1
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Shu L, Lin S, Zhou S, Yuan T. Glycan-Lectin interactions between platelets and tumor cells drive hematogenous metastasis. Platelets 2024; 35:2315037. [PMID: 38372252 DOI: 10.1080/09537104.2024.2315037] [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: 11/02/2023] [Accepted: 01/30/2024] [Indexed: 02/20/2024]
Abstract
Glycosylation is a ubiquitous cellular or microenvironment-specific post-translational modification that occurs on the surface of normal cells and tumor cells. Tumor cell-associated glycosylation is involved in hematogenous metastasis. A wide variety of tumors undergo aberrant glycosylation to interact with platelets. As platelets have many opportunities to engage circulating tumor cells, they represent an important avenue into understanding the role glycosylation plays in tumor metastasis. Platelet involvement in tumor metastasis is evidenced by observations that platelets protect tumor cells from damaging shear forces and immune system attack, aid metastasis through the endothelium at specific sites, and facilitate tumor survival and colonization. During platelet-tumor-cell interactions, many opportunities for glycan-ligand binding emerge. This review integrates the latest information about glycans, their ligands, and how they mediate platelet-tumor interactions. We also discuss adaptive changes that tumors undergo upon glycan-lectin binding and the impact glycans have on targeted therapeutic strategies for treating tumors in clinical settings.
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Affiliation(s)
- Longqiang Shu
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shanyi Lin
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Orthopedic Surgery, Peking University People's Hospital, Beijing, China
| | - Shumin Zhou
- Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Yuan
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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2
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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 2024:10.1007/s00216-024-05352-3. [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] [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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Hu Q, Wu HJ. Direct Glycan Analysis of Biological Samples and Intact Glycoproteins by Integrating Machine Learning-Driven Surface-Enhanced Raman Scattering and Boronic Acid Arrays. ACS MEASUREMENT SCIENCE AU 2024; 4:307-314. [PMID: 38910864 PMCID: PMC11191725 DOI: 10.1021/acsmeasuresciau.4c00014] [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: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 06/25/2024]
Abstract
Frequent monitoring of glycan patterns is a critical step in studying glycan-mediated cellular processes. However, the current glycan analysis tools are resource-intensive and less suitable for routine use in standard laboratories. We developed a novel glycan detection platform by integrating surface-enhanced Raman spectroscopy (SERS), boronic acid (BA) receptors, and machine learning tools. This sensor monitors the molecular fingerprint spectra of BA binding to cis-diol-containing glycans. Different types of BA receptors could yield different stereoselective reactions toward different glycans and exhibit unique vibrational spectra. By integration of the Raman spectra collected from different BA receptors, the structural information can be enriched, eventually improving the accuracy of glycan classification and quantification. Here, we established a SERS-based sensor incorporating multiple different BA receptors. This sensing platform could directly analyze the biological samples, including whole milk and intact glycoproteins (fetuin and asialofetuin), without tedious glycan release and purification steps. The results demonstrate the platform's ability to classify milk oligosaccharides with remarkable classification accuracy, despite the presence of other non-glycan constituents in the background. This sensor could also directly quantify sialylation levels of a fetuin/asialofetuin mixture without glycan release procedures. Moreover, by selecting appropriate BA receptors, the sensor exhibits an excellent performance of differentiating between α2,3 and α2,6 linkages of sialic acids. This low-cost, rapid, and highly accessible sensor will provide the scientific community with an invaluable tool for routine glycan screening in standard laboratories.
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Affiliation(s)
- Qiang Hu
- The Artie McFerrin Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Hung-Jen Wu
- The Artie McFerrin Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
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4
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Liu M, Duan Y, Dong J, Zhang K, Jin X, Gao M, Jia H, Chen J, Liu M, Wei M, Zhong X. Early signs of neurodegenerative diseases: Possible mechanisms and targets for Golgi stress. Biomed Pharmacother 2024; 175:116646. [PMID: 38692058 DOI: 10.1016/j.biopha.2024.116646] [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: 02/28/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
The Golgi apparatus plays a crucial role in mediating the modification, transport, and sorting of intracellular proteins and lipids. The morphological changes occurring in the Golgi apparatus are exceptionally important for maintaining its function. When exposed to external pressure or environmental stimulation, the Golgi apparatus undergoes adaptive changes in both structure and function, which are known as Golgi stress. Although certain signal pathway responses or post-translational modifications have been observed following Golgi stress, further research is needed to comprehensively summarize and understand the related mechanisms. Currently, there is evidence linking Golgi stress to neurodegenerative diseases; however, the role of Golgi stress in the progression of neurodegenerative diseases such as Alzheimer's disease remains largely unexplored. This review focuses on the structural and functional alterations of the Golgi apparatus during stress, elucidating potential mechanisms underlying the involvement of Golgi stress in regulating immunity, autophagy, and metabolic processes. Additionally, it highlights the pivotal role of Golgi stress as an early signaling event implicated in the pathogenesis and progression of neurodegenerative diseases. Furthermore, this study summarizes prospective targets that can be therapeutically exploited to mitigate neurodegenerative diseases by targeting Golgi stress. These findings provide a theoretical foundation for identifying novel breakthroughs in preventing and treating neurodegenerative diseases.
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Affiliation(s)
- Mengyu Liu
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Ying Duan
- Liaoning Maternal and Child Health Hospital, Shayang, Liaoning 110005, China
| | - Jianru Dong
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Kaisong Zhang
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Xin Jin
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Menglin Gao
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Huachao Jia
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Ju Chen
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Mingyan Liu
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China.
| | - Minjie Wei
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China; Liaoning Medical Diagnosis and Treatment Center, Shenyang, Liaoning 110167, China.
| | - Xin Zhong
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China.
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5
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Yom A, Chiang A, Lewis NE. Boltzmann Model Predicts Glycan Structures from Lectin Binding. Anal Chem 2024; 96:8332-8341. [PMID: 38720429 PMCID: PMC11162346 DOI: 10.1021/acs.analchem.3c04992] [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: 05/20/2024]
Abstract
Glycans are complex oligosaccharides that are involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese hamster ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego, California 92093, United States
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Immunology Center of Georgia, Augusta University, Augusta, Georgia 30912, United States
- Department of Medicine, Augusta University, Augusta, Georgia 30912, United States
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Department of Bioengineering, University of California, San Diego, California 92093, United States
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6
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Domma AJ, Henderson LA, Nurdin JA, Kamil JP. Uncloaking the viral glycocalyx: How do viruses exploit glycoimmune checkpoints? Adv Virus Res 2024; 119:63-110. [PMID: 38897709 PMCID: PMC11192240 DOI: 10.1016/bs.aivir.2024.03.001] [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: 06/21/2024]
Abstract
The surfaces of cells and enveloped viruses alike are coated in carbohydrates that play multifarious roles in infection and immunity. Organisms across all kingdoms of life make use of a diverse set of monosaccharide subunits, glycosidic linkages, and branching patterns to encode information within glycans. Accordingly, sugar-patterning enzymes and glycan binding proteins play integral roles in cell and organismal biology, ranging from glycoprotein quality control within the endoplasmic reticulum to lymphocyte migration, coagulation, inflammation, and tissue homeostasis. Unsurprisingly, genes involved in generating and recognizing oligosaccharide patterns are playgrounds for evolutionary conflicts that abound in cross-species interactions, exemplified by the myriad plant lectins that function as toxins. In vertebrates, glycans bearing acidic nine-carbon sugars called sialic acids are key regulators of immune responses. Various bacterial and fungal pathogens adorn their cells in sialic acids that either mimic their hosts' or are stolen from them. Yet, how viruses commandeer host sugar-patterning enzymes to thwart immune responses remains poorly studied. Here, we review examples of viruses that interact with sialic acid-binding immunoglobulin-like lectins (Siglecs), a family of immune cell receptors that regulate toll-like receptor signaling and govern glycoimmune checkpoints, while highlighting knowledge gaps that merit investigation. Efforts to illuminate how viruses leverage glycan-dependent checkpoints may translate into new clinical treatments that uncloak viral antigens and infected cell surfaces by removing or masking immunosuppressive sialoglycans, or by inhibiting viral gene products that induce their biosynthesis. Such approaches may hold the potential to unleash the immune system to clear long intractable chronic viral infections.
