkac J. How to choose proper magnetic particles for bioaffinity interactions? The case for immobilised glyconanoconjugate. Anal Chim Acta 2023; 1242:340794. [PMID: 36657889 DOI: 10.1016/j.aca.2023.340794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023]
Abstract
In this study, an assay for detection of the cancer biomarker Thomsen-nouvelle (Tn) antigen on the ELISA plates format was designed and developed. The effects of size and the interfacial density of the negative charge of magnetic beads (MBs) on the specific sensitivity of the bioaffinity interaction were studied. In particular, glyconanoconjugate, i.e. glycan Tn antigen conjugated to bovine serum albumin (BSA) was covalently immobilised on MBs for the bioaffinity detection of anti-Tn antibodies as cancer biomarkers. Six different MBs were used in the study, i.e. carboxy-modified MBs of 250 nm, 500 nm, 1000 nm and 2800 nm and epoxy-modified MBs of 2800 nm and 4500 nm. In order to evaluate which MBs are the best suited for detection of the analyte anti-Tn antibodies, sensitivities of detection (slopes from calibration curves) were calculated. Next, specific sensitivities were calculated for each type of MBs as a ratio of sensitivity of detection to the mass of MBs. From zeta potential ζ for each type of MBs, the interfacial charge density on MBs was calculated, expressed as the density of zeta potential ζd (ratio of zeta potential to surface area of MBs, i.e. ζd = ζ/A). Then, we evaluated the effect of size and ζd on the specific sensitivity of detection of anti-Tn antibodies in order to understand the immobilisation process on nanoscale. We also identified an optimal value of ζd on MBs; this was essential to achieve highly sensitive detection of the analyte, which made it possible to attain limit of detection (LOD) of (0.31 ± 0.01) ng mL-1 or (2.10 ± 0.04) pM for analyte detection. In addition, the optimal assay configuration was highly selective and enabled reliable detection of the analyte in human serum with a recovery index in the range of 102-104%.
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Affiliation(s)
- Veronika Vrablova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38, Bratislava, Slovakia
| | - Anna Blsakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38, Bratislava, Slovakia
| | - Lenka Lorencova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38, Bratislava, Slovakia
| | - Jozef Kollar
- Polymer Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 41, Bratislava, Slovakia
| | - Alica Vikartovska
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38, Bratislava, Slovakia
| | - Peter Kasak
- Center for Advanced Materials, Qatar University, P.O. Box 2713, Doha, Qatar.
| | - Jan Tkac
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38, Bratislava, Slovakia.
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Ramos-Martínez I, Ramos-Martínez E, Cerbón M, Pérez-Torres A, Pérez-Campos Mayoral L, Hernández-Huerta MT, Martínez-Cruz M, Pérez-Santiago AD, Sánchez-Medina MA, García-Montalvo IA, Zenteno E, Matias-Cervantes CA, Ojeda-Meixueiro V, Pérez-Campos E. The Role of B Cell and T Cell Glycosylation in Systemic Lupus Erythematosus. Int J Mol Sci 2023; 24:ijms24010863. [PMID: 36614306 PMCID: PMC9820943 DOI: 10.3390/ijms24010863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023] Open
Abstract
Glycosylation is a post-translational modification that affects the stability, structure, antigenicity and charge of proteins. In the immune system, glycosylation is involved in the regulation of ligand-receptor interactions, such as in B-cell and T-cell activating receptors. Alterations in glycosylation have been described in several autoimmune diseases, such as systemic lupus erythematosus (SLE), in which alterations have been found mainly in the glycosylation of B lymphocytes, T lymphocytes and immunoglobulins. In immunoglobulin G of lupus patients, a decrease in galactosylation, sialylation, and nucleotide fucose, as well as an increase in the N-acetylglucosamine bisector, are observed. These changes in glycoisolation affect the interactions of immunoglobulins with Fc receptors and are associated with pericarditis, proteinuria, nephritis, and the presence of antinuclear antibodies. In T cells, alterations have been described in the glycosylation of receptors involved in activation, such as the T cell receptor; these changes affect the affinity with their ligands and modulate the binding to endogenous lectins such as galectins. In T cells from lupus patients, a decrease in galectin 1 binding is observed, which could favor activation and reduce apoptosis. Furthermore, these alterations in glycosylation correlate with disease activity and clinical manifestations, and thus have potential use as biomarkers. In this review, we summarize findings on glycosylation alterations in SLE and how they relate to immune system defects and their clinical manifestations.
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Affiliation(s)
- Ivan Ramos-Martínez
- Departamento de Medicina y Zootecnia de Cerdos, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Edgar Ramos-Martínez
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Escuela de Ciencias, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68120, Mexico
| | - Marco Cerbón
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología “Isidro Espinosa de los Reyes”—Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Armando Pérez-Torres
- Departamento de Biología Celular y Tisular, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | | | - María Teresa Hernández-Huerta
- CONACyT, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | | | | | | | | | - Edgar Zenteno
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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Doud EH, Yeh ES. Mass Spectrometry-Based Glycoproteomic Workflows for Cancer Biomarker Discovery. Technol Cancer Res Treat 2023; 22:15330338221148811. [PMID: 36740994 PMCID: PMC9903044 DOI: 10.1177/15330338221148811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Glycosylation has a clear role in cancer initiation and progression, with numerous studies identifying distinct glycan features or specific glycoproteoforms associated with cancer. Common findings include that aggressive cancers tend to have higher expression levels of enzymes that regulate glycosylation as well as glycoproteins with greater levels of complexity, increased branching, and enhanced chain length1. Research in cancer glycoproteomics over the last 50-plus years has mainly focused on technology development used to observe global changes in glycosylation. Efforts have also been made to connect glycans to their protein carriers as well as to delineate the role of these modifications in intracellular signaling and subsequent cell function. This review discusses currently available techniques utilizing mass spectrometry-based technologies used to study glycosylation and highlights areas for future advancement.
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Affiliation(s)
- Emma H. Doud
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, USA
- IU Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, USA
| | - Elizabeth S. Yeh
- IU Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, USA
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, USA
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Yang Y, Yang Y, Liu J, Zeng Y, Guo Q, Guo J, Guo L, Lu H, Liu W. Establishment and validation of a carbohydrate metabolism-related gene signature for prognostic model and immune response in acute myeloid leukemia. Front Immunol 2022; 13:1038570. [PMID: 36544784 PMCID: PMC9761472 DOI: 10.3389/fimmu.2022.1038570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/21/2022] [Indexed: 12/10/2022] Open
Abstract
Introduction The heterogeneity of treatment response in acute myeloid leukemia (AML) patients poses great challenges for risk scoring and treatment stratification. Carbohydrate metabolism plays a crucial role in response to therapy in AML. In this multicohort study, we investigated whether carbohydrate metabolism related genes (CRGs) could improve prognostic classification and predict response of immunity and treatment in AML patients. Methods Using univariate regression and LASSO-Cox stepwise regression analysis, we developed a CRG prognostic signature that consists of 10 genes. Stratified by the median risk score, patients were divided into high-risk group and low-risk group. Using TCGA and GEO public data cohorts and our cohort (1031 non-M3 patients in total), we demonstrated the consistency and accuracy of the CRG score on the predictive performance of AML survival. Results The overall survival (OS) was significantly shorter in high-risk group. Differentially expressed genes (DEGs) were identified in the high-risk group compared to the low-risk group. GO and GSEA analysis showed that the DEGs were mainly involved in immune response signaling pathways. Analysis of tumor-infiltrating immune cells confirmed that the immune microenvironment was strongly suppressed in high-risk group. The results of potential drugs for risk groups showed that inhibitors of carbohydrate metabolism were effective. Discussion The CRG signature was involved in immune response in AML. A novel risk model based on CRGs proposed in our study is promising prognostic classifications in AML, which may provide novel insights for developing accurate targeted cancer therapies.