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Affiliation(s)
- Anthony J Domma
- LSU Health Sciences Center at Shreveport, Shreveport, LA, United States
| | | | - Jeffery A Nurdin
- LSU Health Sciences Center at Shreveport, Shreveport, LA, United States
| | - Jeremy P Kamil
- LSU Health Sciences Center at Shreveport, Shreveport, LA, United States.
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7
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Chatham JC, Patel RP. Protein glycosylation in cardiovascular health and disease. Nat Rev Cardiol 2024:10.1038/s41569-024-00998-z. [PMID: 38499867 DOI: 10.1038/s41569-024-00998-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/13/2024] [Indexed: 03/20/2024]
Abstract
Protein glycosylation, which involves the attachment of carbohydrates to proteins, is one of the most abundant protein co-translational and post-translational modifications. Advances in technology have substantially increased our knowledge of the biosynthetic pathways involved in protein glycosylation, as well as how changes in glycosylation can affect cell function. In addition, our understanding of the role of protein glycosylation in disease processes is growing, particularly in the context of immune system function, infectious diseases, neurodegeneration and cancer. Several decades ago, cell surface glycoproteins were found to have an important role in regulating ion transport across the cardiac sarcolemma. However, with very few exceptions, our understanding of how changes in protein glycosylation influence cardiovascular (patho)physiology remains remarkably limited. Therefore, in this Review, we aim to provide an overview of N-linked and O-linked protein glycosylation, including intracellular O-linked N-acetylglucosamine protein modification. We discuss our current understanding of how all forms of protein glycosylation contribute to normal cardiovascular function and their roles in cardiovascular disease. Finally, we highlight potential gaps in our knowledge about the effects of protein glycosylation on the heart and vascular system, highlighting areas for future research.
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Affiliation(s)
- John C Chatham
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Rakesh P Patel
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
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8
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Yom A, Chiang A, Lewis NE. A Boltzmann model predicts glycan structures from lectin binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.03.543532. [PMID: 37333412 PMCID: PMC10274649 DOI: 10.1101/2023.06.03.543532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Glycans are complex oligosaccharides involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese Hamster Ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego. CA 92093, USA
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
- Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Medicine, Augusta University, Augusta, GA 30912, USA
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego. CA 92093, USA
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
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9
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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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10
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Ma S, Liu L, Eggink D, Herfst S, Fouchier RAM, de Vries RP, Boons GJ. Asymmetrical Biantennary Glycans Prepared by a Stop-and-Go Strategy Reveal Receptor Binding Evolution of Human Influenza A Viruses. JACS AU 2024; 4:607-618. [PMID: 38425896 PMCID: PMC10900492 DOI: 10.1021/jacsau.3c00695] [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: 11/08/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 03/02/2024]
Abstract
Glycan binding properties of respiratory viruses have been difficult to probe due to a lack of biologically relevant glycans for binding studies. Here, a stop-and-go chemoenzymatic methodology is presented that gave access to a panel of 32 asymmetrical biantennary N-glycans having various numbers of N-acetyl lactosamine (LacNAc) repeating units capped by α2,3- or α2,6-sialosides resembling structures found in airway tissues. It exploits that the branching enzymes MGAT1 and MGAT2 can utilize unnatural UDP-2-deoxy-2-trifluoro-N-acetamido-glucose (UDP-GlcNTFA) as donor. The TFA moiety of the resulting glycans can be hydrolyzed to give GlcNH2 at one of the antennae, which temporarily blocks extension by glycosyl transferases. The N-glycans were printed as a microarray that was probed for receptor binding specificities of the evolutionary distinct human A(H3N2) and A(H1N1)pdm09 viruses. It was found that not only the sialoside type but also the length of the LacNAc chain and presentation at the α1,3-antenna of N-glycans are critical for binding. Early A(H3N2) viruses bound to 2,6-sialosides at a single LacNAc moiety at the α1,3-antenna whereas later viruses required the sialoside to be presented at a tri-LacNAc moiety. Surprisingly, most of the A(H3N2) viruses that appeared after 2021 regained binding capacity to sialosides presented at a di-LacNAc moiety. As a result, these viruses again agglutinate erythrocytes, commonly employed for antigenic characterization of influenza viruses. Human A(H1N1)pdm09 viruses have similar receptor binding properties as recent A(H3N2) viruses. The data indicate that an asymmetric N-glycan having 2,6-sialoside at a di-LacNAc moiety is a commonly employed receptor by human influenza A viruses.
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Affiliation(s)
- Shengzhou Ma
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Lin Liu
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Dirk Eggink
- Amsterdam
UMC Location University of Amsterdam, Department
of Medical Microbiology and Infection prevention, Laboratory of Applied
Evolutionary Biology, 1105
AZ Amsterdam, The
Netherlands
- Center
for Infectious Disease Control, National
Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands
| | - Sander Herfst
- Department
of Viroscience, Erasmus University Medical
Center, 3015 CD Rotterdam, The Netherlands
| | - Ron A. M. Fouchier
- Department
of Viroscience, Erasmus University Medical
Center, 3015 CD Rotterdam, The Netherlands
| | - Robert P. de Vries
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Geert-Jan Boons
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Bijvoet
Center for Biomolecular Research, Utrecht
University, Padualaan
8, 3584 CH Utrecht, The Netherlands
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11
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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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12
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Lado-Baleato Ó, Torre J, O’Flaherty R, Alonso-Sampedro M, Carballo I, Fernández-Merino C, Vidal C, Gude F, Saldova R, González-Quintela A. Age-Related Changes in Serum N-Glycome in Men and Women-Clusters Associated with Comorbidity. Biomolecules 2023; 14:17. [PMID: 38254617 PMCID: PMC10813383 DOI: 10.3390/biom14010017] [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: 11/15/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
(1) Aim: To describe, in a general adult population, the serum N-glycome in relation to age in men and women, and investigate the association of N-glycome patterns with age-related comorbidity; (2) Methods: The serum N-glycome was studied by hydrophilic interaction chromatography with ultra-performance liquid chromatography in 1516 randomly selected adults (55.3% women; age range 18-91 years). Covariates included lifestyle factors, metabolic disorders, inflammatory markers, and an index of comorbidity. Principal component analysis was used to define clusters of individuals based on the 46 glycan peaks obtained in chromatograms; (3) Results: The serum N-glycome changed with ageing, with significant differences between men and women, both in individual N-glycan peaks and in groups defined by common features (branching, galactosylation, sialylation, fucosylation, and oligomannose). Through K-means clustering algorithm, the individuals were grouped into a cluster characterized by abundance of simpler N-glycans and a cluster characterized by abundance of higher-order N-glycans. The individuals of the first cluster were older, showed higher concentrations of glucose and glycation markers, higher levels of some inflammatory markers, lower glomerular filtration rate, and greater comorbidity index; (4) Conclusions: The serum N-glycome changes with ageing with sex dimorphism. The N-glycome could be, in line with the inflammaging hypothesis, a marker of unhealthy aging.