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Affiliation(s)
- You Yang
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Yan Yang
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Jing Liu
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Yan Zeng
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Qulian Guo
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Jing Guo
- The Second Hospital, Center for Reproductive Medicine, Advanced Medical Research Institute, and Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ling Guo
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China,*Correspondence: Ling Guo, ; Haiquan Lu, ; Wenjun Liu,
| | - Haiquan Lu
- Department of Hematology, The Affiliated Hospital of Southwest Medical University. Luzhou, Sichuan, China,*Correspondence: Ling Guo, ; Haiquan Lu, ; Wenjun Liu,
| | - Wenjun Liu
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China,*Correspondence: Ling Guo, ; Haiquan Lu, ; Wenjun Liu,
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Xiang T, Qiao M, Xie J, Li Z, Xie H. Emerging Roles of the Unique Molecular Chaperone Cosmc in the Regulation of Health and Disease. Biomolecules 2022; 12:biom12121732. [PMID: 36551160 PMCID: PMC9775496 DOI: 10.3390/biom12121732] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/12/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022] Open
Abstract
The core-1 β1-3galactosyltransferase-specific chaperone 1 (Cosmc) is a unique molecular chaperone of core-1 β1-3galactosyltransferase(C1GALT1), which typically functions inside the endoplasmic reticulum (ER). Cosmc helps C1GALT1 to fold correctly and maintain activity. It also participates in the synthesis of the T antigen, O-glycan, together with C1GALT1. Cosmc is a multifaceted molecule with a wide range of roles and functions. It involves platelet production and the regulation of immune cell function. Besides that, the loss of function of Cosmc also facilitates the development of several diseases, such as inflammation diseases, immune-mediated diseases, and cancer. It suggests that Cosmc is a critical control point in diseases and that it should be regarded as a potential target for oncotherapy. It is essential to fully comprehend Cosmc's roles, as they may provide critical information about its involvement in disease development and pathogenesis. In this review, we summarize the recent progress in understanding the role of Cosmc in normal development and diseases.
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Affiliation(s)
- Ting Xiang
- Hunan Province Key Laboratory of Tumor cellular Molecular Pathology, Cancer Research Institute, Heng yang School of Medicine, University of South China, Hengyang 421009, China
| | - Muchuan Qiao
- Hunan Province Key Laboratory of Tumor cellular Molecular Pathology, Cancer Research Institute, Heng yang School of Medicine, University of South China, Hengyang 421009, China
| | - Jiangbo Xie
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410013, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an 710069, China
- Correspondence: (Z.L.); (H.X.)
| | - Hailong Xie
- Hunan Province Key Laboratory of Tumor cellular Molecular Pathology, Cancer Research Institute, Heng yang School of Medicine, University of South China, Hengyang 421009, China
- Correspondence: (Z.L.); (H.X.)
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Zhang Y, Zhang S, Liu J, Zhang Y, Liu Y, Shen S, Tian F, Yan G, Gao Y, Qin X. Identification of serum glycobiomarkers for Hepatocellular Carcinoma using lectin microarrays. Front Immunol 2022; 13:973993. [PMID: 36341438 PMCID: PMC9634732 DOI: 10.3389/fimmu.2022.973993] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/10/2022] [Indexed: 11/24/2022] Open
Abstract
Objective Hepatocellular carcinoma (HCC) is the sixth most commonly occurring cancer and ranks third in mortality among all malignant tumors; as a result, HCC represents a major human health issue. Although aberrant glycosylation is clearly implicated in HCC, changes in serum immunoglobulin (Ig)G and IgM glycosylation have not been comprehensively characterized. In this study, we used lectin microarrays to evaluate differences in serum IgG and IgM glycosylation among patients with HCC, hepatitis B cirrhosis (HBC), or chronic hepatitis B (CHB), and healthy normal controls (NC) and aimed to establish a model to improve the diagnostic accuracy of HCC. Methods In total, 207 serum samples collected in 2019–2020 were used for lectin microarray analyses, including 97 cases of HCC, 50 cases of HBC, 30 cases of CHB, and 30 cases of NC. Samples were randomly divided into training and validation groups at a 2:1 ratio. Training group data were used to investigate the diagnostic value of the relative signal intensity for the lectin probe combined with alpha-fetoprotein (AFP). The efficacy of models for HCC diagnosis were analyzed by receiver operating characteristic (ROC) curves. Results In terms of IgG, a model combining three lectins and AFP had good diagnostic accuracy for HCC. The area under the ROC curve was 0.96 (P < 0.05), the sensitivity was 82.54%, and the specificity was 100%. In terms of IgM, a model including one lectin combined with AFP had an area under the curve of 0.90 (P < 0.05), sensitivity of 75.41%, and specificity of 100%. Conclusion Estimation of serum IgG and IgM glycosylation could act as complementary techniques to improve diagnosis and shed light on the occurrence and development of the HCC
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Affiliation(s)
- Yue Zhang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Clinical Research Center for Laboratory Medicine, Shenyang, China
| | - Sihua Zhang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Clinical Research Center for Laboratory Medicine, Shenyang, China
| | - Jianhua Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Clinical Research Center for Laboratory Medicine, Shenyang, China
| | - Yunli Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yanjie Liu
- Department of Laboratory Medicine, Chaoyang Central Hospital, Chaoyang, China
| | - Shuang Shen
- Department of Laboratory Medicine, Huludao Central Hospital, Huludao, China
| | - Fangfang Tian
- Department of Laboratory Medicine, Fuxin Central Hospital, Fuxin, China
| | - Gaobo Yan
- Department of Laboratory Medicine, Dandong Central Hospital, Dandong, China
| | - Yongqing Gao
- Department of Laboratory Medicine, Tieling Central Hospital, Tieling, China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Clinical Research Center for Laboratory Medicine, Shenyang, China
- *Correspondence: Xiaosong Qin,
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Riley NM, Wen RM, Bertozzi CR, Brooks JD, Pitteri SJ. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Adv Cancer Res 2022; 157:83-121. [PMID: 36725114 PMCID: PMC10582998 DOI: 10.1016/bs.acr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mucin-domain glycoproteins are highly O-glycosylated cell surface and secreted proteins that serve as both biochemical and biophysical modulators. Aberrant expression and glycosylation of mucins are known hallmarks in numerous malignancies, yet mucin-domain glycoproteins remain enigmatic in the broad landscape of cancer glycobiology. Here we review the multifaceted roles of mucins in cancer through the lens of the analytical and biochemical methods used to study them. We also describe a collection of emerging tools that are specifically equipped to characterize mucin-domain glycoproteins in complex biological backgrounds. These approaches are poised to further elucidate how mucin biology can be understood and subsequently targeted for the next generation of cancer therapeutics.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States.
| | - Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, Stanford, CA, United States
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States.
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Choi W, Kang S, Kim J. New insights into the role of the Golgi apparatus in the pathogenesis and therapeutics of human diseases. Arch Pharm Res 2022; 45:671-692. [PMID: 36178581 DOI: 10.1007/s12272-022-01408-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022]
Abstract
The Golgi apparatus is an essential cellular organelle that mediates homeostatic functions, including vesicle trafficking and the post-translational modification of macromolecules. Its unique stacked structure and dynamic functions are tightly regulated, and several Golgi proteins play key roles in the functioning of unconventional protein secretory pathways triggered by cellular stress responses. Recently, an increasing number of studies have implicated defects in Golgi functioning in human diseases such as cancer, neurodegenerative, and immunological disorders. Understanding the extraordinary characteristics of Golgi proteins is important for elucidating its associated intracellular signaling mechanisms and has important ramifications for human health. Therefore, analyzing the mechanisms by which the Golgi participates in disease pathogenesis may be useful for developing novel therapeutic strategies. This review articulates the structural features and abnormalities of the Golgi apparatus reported in various diseases and the suspected mechanisms underlying the Golgi-associated pathologies. Furthermore, we review the potential therapeutic strategies based on Golgi function.