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Affiliation(s)
- Óscar Lado-Baleato
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
- ISCIII Support Platforms for Clinical Research, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostel, 15706 Santiago de Compostela, Spain
| | - Jorge Torre
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
| | - Róisín O’Flaherty
- GlycoScience Group, National Institute for Bioprocessing Research and Training, Fosters Avenue, A94 X099 Dublin, Ireland (R.S.)
- Department of Chemistry, Maynooth University, W23 F2K8 Maynooth, Ireland
| | - Manuela Alonso-Sampedro
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
| | - Iago Carballo
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
| | - Carmen Fernández-Merino
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
- Primary Care, Santiago de Compostela Area, 15706 Santiago de Compostela, Spain
| | - Carmen Vidal
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
| | - Francisco Gude
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
- Primary Care, Santiago de Compostela Area, 15706 Santiago de Compostela, Spain
| | - Radka Saldova
- GlycoScience Group, National Institute for Bioprocessing Research and Training, Fosters Avenue, A94 X099 Dublin, Ireland (R.S.)
- UCD School of Medicine, College of Health and Agricultural Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Arturo González-Quintela
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
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13
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Ma S, Liu L, Eggink D, Herfst S, Fouchier RAM, de Vries RP, Boons GJ. Asymmetrical Bi-antennary Glycans Prepared by a Stop-and-Go Strategy Reveal Receptor Binding Evolution of Human Influenza A Viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566285. [PMID: 37986780 PMCID: PMC10659364 DOI: 10.1101/2023.11.08.566285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Glycan binding properties of respiratory viruses have been difficult to probe due to a lack of biological relevant glycans for binding studies. Here, a stop-and-go chemoenzymatic methodology is presented that gave access to a panel of 32 asymmetrical bi-antennary N-glycans having various numbers of N-acetyl lactosamine (LacNAc) repeating units capped by α2,3- or α2,6-sialosides resembling structures found in airway tissues. It exploits that the branching enzymes MGAT1 and MGAT2 can utilize unnatural UDP-2-deoxy-2-trifluoro-N-acetamido-glucose (UDP-GlcNTFA) as donor. The TFA moiety of the resulting glycans can be hydrolyzed to give GlcNH2 at one of the antennae that temporarily blocks extension by glycosyl transferases. The N-glycans were printed as a microarray that was probed for receptor binding specificities of evolutionary distinct human A(H3N2) and A(H1N1)pdm09 viruses. It was found that not only the sialoside type but also the length of the LacNAc chain and presentation at the α1,3-antenna of N-glycans is critical for binding. Early A(H3N2) viruses bound to 2,6-sialosides at a single LacNAc moiety at the α1,3-antenna whereas later viruses required the sialoside to be presented at a tri-LacNAc moiety. Surprisingly, most of the A(H3N2) viruses that appeared after 2021 regained binding capacity to sialosides presented at a di-LacNAc moiety. As a result, these viruses agglutinate erythrocytes again, commonly employed for antigenic characterization of influenza viruses. Human A(H1N1)pdm09 viruses have similar receptor binding properties as recent A(H3N2) viruses. The data indicates that an asymmetric N-glycan having 2,6-sialoside at a di-LacNAc moiety is a commonly employed receptor by human influenza A viruses.
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Affiliation(s)
- Shengzhou Ma
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Dirk Eggink
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Applied Evolutionary Biology, Amsterdam, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert P de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Department of Chemistry, University of Georgia, Athens, GA, USA
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14
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Niazi SK. A Critical Analysis of the FDA's Omics-Driven Pharmacodynamic Biomarkers to Establish Biosimilarity. Pharmaceuticals (Basel) 2023; 16:1556. [PMID: 38004421 PMCID: PMC10675618 DOI: 10.3390/ph16111556] [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: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 11/26/2023] Open
Abstract
Demonstrating biosimilarity entails comprehensive analytical assessment, clinical pharmacology profiling, and efficacy testing in patients for at least one medical indication, as required by the U.S. Biologics Price Competition and Innovation Act (BPCIA). The efficacy testing can be waived if the drug has known pharmacodynamic (PD) markers, leaving most therapeutic proteins out of this concession. To overcome this, the FDA suggests that biosimilar developers discover PD biomarkers using omics technologies such as proteomics, glycomics, transcriptomics, genomics, epigenomics, and metabolomics. This approach is redundant since the mode-action-action biomarkers of approved therapeutic proteins are already available, as compiled in this paper for the first time. Other potential biomarkers are receptor binding and pharmacokinetic profiling, which can be made more relevant to ensure biosimilarity without requiring biosimilar developers to conduct extensive research, for which they are rarely qualified.
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Affiliation(s)
- Sarfaraz K Niazi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, IL 60612, USA
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15
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Weigand MR, Moore AM, Hu H, Angel PM, Drake RR, Laskin J. Imaging of N-Linked Glycans in Biological Tissue Sections Using Nanospray Desorption Electrospray Ionization (nano-DESI) Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2481-2490. [PMID: 37779241 DOI: 10.1021/jasms.3c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
N-linked glycans are complex biomolecules vital to cellular functions that have been linked to a wide range of pathological conditions. Mass spectrometry imaging (MSI) has been used to study the localization of N-linked glycans in cells and tissues. However, their structural diversity presents a challenge for MSI techniques, which stimulates the development of new approaches. In this study, we demonstrate for the first time spatial mapping of N-linked glycans in biological tissues using nanospray desorption electrospray ionization mass spectrometry imaging (nano-DESI MSI). Nano-DESI MSI is an ambient ionization technique that has been previously used for imaging of metabolites, lipids, and proteins in biological tissue samples without special sample pretreatment. N-linked glycans are released from glycoproteins using an established enzymatic digestion with peptide N-glycosidase F, and their spatial localization is examined using nano-DESI MSI. We demonstrate imaging of N-linked glycans in formalin-fixed paraffin-embedded human hepatocellular carcinoma and human prostate tissues in both positive and negative ionization modes. We examine the localization of 38 N-linked glycans consisting of high mannose, hybrid fucosylated, and sialyated glycans. We demonstrate that negative mode nano-DESI MSI is well-suited for imaging of underivatized sialylated N-linked glycans. On-tissue MS/MS of different adducts of N-linked glycans proves advantageous for elucidation of the glycan sequence. This study demonstrates the applicability of liquid extraction techniques for spatial mapping of N-linked glycans in biological samples, providing an additional tool for glycobiology research.
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Affiliation(s)
- Miranda R Weigand
- Department of Chemistry, College of Science, Purdue University, West Lafayette, Indiana 47907, United States
| | - Alyssa M Moore
- Department of Chemistry, College of Science, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hang Hu
- Department of Chemistry, College of Science, Purdue University, West Lafayette, Indiana 47907, United States
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Julia Laskin
- Department of Chemistry, College of Science, Purdue University, West Lafayette, Indiana 47907, United States
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16
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Williamson DL, Nagy G. Coupling Isotopic Shifts with Collision Cross-Section Measurements for Carbohydrate Characterization in High-Resolution Ion Mobility Separations. Anal Chem 2023; 95:13992-14000. [PMID: 37683280 PMCID: PMC10538943 DOI: 10.1021/acs.analchem.3c02619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
Herein, we introduce a two-dimensional strategy to better characterize carbohydrate isomers. In a single experiment, we can derive cyclic ion mobility-mass spectrometry (cIMS-MS)-based collision cross-section (CCS) values in conjunction with measuring isotopic shifts through the relative arrival times of light and heavy isotopologues. These isotopic shifts were introduced by permethylating carbohydrates with either light, CH3, or heavy, CD3, labels at every available hydroxyl group to generate a light/heavy pair of isotopologues for every individual species analyzed. We observed that our calculated CCS values, which were exclusively measured for the light isotopologues, were orthogonal to our measured isotopic shifts (i.e., relative arrival time values between heavy and light permethylated isotopologues). Our permethylation-induced isotopic shifts scaled well with increasing molecular weight, up to ∼m/z 1300, expanding the analysis of isotopic shifts to molecules 3-4 times as large as those previously studied. Our presented use of coupling CCS values with the measurement of isotopic shifts in a single cIMS-MS experiment is a proof-of-concept demonstration that our two-dimensional approach can improve the characterization of challenging isomeric carbohydrates. We envision that our presented 2D approach will have broad utility for varying molecular classes as well as being amenable to many forms of derivatization.