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Affiliation(s)
- Wooseon Choi
- Department of Pharmacology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea
| | - Shinwon Kang
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jiyoon Kim
- Department of Pharmacology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.
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Marciel MP, Haldar B, Hwang J, Bhalerao N, Bellis SL. Role of tumor cell sialylation in pancreatic cancer progression. Adv Cancer Res 2022; 157:123-155. [PMID: 36725107 DOI: 10.1016/bs.acr.2022.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest malignancies and is currently the third leading cause of cancer death. The aggressiveness of PDAC stems from late diagnosis, early metastasis, and poor efficacy of current chemotherapies. Thus, there is an urgent need for effective biomarkers for early detection of PDAC and development of new therapeutic strategies. It has long been known that cellular glycosylation is dysregulated in pancreatic cancer cells, however, tumor-associated glycans and their cognate glycosylating enzymes have received insufficient attention as potential clinical targets. Aberrant glycosylation affects a broad range of pathways that underpin tumor initiation, metastatic progression, and resistance to cancer treatment. One of the prevalent alterations in the cancer glycome is an enrichment in a select group of sialylated glycans including sialylated, branched N-glycans, sialyl Lewis antigens, and sialylated forms of truncated O-glycans such as the sialyl Tn antigen. These modifications affect the activity of numerous cell surface receptors, which collectively impart malignant characteristics typified by enhanced cell proliferation, migration, invasion and apoptosis-resistance. Additionally, sialic acids on tumor cells engage inhibitory Siglec receptors on immune cells to dampen anti-tumor immunity, further promoting cancer progression. The goal of this review is to summarize the predominant changes in sialylation occurring in pancreatic cancer, the biological functions of sialylated glycoproteins in cancer pathogenesis, and the emerging strategies for targeting sialoglycans and Siglec receptors in cancer therapeutics.
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Affiliation(s)
- Michael P Marciel
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Barnita Haldar
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jihye Hwang
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nikita Bhalerao
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Susan L Bellis
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
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Garay YC, Cejas RB, Lorenz V, Zlocowski N, Parodi P, Ferrero FA, Angeloni G, García VA, Sendra VG, Lardone RD, Irazoqui FJ. Polypeptide N-acetylgalactosamine transferase 3: a post-translational writer on human health. J Mol Med (Berl) 2022; 100:1387-1403. [PMID: 36056254 DOI: 10.1007/s00109-022-02249-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 10/14/2022]
Abstract
Polypeptide N-acetylgalactosamine transferase 3 (ppGalNAc-T3) is an enzyme involved in the initiation of O-GalNAc glycan biosynthesis. Acting as a writer of frequent post-translational modification (PTM) on human proteins, ppGalNAc-T3 has key functions in the homeostasis of human cells and tissues. We review the relevant roles of this molecule in the biosynthesis of O-GalNAc glycans, as well as in biological functions related to human physiological and pathological conditions. With main emphasis in ppGalNAc-T3, we draw attention to the different ways involved in the modulation of ppGalNAc-Ts enzymatic activity. In addition, we take notice on recent reports of ppGalNAc-T3 having different subcellular localizations, highlight critical intrinsic and extrinsic functions in cellular physiology that are exerted by ppGalNAc-T3-synthesized PTMs, and provide an update on several human pathologies associated with dysfunctional ppGalNAc-T3. Finally, we propose biotechnological tools as new therapeutic options for the treatment of pathologies related to altered ppGalNAc-T3. KEY MESSAGES: ppGalNAc-T3 is a key enzyme in the human O-GalNAc glycans biosynthesis. enzyme activity is regulated by PTMs, lectin domain and protein-protein interactions. ppGalNAc-T3 is located in human Golgi apparatus and cell nucleus. ppGalNAc-T3 has a central role in cell physiology as well as in several pathologies. Biotechnological tools for pathological management are proposed.
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Affiliation(s)
- Yohana Camila Garay
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Romina Beatriz Cejas
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Virginia Lorenz
- Facultad de Bioquímica Y Ciencias Biológicas, Instituto de Salud Y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Santa Fe, Argentina
| | - Natacha Zlocowski
- Centro de Microscopía Electrónica, Facultad de Ciencias Médicas, Instituto de Investigaciones en Ciencias de La Salud (INICSA-CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Pedro Parodi
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Franco Alejandro Ferrero
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Genaro Angeloni
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Valentina Alfonso García
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Victor German Sendra
- Center for Translational Ocular Immunology, Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA
| | - Ricardo Dante Lardone
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Fernando José Irazoqui
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.
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Zheng PF, Chen LZ, Liu P, Liu ZY, Pan HW. Integrative identification of immune-related key genes in atrial fibrillation using weighted gene coexpression network analysis and machine learning. Front Cardiovasc Med 2022; 9:922523. [PMID: 35966550 PMCID: PMC9363882 DOI: 10.3389/fcvm.2022.922523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe immune system significantly participates in the pathologic process of atrial fibrillation (AF). However, the molecular mechanisms underlying this participation are not completely explained. The current research aimed to identify critical genes and immune cells that participate in the pathologic process of AF.MethodsCIBERSORT was utilized to reveal the immune cell infiltration pattern in AF patients. Meanwhile, weighted gene coexpression network analysis (WGCNA) was utilized to identify meaningful modules that were significantly correlated with AF. The characteristic genes correlated with AF were identified by the least absolute shrinkage and selection operator (LASSO) logistic regression and support vector machine recursive feature elimination (SVM-RFE) algorithm.ResultsIn comparison to sinus rhythm (SR) individuals, we observed that fewer activated mast cells and regulatory T cells (Tregs), as well as more gamma delta T cells, resting mast cells, and M2 macrophages, were infiltrated in AF patients. Three significant modules (pink, red, and magenta) were identified to be significantly associated with AF. Gene enrichment analysis showed that all 717 genes were associated with immunity- or inflammation-related pathways and biological processes. Four hub genes (GALNT16, HTR2B, BEX2, and RAB8A) were revealed to be significantly correlated with AF by the SVM-RFE algorithm and LASSO logistic regression. qRT–PCR results suggested that compared to the SR subjects, AF patients exhibited significantly reduced BEX2 and GALNT16 expression, as well as dramatically elevated HTR2B expression. The AUC measurement showed that the diagnostic efficiency of BEX2, HTR2B, and GALNT16 in the training set was 0.836, 0.883, and 0.893, respectively, and 0.858, 0.861, and 0.915, respectively, in the validation set.ConclusionsThree novel genes, BEX2, HTR2B, and GALNT16, were identified by WGCNA combined with machine learning, which provides potential new therapeutic targets for the early diagnosis and prevention of AF.