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Affiliation(s)
- David L Williamson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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17
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Katner S, Ginsburg EP, Hampton JD, Peterson EJ, Koblinski JE, Farrell NP. A Comparison of Di- and Trinuclear Platinum Complexes Interacting with Glycosaminoglycans for Targeted Chemotherapy. ACS Med Chem Lett 2023; 14:1224-1230. [PMID: 37736178 PMCID: PMC10510529 DOI: 10.1021/acsmedchemlett.3c00244] [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: 06/01/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
Heparan sulfate proteoglycans (HSPGs) and their associated proteins aid in tumor progression through modulation of biological events such as cell invasion, angiogenesis, metastasis, and immunological responses. Metalloshielding of the anionic heparan sulfate (HS) chains by cationic polynuclear platinum complexes (PPCs) prevents the HS from interacting with HS-associated proteins and thus diminishes the critical functions of HSPG. Studies herein exploring the PPC-HS interactions demonstrated that a series of PPCs varying in charge, nuclearity, distance between Pt centers, and hydrogen-bonding ability influence HS affinity. We report that the polyamine-linked complexes have high HS affinity and display excellent in vivo activity against breast cancer metastases and those arising in the bone and liver compared to carboplatin. Overall, the PPC-HS niche offers an attractive approach for targeting HSPG-expressing tumor cells.
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Affiliation(s)
- Samantha
J. Katner
- Department
of Biochemistry, Chemistry, and Geology, Minnesota State University, Mankato, Mankato, Minnesota 56001, United States
| | - Eric P. Ginsburg
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - James D. Hampton
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- Massey
Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Erica J. Peterson
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- Massey
Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Jennifer E. Koblinski
- Massey
Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Department
of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Nicholas P. Farrell
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- Massey
Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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18
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Christian JM, Zoepfl M, Johnson WE, Ginsburg E, Peterson EJ, Hampton JD, Farrell NP. Glycosaminoglycan-directed cobalt complexes. J Inorg Biochem 2023; 245:112254. [PMID: 37182504 DOI: 10.1016/j.jinorgbio.2023.112254] [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: 03/15/2023] [Revised: 04/20/2023] [Accepted: 05/08/2023] [Indexed: 05/16/2023]
Abstract
The biological activity of the 6+ Co containing Werner's Complex has been described and mechanistic considerations suggest that the highly anionic glycosaminoglycans (heparan sulfate, HS, GAGs) are implicated in this activity [Paiva et al. 2021]. To examine in detail the molecular basis of Werner's Complex biological properties we have examined a selection of simple mononuclear Co3+ compounds for their interactions with HS and Fondaparinux (FPX). FPX is a highly sulfated synthetic pentasaccharide used as a model HS substrate [Mangrum et al. 2014, Peterson et al. 2017]. The Co complexes were chosen to be formally substitution-inert and/or have the potential for covalent binding to the biomolecule. Using both indirect competitive inhibition assays and direct mass spectrometric assays, formally substitution-inert complexes bound to FPX with protection from multiple sulfate loss in the gas phase through metalloshielding. Covalent binding of Co-Cl complexes as in [CoCl(NH3)5]2+ and cis-[CoCl2(en)2]+ was confirmed by mass spectrometry. Interestingly, the former complex was shown to be an effective inhibitor of bacterial heparinase enzyme activity and to inhibit heparanase-dependent cellular invasion through the extracellular matrix (ECM). Pursuing the theme of metalloglycomics, we have observed the hitherto unappreciated biological activity of the simple [CoCl(NH3)5]2+ compound, a staple of most inorganic chemistry lab curricula.
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Affiliation(s)
- Jessica M Christian
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, VA 23284, United States of America
| | - Mary Zoepfl
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, VA 23284, United States of America
| | - Wyatt E Johnson
- Massey Cancer Center, Virginia Commonwealth University, 1300 E Marshall Street, Richmond, VA 23298-0037, United States of America
| | - Eric Ginsburg
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, VA 23284, United States of America
| | - Erica J Peterson
- Massey Cancer Center, Virginia Commonwealth University, 1300 E Marshall Street, Richmond, VA 23298-0037, United States of America
| | - J David Hampton
- Massey Cancer Center, Virginia Commonwealth University, 1300 E Marshall Street, Richmond, VA 23298-0037, United States of America
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, VA 23284, United States of America; Massey Cancer Center, Virginia Commonwealth University, 1300 E Marshall Street, Richmond, VA 23298-0037, United States of America.
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19
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Kadirvelraj R, Boruah BM, Wang S, Chapla D, Huang C, Ramiah A, Hudson KL, Prudden AR, Boons GJ, Withers SG, Wood ZA, Moremen KW. Structural basis for Lewis antigen synthesis by the α1,3-fucosyltransferase FUT9. Nat Chem Biol 2023; 19:1022-1030. [PMID: 37202521 PMCID: PMC10726971 DOI: 10.1038/s41589-023-01345-y] [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: 07/26/2022] [Accepted: 04/20/2023] [Indexed: 05/20/2023]
Abstract
Mammalian cell surface and secreted glycoproteins exhibit remarkable glycan structural diversity that contributes to numerous physiological and pathogenic interactions. Terminal glycan structures include Lewis antigens synthesized by a collection of α1,3/4-fucosyltransferases (CAZy GT10 family). At present, the only available crystallographic structure of a GT10 member is that of the Helicobacter pylori α1,3-fucosyltransferase, but mammalian GT10 fucosyltransferases are distinct in sequence and substrate specificity compared with the bacterial enzyme. Here, we determined crystal structures of human FUT9, an α1,3-fucosyltransferase that generates Lewisx and Lewisy antigens, in complex with GDP, acceptor glycans, and as a FUT9-donor analog-acceptor Michaelis complex. The structures reveal substrate specificity determinants and allow prediction of a catalytic model supported by kinetic analyses of numerous active site mutants. Comparisons with other GT10 fucosyltransferases and GT-B fold glycosyltransferases provide evidence for modular evolution of donor- and acceptor-binding sites and specificity for Lewis antigen synthesis among mammalian GT10 fucosyltransferases.
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Affiliation(s)
- Renuka Kadirvelraj
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - Bhargavi M Boruah
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Shuo Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Chin Huang
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Annapoorani Ramiah
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Kieran L Hudson
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zachary A Wood
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Kelley W Moremen
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
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20
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Clarke HA, Ma X, Shedlock CJ, Medina T, Hawkinson TR, Wu L, Ribas RA, Keohane S, Ravi S, Bizon J, Burke S, Abisambra JF, Merritt M, Prentice B, Vander Kooi CW, Gentry MS, Chen L, Sun RC. Spatial Metabolome Lipidome and Glycome from a Single brain Section. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.22.550155. [PMID: 37546843 PMCID: PMC10401929 DOI: 10.1101/2023.07.22.550155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Metabolites, lipids, and glycans are fundamental biomolecules involved in complex biological systems. They are metabolically channeled through a myriad of pathways and molecular processes that define the physiology and pathology of an organism. Here, we present a blueprint for the simultaneous analysis of spatial metabolome, lipidome, and glycome from a single tissue section using mass spectrometry imaging. Complimenting an original experimental protocol, our workflow includes a computational framework called Spatial Augmented Multiomics Interface (Sami) that offers multiomics integration, high dimensionality clustering, spatial anatomical mapping with matched multiomics features, and metabolic pathway enrichment to providing unprecedented insights into the spatial distribution and interaction of these biomolecules in mammalian tissue biology.
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21
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Abstract
It has been widely appreciated that numerous bacterial species express chitinases for the purpose of degrading environmental chitin. However, chitinases and chitin-binding proteins are also expressed by pathogenic bacterial species during infection even though mammals do not produce chitin. Alternative molecular targets are therefore likely present within the host. Here, we will describe our current understanding of chitinase/chitin-binding proteins as virulence factors that promote bacterial colonization and infection. The targets of these chitinases in the host have been shown to include immune system components, mucins, and surface glycans. Bacterial chitinases have also been shown to interact with other microorganisms, targeting the peptidoglycan or chitin in the bacterial and fungal cell wall, respectively. This review highlights that even though the name "chitinase" implies activity toward chitin, chitinases can have a wide diversity of targets, including ones relevant to host infection. Chitinases may therefore be useful as a target of future anti-infective therapeutics.
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Affiliation(s)
- Jason R. Devlin
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
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22
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Plećaš D, Mraz N, Patanaude AM, Pribić T, Pavlinac Dodig I, Pecotić R, Lauc G, Polašek O, Đogaš Z. Not-So-Sweet Dreams: Plasma and IgG N-Glycome in the Severe Form of the Obstructive Sleep Apnea. Biomolecules 2023; 13:880. [PMID: 37371460 DOI: 10.3390/biom13060880] [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: 04/20/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Obstructive sleep apnea (OSA) is a prevalent disease associated with increased risk for cardiovascular and metabolic diseases and shortened lifespan. The aim of this study was to explore the possibility of using N-glycome as a biomarker for the severe form of OSA. Seventy subjects who underwent a whole-night polysomnography/polygraphy and had apnea-hypopnea index (AHI) over 30 were compared to 23 controls (AHI under 5). Plasma samples were used to extract 39 glycan peaks using ultra-high-performance liquid chromatography (UPLC) and 27 IgG peaks using capillary gel electrophoresis (CGE). We also measured glycan age, a molecular proxy for biological aging. Three plasma and one IgG peaks were significant in a multivariate model controlling for the effects of age, sex, and body mass index. These included decreased GP24 (disialylated triantennary glycans as major structure) and GP28 (trigalactosylated, triantennary, disialylated, and trisialylated glycans), and increased GP32 (trisialylated triantennary glycan). Only one IgG glycan peak was significantly increased (P26), which contains biantennary digalactosylated glycans with core fucose. Patients with severe OSA exhibited accelerated biological aging, with a median of 6.9 years more than their chronological age (p < 0.001). Plasma N-glycome can be used as a biomarker for severe OSA.
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Affiliation(s)
- Doris Plećaš
- Mediterranean Institute for Life Sciences, 21000 Split, Croatia
| | - Nikol Mraz
- Genos Glycoscience Ltd., 10000 Zagreb, Croatia
| | | | - Tea Pribić
- Genos Glycoscience Ltd., 10000 Zagreb, Croatia
| | - Ivana Pavlinac Dodig
- Department for Neuroscience, School of Medicine, Sleep Medicine Center, University of Split, 21000 Split, Croatia
| | - Renata Pecotić
- Department for Neuroscience, School of Medicine, Sleep Medicine Center, University of Split, 21000 Split, Croatia
| | - Gordan Lauc
- Genos Glycoscience Ltd., 10000 Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Ozren Polašek
- Department of Public Health, School of Medicine, University of Split, 21000 Split, Croatia
- Department of General Courses, Algebra University, 10000 Zagreb, Croatia
| | - Zoran Đogaš
- Department for Neuroscience, School of Medicine, Sleep Medicine Center, University of Split, 21000 Split, Croatia
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23
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Bueno-Sánchez JC, Gómez-Gutiérrez AM, Maldonado-Estrada JG, Quintana-Castillo JC. Expression of placental glycans and its role in regulating peripheral blood NK cells during preeclampsia: a perspective. Front Endocrinol (Lausanne) 2023; 14:1087845. [PMID: 37206444 PMCID: PMC10190602 DOI: 10.3389/fendo.2023.1087845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/03/2023] [Indexed: 05/21/2023] Open
Abstract
Preeclampsia is a pregnancy-related multisystem disorder characterized by altered trophoblast invasion, oxidative stress, exacerbation of systemic inflammatory response, and endothelial damage. The pathogenesis includes hypertension and mild-to-severe microangiopathy in the kidney, liver, placenta, and brain. The main mechanisms involved in its pathogenesis have been proposed to limit trophoblast invasion and increase the release of extracellular vesicles from the syncytiotrophoblast into the maternal circulation, exacerbating the systemic inflammatory response. The placenta expresses glycans as part of its development and maternal immune tolerance during gestation. The expression profile of glycans at the maternal-fetal interface may play a fundamental role in physiological pregnancy changes and disorders such as preeclampsia. It is unclear whether glycans and their lectin-like receptors are involved in the mechanisms of maternal-fetal recognition by immune cells during pregnancy homeostasis. The expression profile of glycans appears to be altered in hypertensive disorders of pregnancy, which could lead to alterations in the placental microenvironment and vascular endothelium in pregnancy conditions such as preeclampsia. Glycans with immunomodulatory properties at the maternal-fetal interface are altered in early-onset severe preeclampsia, implying that innate immune system components, such as NK cells, exacerbate the systemic inflammatory response observed in preeclampsia. In this article, we discuss the evidence for the role of glycans in gestational physiology and the perspective of glycobiology on the pathophysiology of hypertensive disorders in gestation.
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Affiliation(s)
- Julio C. Bueno-Sánchez
- Reproduction Group, Department of Physiology and Biochemistry, School of Medicine, Universidad de Antioquia, Medellín, Colombia
- Department of Obstetrics and Gynecology, School of Medicine, Universidad de Antioquia, Medellín, Colombia
- Red Iberoamericana de Alteraciones Vasculares en Trastornos del Embarazo (RIVATREM), Chillan, Chile
| | - Alejandra M. Gómez-Gutiérrez
- Reproduction Group, Department of Physiology and Biochemistry, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Juan G. Maldonado-Estrada
- One Health and Veterinary Innovative Research & Development (OHVRI) Research Group, Escuela de Medicina Veterinaria, Universidad de Antioquia, Medellín, Colombia
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24
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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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25
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Bansal P, Ben Faleh A, Warnke S, Rizzo TR. Multistage Ion Mobility Spectrometry Combined with Infrared Spectroscopy for Glycan Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:695-700. [PMID: 36881006 PMCID: PMC10080682 DOI: 10.1021/jasms.2c00361] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 05/26/2023]
Abstract
The structural complexity of glycans makes their characterization challenging, not only because of the presence of various isomeric forms of the precursor molecule but also because the fragments can themselves be isomeric. We have recently developed an IMS-CID-IMS approach using structures for lossless ion manipulations (SLIM) combined with cryogenic infrared (IR) spectroscopy for glycan analysis. It allows mobility separation and collision-induced dissociation of a precursor glycan followed by mobility separation and IR spectroscopy of the fragments. While this approach holds great promise for glycan analysis, we often encounter fragments for which we have no standards to identify their spectroscopic fingerprint. In this work, we perform proof-of-principle experiments employing a multistage SLIM-based IMS-CID technique to generate second-generation fragments, followed by their mobility separation and spectroscopic interrogation. This approach provides detailed structural information about the first-generation fragments, including their anomeric form, which in turn can be used to identify the precursor glycan.