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Affiliation(s)
- Peng-Fei Zheng
- Department of Cardiology, Hunan Provincial People's Hospital, Changsha, China
- Clinical Research Center for Heart Failure in Hunan Province, Changsha, China
- Hunan Provincial People's Hospital, Institute of Cardiovascular Epidemiology, Changsha, China
| | - Lu-Zhu Chen
- Department of Cardiology, The Central Hospital of ShaoYang, Shaoyang, China
| | - Peng Liu
- Department of Cardiology, The Central Hospital of ShaoYang, Shaoyang, China
| | - Zheng-Yu Liu
- Department of Cardiology, Hunan Provincial People's Hospital, Changsha, China
- Clinical Research Center for Heart Failure in Hunan Province, Changsha, China
- Hunan Provincial People's Hospital, Institute of Cardiovascular Epidemiology, Changsha, China
- *Correspondence: Zheng-Yu Liu
| | - Hong Wei Pan
- Department of Cardiology, Hunan Provincial People's Hospital, Changsha, China
- Clinical Research Center for Heart Failure in Hunan Province, Changsha, China
- Hunan Provincial People's Hospital, Institute of Cardiovascular Epidemiology, Changsha, China
- Hong Wei Pan
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Liao C, Wang Q, An J, Chen J, Li X, Long Q, Xiao L, Guan X, Liu J. CD44 Glycosylation as a Therapeutic Target in Oncology. Front Oncol 2022; 12:883831. [PMID: 35936713 PMCID: PMC9351704 DOI: 10.3389/fonc.2022.883831] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/10/2022] [Indexed: 11/27/2022] Open
Abstract
The interaction of non-kinase transmembrane glycoprotein CD44 with ligands including hyaluronic acid (HA) is closely related to the occurrence and development of tumors. Changes in CD44 glycosylation can regulate its binding to HA, Siglec-15, fibronectin, TM4SF5, PRG4, FGF2, collagen and podoplanin and activate or inhibit c-Src/STAT3/Twist1/Bmi1, PI3K/AKT/mTOR, ERK/NF-κB/NANOG and other signaling pathways, thereby having a profound impact on the tumor microenvironment and tumor cell fate. However, the glycosylation of CD44 is complex and largely unknown, and the current understanding of how CD44 glycosylation affects tumors is limited. These issues must be addressed before targeted CD44 glycosylation can be applied to treat human cancers.
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Affiliation(s)
- Chengcheng Liao
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Qian Wang
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Life Sciences Institute, Zunyi Medical University, Zunyi, China
| | - Jiaxing An
- Department of Gastroenterology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jie Chen
- Department of Urology, The Third Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xiaolan Li
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Life Sciences Institute, Zunyi Medical University, Zunyi, China
| | - Qian Long
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Linlin Xiao
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
- *Correspondence: Linlin Xiao, ; Xiaoyan Guan, ; Jianguo Liu,
| | - Xiaoyan Guan
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
- *Correspondence: Linlin Xiao, ; Xiaoyan Guan, ; Jianguo Liu,
| | - Jianguo Liu
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
- *Correspondence: Linlin Xiao, ; Xiaoyan Guan, ; Jianguo Liu,
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Thongboonkerd V, Chaiyarit S. Gel-Based and Gel-Free Phosphoproteomics to Measure and Characterize Mitochondrial Phosphoproteins. Curr Protoc 2022; 2:e390. [PMID: 35275445 DOI: 10.1002/cpz1.390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mitochondrion is a key intracellular organelle regulating metabolic processes, oxidative stress, energy production, calcium homeostasis, and cell survival. Protein phosphorylation plays an important role in regulating mitochondrial functions and cellular signaling pathways. Dysregulation of protein phosphorylation status can cause protein malfunction and abnormal signal transduction, leading to organ dysfunction and disease. Investigating the mitochondrial phosphoproteins is therefore crucial to better understand the molecular and pathogenic mechanisms of many metabolic disorders. Conventional analyses of phosphoproteins, for instance, via western blotting, can be done only for proteins for which specific antibodies to their phosphorylated forms are available. Moreover, such an approach is not suitable for large-scale study of phosphoproteins. Currently, proteomics represents an important tool for large-scale analysis of proteins and their post-translational modifications, including phosphorylation. Here, we provide step-by-step protocols for the proteomics analysis of mitochondrial phosphoproteins (the phosphoproteome), using renal tubular cells as an example. These protocols include methods to effectively isolate mitochondria and to validate the efficacy of mitochondrial enrichment as well as its purity. We also provide detailed protocols for performing both gel-based and gel-free phosphoproteome analyses. The gel-based analysis involves two-dimensional gel electrophoresis and phosphoprotein-specific staining, followed by protein identification via mass spectrometry, whereas the gel-free approach is based on in-solution mass spectrometric identification of specific phosphorylation sites and residues. In all, these approaches allow large-scale analyses of mitochondrial phosphoproteins that can be applied to other cells and tissues of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Mitochondrial isolation/purification from renal tubular cells Support Protocol: Validation of enrichment efficacy and purity of mitochondrial isolation Basic Protocol 2: Gel-based phosphoproteome analysis Basic Protocol 3: Gel-free phosphoproteome analysis.