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Affiliation(s)
| | | | | | - Thomas R. Rizzo
- Laboratoire
de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale
de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
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26
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Bochner BS, O'Sullivan JA, Chang AT, Youngblood BA. Siglecs in allergy and asthma. Mol Aspects Med 2023; 90:101104. [PMID: 35835621 PMCID: PMC10757266 DOI: 10.1016/j.mam.2022.101104] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/28/2022] [Accepted: 07/03/2022] [Indexed: 01/21/2023]
Abstract
The term "allergic diseases" encompasses several common, IgE-mediated conditions that range from being annoying to those that are life-threatening. Available treatments include active avoidance of the instigating allergen and the use of a variety of oral, inhaled, intranasal, intraocular and injected agents. While most individuals with allergies do well with existing therapies, there are still unmet therapeutic needs. Siglecs (sialic acid-binding, immunoglobulin-like lectins) are a family of single-pass transmembrane I-type lectins found on various subsets of cells, especially those of the immune system. All Siglecs have extracellular domains recognizing sialoside ligands, and most contain cytoplasmic domains with inhibitory signaling activity. This review focuses on Siglecs that likely play a role in regulating allergic and asthmatic responses, and how specific Siglecs, expressed on cells such as eosinophils and mast cells, are being targeted for therapeutic benefit.
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Affiliation(s)
- Bruce S Bochner
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Jeremy A O'Sullivan
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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27
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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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28
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Wang BX, Takagi J, McShane A, Park JH, Aoki K, Griffin C, Teschler J, Kitts G, Minzer G, Tiemeyer M, Hevey R, Yildiz F, Ribbeck K. Host-derived O-glycans inhibit toxigenic conversion by a virulence-encoding phage in Vibrio cholerae. EMBO J 2023; 42:e111562. [PMID: 36504455 PMCID: PMC9890226 DOI: 10.15252/embj.2022111562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 12/14/2022] Open
Abstract
Pandemic and endemic strains of Vibrio cholerae arise from toxigenic conversion by the CTXφ bacteriophage, a process by which CTXφ infects nontoxigenic strains of V. cholerae. CTXφ encodes the cholera toxin, an enterotoxin responsible for the watery diarrhea associated with cholera infections. Despite the critical role of CTXφ during infections, signals that affect CTXφ-driven toxigenic conversion or expression of the CTXφ-encoded cholera toxin remain poorly characterized, particularly in the context of the gut mucosa. Here, we identify mucin polymers as potent regulators of CTXφ-driven pathogenicity in V. cholerae. Our results indicate that mucin-associated O-glycans block toxigenic conversion by CTXφ and suppress the expression of CTXφ-related virulence factors, including the toxin co-regulated pilus and cholera toxin, by interfering with the TcpP/ToxR/ToxT virulence pathway. By synthesizing individual mucin glycan structures de novo, we identify the Core 2 motif as the critical structure governing this virulence attenuation. Overall, our results highlight a novel mechanism by which mucins and their associated O-glycan structures affect CTXφ-mediated evolution and pathogenicity of V. cholerae, underscoring the potential regulatory power housed within mucus.
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Affiliation(s)
- Benjamin X Wang
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Microbiology and ImmunologyStanford UniversityStanfordCAUSA
| | - Julie Takagi
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Abigail McShane
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Jin Hwan Park
- Department of Microbiology and Environmental ToxicologyUniversity of CaliforniaSanta CruzCAUSA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research CenterUniversity of GeorgiaAthensGAUSA
| | - Catherine Griffin
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Jennifer Teschler
- Department of Microbiology and Environmental ToxicologyUniversity of CaliforniaSanta CruzCAUSA
| | - Giordan Kitts
- Department of Microbiology and Environmental ToxicologyUniversity of CaliforniaSanta CruzCAUSA
| | - Giulietta Minzer
- Department of Pharmaceutical SciencesUniversity of BaselBaselSwitzerland
| | - Michael Tiemeyer
- Complex Carbohydrate Research CenterUniversity of GeorgiaAthensGAUSA
| | - Rachel Hevey
- Department of Pharmaceutical SciencesUniversity of BaselBaselSwitzerland
| | - Fitnat Yildiz
- Department of Microbiology and Environmental ToxicologyUniversity of CaliforniaSanta CruzCAUSA
| | - Katharina Ribbeck
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
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29
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Wang H, Gao Y, He Q, Liao J, Zhou S, Liu Y, Guo C, Li X, Zhao X, Pan Y. 2-Hydrazinoterephthalic Acid as a Novel Negative-Ion Matrix-Assisted Laser Desorption/Ionization Matrix for Qualitative and Quantitative Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Analysis of N-Glycans in Peach Allergy Research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:952-962. [PMID: 36541565 DOI: 10.1021/acs.jafc.2c06822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Glycans recently attracted considerable attention as the proposal of cross-reactive carbohydrate determinants for food allergy. Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is powerful in analyzing biomolecules, while its applications in glycans are still challenging. Herein, a novel reactive matrix-assisted laser desorption/ionization (MALDI) matrix, 2-hydrazinoterephthalic acid, was rationally designed and synthesized. It provides uniform co-crystallization with glycans and only produces deprotonated ions with high intensities in the negative-ion mode. In combination with sinapic acid, a rapid and high-throughput method was established for on-target analysis of glycans with a superior limit of detection at the femtomole level and a good linearity (R2 > 0.999). Furthermore, the established method was successfully applied to quantify N-glycans in different cultivars and tissues of peach [Prunus persica (L.) Batsch]. Our work suggests the potential role of N-glycans as biomarkers for food-borne allergy and lays a methodological foundation for the elucidation of the possible relationship between carbohydrate epitopes and food allergy.
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Affiliation(s)
- Huiwen Wang
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, People's Republic of China
| | - Yuexia Gao
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Quan He
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, People's Republic of China
| | - Jiancong Liao
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, People's Republic of China
| | - Shiwen Zhou
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, People's Republic of China
| | - Yaqin Liu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, People's Republic of China
| | - Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, People's Republic of China
| | - Xian Li
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Xiaoyong Zhao
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, People's Republic of China
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30
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Koch KC, Tew GN. Functional antibody delivery: Advances in cellular manipulation. Adv Drug Deliv Rev 2023; 192:114586. [PMID: 36280179 DOI: 10.1016/j.addr.2022.114586] [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: 07/19/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 02/03/2023]
Abstract
The current therapeutic antibody market in the U.S. consists of 100 antibody-based products and their market value is expected to explode beyond $300 billion by 2025. These therapies are presently limited to extracellular targets due to the innate inability of antibodies to transverse membranes. To expand the number of accessible therapeutic targets, intracellular antibody delivery is necessary. Many delivery vehicles for antibodies have been used with some promising results, such as nanoparticles and cell penetrating polymers. Despite the success of these delivery platforms using model antibody cargo, there is a surprisingly small number of studies that focus on functional antibody delivery into the cytosol that also measures a cellular response. Antibodies can be designed for essentially unlimited targets, including proteins and DNA, that will ultimately control cell function once delivered inside cells. Advancement in cellular manipulation depends on the application of intracellularly delivering functional antibodies to achieve a desired result. This review focuses on the emerging field of functional antibody delivery which enables various cellular responses and cell manipulation.
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Affiliation(s)
- Kayla C Koch
- Department of Polymer Science & Engineering, University of Massachusetts, Amherst, MA 01003, United States
| | - Gregory N Tew
- Department of Polymer Science & Engineering, University of Massachusetts, Amherst, MA 01003, United States; Molecular & Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, United States; Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA 01003, United States.
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31
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Firdous A, Gopalakrishnan V, Vo N, Sowa G. Challenges and opportunities for omics-based precision medicine in chronic low back pain. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2022:10.1007/s00586-022-07457-8. [PMID: 36565345 DOI: 10.1007/s00586-022-07457-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/27/2022] [Accepted: 11/07/2022] [Indexed: 12/25/2022]
Abstract
PURPOSE Chronic low back pain (cLBP) is a common health condition worldwide and a leading cause of disability with an estimated lifetime prevalence of 80-90% in industrialized countries. However, we have had limited success in treating cLBP likely due to its non-specific heterogeneous nature that goes beyond detectable anatomical changes. We propose that omics technologies as precision medicine tools are well suited to provide insight into its pathophysiology and provide diagnostic markers and therapeutic targets. Therefore, in this review, we explore the current state of omics technologies in the diagnosis and classification of cLBP. We identify factors that may serve as markers to differentiate between acute and chronic cases of low back pain (LBP). Finally, we also discuss some challenges that must be overcome to successfully apply precision medicine to the diagnosis and treatment of cLBP. METHODS A literature search for the current applications of omics technologies to chronic low back pain was performed using the following search terms- "back pain," "low back pain," "proteomics," "transcriptomics", "epigenomics," "genomics," "omics." We reviewed molecular markers identified from 35 studies which hold promise in providing information regarding molecular insights into cLBP. RESULTS GWAS studies have found evidence for the role of single nucleotide polymorphisms (SNPs) associated with pain pathways in individuals with cLBP. Epigenomic modifications in patients with cLBP have been found to be enriched among genes involved in immune signaling and inflammation. Transcriptomics profiles of patients with cLBP show multiple lines of evidence for the role of inflammation in cLBP. The glycomics profiles of patients with cLBP are similar to those of patients with inflammatory conditions. Proteomics and microbiomics show promise but have limited studies currently. CONCLUSION Omics technologies have identified associations between inflammatory and pain pathways in the pathophysiology of cLBP. However, in order to integrate information across the range of studies, it is important for the field to identify and adopt standardized definitions of cLBP and control patients. Additionally, most papers have applied a single omics method to a sampling of cLBP patients which have yielded limited insight into the pathophysiology of cLBP. Therefore, we recommend a multi-omics approach applied to large global consortia for advancing subphenotyping and better management of cLBP, via improved identification of diagnostic markers and therapeutic targets.
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Affiliation(s)
- Ayesha Firdous
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh, Pittsburgh, PA, USA.
| | | | - Nam Vo
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gwendolyn Sowa
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh, Pittsburgh, PA, USA
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32
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Ding P, Wei Q, Tian N, Ding X, Wang L, Wang B, Okoro OV, Shavandi A, Nie L. Enzymatically crosslinked hydrogel based on tyramine modified gelatin and sialylated chitosan. Biomed Mater 2022; 18. [PMID: 36322975 DOI: 10.1088/1748-605x/ac9f90] [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: 09/17/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
The enzymatically crosslinked hydrogel could replicate the cellular microenvironment for biomedical applications. In the present study, to improve the cytocompatibility of chitosan (CS), sialic acid (SA) was introduced to CS to synthesize sialylated CS (CS-SA), and the tyramine (TA) was grafted to gelatin (G) to obtain TA modified gelatin (G-TA). The successful synthesis of CS-SA and G-TA was confirmed using1H NMR and UV-Vis absorption spectra. The interpenetrating polymer networks G-TA/CS-SA (GC) hydrogel was then fabricated via blending G-TA and CS-SA solutions and crosslinked using horseradish peroxidase. The storage modulus (G') of the fabricated GC hydrogels with different ratios of G-TA/CS-SA greatly varied during the formation and strain of hydrogels. With the increase of CS-SA concentration from 0% to 2%, the storage modulus of GC hydrogels was also observed to decrease from 1500 Pa to 101 Pa; the water uptake capacity of GC hydrogels increased from 1000% to 4500%. Additionally, the cell counting kit-8 and fluorescent images demonstrated the excellent cytocompatibility of GC hydrogels after culturing with NIH 3T3 cells. The obtained results indicated that the fabricated GC hydrogels might have potential in biomedical fields, such as wound dressing.
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Affiliation(s)
- Peng Ding
- School of Life Science, Xinyang Normal University, Xinyang 464000, People's Republic of China.,Tea Plant Biology Key Laboratory of Henan Province, Xinyang 464000, People's Republic of China
| | - Qianqian Wei
- School of Life Science, Xinyang Normal University, Xinyang 464000, People's Republic of China
| | - Ning Tian
- School of Life Science, Xinyang Normal University, Xinyang 464000, People's Republic of China
| | - Xiaoyue Ding
- School of Life Science, Xinyang Normal University, Xinyang 464000, People's Republic of China
| | - Ling Wang
- School of Life Science, Xinyang Normal University, Xinyang 464000, People's Republic of China
| | - Bin Wang
- School of Life Science, Xinyang Normal University, Xinyang 464000, People's Republic of China
| | - Oseweuba Valentine Okoro
- Université libre de Bruxelles (ULB), École polytechnique de Bruxelles, 3BIO-BioMatter, Avenue F.D. Roosevelt, 50 - CP 165/61, 1050 Brussels, Belgium
| | - Amin Shavandi
- Université libre de Bruxelles (ULB), École polytechnique de Bruxelles, 3BIO-BioMatter, Avenue F.D. Roosevelt, 50 - CP 165/61, 1050 Brussels, Belgium
| | - Lei Nie
- School of Life Science, Xinyang Normal University, Xinyang 464000, People's Republic of China.,Université libre de Bruxelles (ULB), École polytechnique de Bruxelles, 3BIO-BioMatter, Avenue F.D. Roosevelt, 50 - CP 165/61, 1050 Brussels, Belgium
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33
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Xu S, Zhao M, Gu Z, Lu H, Liu Z. Photothermal Therapy of Neuroblastoma via Polysialic Acid-Targeting Nanomissiles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201671. [PMID: 36161701 DOI: 10.1002/smll.202201671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 08/06/2022] [Indexed: 06/16/2023]
Abstract
Exploring new targets and developing novel targeted therapies are urgently needed for neuroblastoma therapy. Polysialic acid (polySia), a linear homopolymer of sialic acid units that correlates well with tumor progression and poor prognosis, has emerged as a potential target for neuroblastoma. However, the lack of polySia-specific binding reagents has severely limited the development of polySia-targeting therapeutics for neuroblastoma. Herein, the construction of polySia-targeting nanomissiles via molecular imprinting for the photothermal therapy of neuroblastoma is reported. Oligosialic acid (oligoSia) containing 3-4 units is considered as a characteristic structure for the recognition of polySia, while oligoSia containing 4-7 units digested from polySia is employed as the template. Via boronate-affinity controllable oriented surface imprinting, oligoSia-imprinted nanoparticles (oSia-MIP) are prepared. The oSia-MIP allows for specifically recognizing polySia and targeting polySia overexpressed neuroblastoma cells in vitro and in vivo. oSia-MIP loaded with indocyanine green is prepared and experimentally demonstrated to be a potent targeted photothermal therapeutic for neuroblastoma. Equipping the core substrate with functional entities, the developed polySia targeting nanoplatform can be accommodated to various therapeutic modalities, holding great promise for neuroblastoma targeted therapy.