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Affiliation(s)
- Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sakdithep Chaiyarit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Insights on ErbB glycosylation – contributions to precision oncology. Trends Cancer 2022; 8:448-455. [DOI: 10.1016/j.trecan.2022.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/03/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022]
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47
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Blšákova A, Květoň F, Lorencová L, Blixt O, Vikartovská A, Kasak P, Tkac J. Amplified suspension magnetic bead-based assay for sensitive detection of anti-glycan antibodies as potential cancer biomarkers. Anal Chim Acta 2022; 1195:339444. [DOI: 10.1016/j.aca.2022.339444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/27/2021] [Accepted: 01/03/2022] [Indexed: 11/16/2022]
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Tvaroška I. Glycosyltransferases as targets for therapeutic intervention in cancer and inflammation: molecular modeling insights. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-021-02026-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Groux‐Degroote S, Vicogne D, Cogez V, Schulz C, Harduin‐Lepers A. B4GALNT2 Controls Sd
a
and SLe
x
Antigen Biosynthesis in Healthy and Cancer Human Colon. Chembiochem 2021. [DOI: 10.1002/cbic.202100363
expr 800938655 + 862139822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Sophie Groux‐Degroote
- Univ. Lille CNRS UMR 8576 UGSF Unité de Glycobiologie Structurale et Fonctionnelle 59000 Lille France
| | - Dorothée Vicogne
- Univ. Lille CNRS UMR 8576 UGSF Unité de Glycobiologie Structurale et Fonctionnelle 59000 Lille France
| | - Virginie Cogez
- Univ. Lille CNRS UMR 8576 UGSF Unité de Glycobiologie Structurale et Fonctionnelle 59000 Lille France
| | - Céline Schulz
- Univ. Lille CNRS UMR 8576 UGSF Unité de Glycobiologie Structurale et Fonctionnelle 59000 Lille France
| | - Anne Harduin‐Lepers
- Univ. Lille CNRS UMR 8576 UGSF Unité de Glycobiologie Structurale et Fonctionnelle 59000 Lille France
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Groux-Degroote S, Vicogne D, Cogez V, Schulz C, Harduin-Lepers A. B4GALNT2 Controls Sd a and SLe x Antigen Biosynthesis in Healthy and Cancer Human Colon. Chembiochem 2021; 22:3381-3390. [PMID: 34397142 PMCID: PMC9290495 DOI: 10.1002/cbic.202100363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/11/2021] [Indexed: 12/30/2022]
Abstract
The Sda carbohydrate antigen and the corresponding biosynthetic enzyme B4GALNT2 are primarily expressed in human normal colonic mucosa and are down‐regulated to variable degrees in colon cancer. On the other hand, the tumor associated antigen SLex is not detected in the healthy colon and is upregulated in colon cancer. High level of B4GALNT2 gene expression appears to be a good marker of prognosis in colon cancer; however, the molecular mechanisms regulating these carbohydrate antigens’ expression are still poorly understood. We review here the most recent progress made towards understanding this balanced expression of blood group carbohydrate epitopes Sda and SLex. In particular in recent years, we have attained a better understanding of genetic and epigenetic regulation of the B4GALNT2 gene and of the subcellular fate of B4GALNT2 isoforms.
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Affiliation(s)
- Sophie Groux-Degroote
- Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Dorothée Vicogne
- Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Virginie Cogez
- Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Céline Schulz
- Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Anne Harduin-Lepers
- Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
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