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Affiliation(s)
- Shuxin Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Menghuan Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Zikuan Gu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Haifeng Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
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34
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Takagi J, Aoki K, Turner BS, Lamont S, Lehoux S, Kavanaugh N, Gulati M, Valle Arevalo A, Lawrence TJ, Kim CY, Bakshi B, Ishihara M, Nobile CJ, Cummings RD, Wozniak DJ, Tiemeyer M, Hevey R, Ribbeck K. Mucin O-glycans are natural inhibitors of Candida albicans pathogenicity. Nat Chem Biol 2022; 18:762-773. [PMID: 35668191 PMCID: PMC7613833 DOI: 10.1038/s41589-022-01035-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
Mucins are large gel-forming polymers inside the mucus barrier that inhibit the yeast-to-hyphal transition of Candida albicans, a key virulence trait of this important human fungal pathogen. However, the molecular motifs in mucins that inhibit filamentation remain unclear despite their potential for therapeutic interventions. Here, we determined that mucins display an abundance of virulence-attenuating molecules in the form of mucin O-glycans. We isolated and cataloged >100 mucin O-glycans from three major mucosal surfaces and established that they suppress filamentation and related phenotypes relevant to infection, including surface adhesion, biofilm formation and cross-kingdom competition between C. albicans and the bacterium Pseudomonas aeruginosa. Using synthetic O-glycans, we identified three structures (core 1, core 1 + fucose and core 2 + galactose) that are sufficient to inhibit filamentation with potency comparable to the complex O-glycan pool. Overall, this work identifies mucin O-glycans as host molecules with untapped therapeutic potential to manage fungal pathogens.
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Affiliation(s)
- Julie Takagi
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Bradley S Turner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sabrina Lamont
- Departments of Microbial Infection and Immunity, Microbiology, The Ohio State University, Columbus, OH, USA
| | - Sylvain Lehoux
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, Boston, MA, USA
| | - Nicole Kavanaugh
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Megha Gulati
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, USA
- Molecular Cell, Cell Press, Cambridge, MA, USA
| | - Ashley Valle Arevalo
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, USA
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
| | - Travis J Lawrence
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, USA
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Colin Y Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bhavya Bakshi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, USA
- Health Sciences Research Institute, University of California Merced, Merced, CA, USA
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, Boston, MA, USA
| | - Daniel J Wozniak
- Departments of Microbial Infection and Immunity, Microbiology, The Ohio State University, Columbus, OH, USA
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Rachel Hevey
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Oinam L, Tateno H. Glycan Profiling by Sequencing to Uncover Multicellular Communication: Launching Glycobiology in Single Cells and Microbiomes. Front Cell Dev Biol 2022; 10:919168. [PMID: 35712658 PMCID: PMC9197256 DOI: 10.3389/fcell.2022.919168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Glycans are essential building blocks of life that are located at the outermost surface of all cells from mammals to bacteria and even viruses. Cell surface glycans mediate multicellular communication in diverse biological processes and are useful as “surface markers” to identify cells. Various single-cell sequencing technologies have already emerged that enable the high-throughput analysis of omics information, such as transcriptome and genome profiling on a cell-by-cell basis, which has advanced our understanding of complex multicellular interactions. However, there has been no robust technology to analyze the glycome in single cells, mainly because glycans with branched and heterogeneous structures cannot be readily amplified by polymerase chain reactions like nucleic acids. We hypothesized that the generation of lectins conjugated with DNA barcodes (DNA-barcoded lectins) would enable the conversion of glycan information to gene information, which may be amplified and measured using DNA sequencers. This technology will enable the simultaneous analysis of glycan and RNA in single cells. Based on this concept, we developed a technology to analyze glycans and RNA in single cells, which was referred to as scGR-seq. Using scGR-seq, we acquired glycan and gene expression profiles of individual cells constituting heterogeneous cell populations, such as tissues. We further extended Glycan-seq to the profiling of the surface glycans of bacteria and even gut microbiota. Glycan-seq and scGR-seq are new technologies that enable us to elucidate the function of glycans in cell–cell and cell–microorganism communication, which extends glycobiology to the level of single cells and microbiomes.
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Affiliation(s)
- Lalhaba Oinam
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
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Gao Z, He Y, He Q, Wei W, Luo Y, Ma Z, Chen W, Chu F, Zhang S, Liu Y, Pan Y. Multidimensional identification of disaccharide isomers based on non-covalent complexes and tandem mass spectrometry. Talanta 2022; 249:123674. [PMID: 35717753 DOI: 10.1016/j.talanta.2022.123674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/26/2022]
Abstract
Glycans are the most abundant organic polymers in nature. They are essential to living organisms and regulate a wide range of biological functions. However, mass spectrometry-based identification of glycan isomers remains challenging due to the complexity of their structures including their complex compositions, linkages, and anomeric configurations. In this study, two novel complex ions, the mononuclear copper-bound dimeric ions [(Cu2+)(A)(L-His)-H]+ and the mononuclear copper-bound quaternary ions [(Cu2+)(A)(L-Ser)3-H]+ (where A denotes a disaccharide, and L-Ser/His denotes l-serine/histidine), were designed for the collision-induced dissociation-based identification and relative quantification of 14 disaccharide isomers. When the unique fragmentation patterns of the above two types of complex ions were mapped into a three-dimensional vector, all the isomers were completely distinguished. Of note, the established method is able to identify mixtures of linkage isomers only using tandem mass spectrometry based on linkage-specific fragment ions of histidine-based complex ions. Finally, the method was successfully applied to the identification and relative quantification of two disaccharide isomers (lactose and sucrose) in dairy beverages. In conclusion, the established method is sensitive to subtle structural differences in disaccharide isomers and has the potential to be used for the differentiation of various glycans.
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Affiliation(s)
- Zhan Gao
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yuwen He
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Quan He
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Wei Wei
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yuanqing Luo
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Zihan Ma
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Weiwei Chen
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Fengjian Chu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, 310027, PR China
| | - Shuheng Zhang
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yaqin Liu
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, PR China.
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Du Z, Yang Q, Liu Y, Chen S, Zhao H, Bai H, Shao W, Zhang Y, Qin W. A New Strategy for High-Efficient Tandem Enrichment and Simultaneous Profiling of N-Glycopeptides and Phosphopeptides in Lung Cancer Tissue. Front Mol Biosci 2022; 9:923363. [PMID: 35685241 PMCID: PMC9171396 DOI: 10.3389/fmolb.2022.923363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
N-glycosylation and phosphorylation, two common posttranslational modifications, play important roles in various biological processes and are extensively studied for biomarker and drug target screening. Because of their low abundance, enrichment of N-glycopeptides and phosphopeptides prior to LC–MS/MS analysis is essential. However, simultaneous characterization of these two types of posttranslational modifications in complex biological samples is still challenging, especially for tiny amount of samples obtained in tissue biopsy. Here, we introduced a new strategy for the highly efficient tandem enrichment of N-glycopeptides and phosphopeptides using HILIC and TiO2 microparticles. The N-glycopeptides and phosphosites obtained by tandem enrichment were 21%–377% and 22%–263% higher than those obtained by enriching the two PTM peptides separately, respectively, using 160–20 μg tryptic digested peptides as the starting material. Under the optimized conditions, 2798 N-glycopeptides from 434 N-glycoproteins and 5130 phosphosites from 1986 phosphoproteins were confidently identified from three technical replicates of HeLa cells by mass spectrometry analysis. Application of this tandem enrichment strategy in a lung cancer study led to simultaneous characterization of the two PTM peptides and discovery of hundreds of differentially expressed N-glycosylated and phosphorylated proteins between cancer and normal tissues, demonstrating the high sensitivity of this strategy for investigation of dysregulated PTMs using very limited clinical samples.
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Affiliation(s)
- Zhuokun Du
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Qianying Yang
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Yuanyuan Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Sijie Chen
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Hongxian Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Haihong Bai
- Phase I Clinical Trial Center, Beijing Shijitan Hospital of Capital Medical University, Beijing, China
| | - Wei Shao
- School of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Yangjun Zhang
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
- *Correspondence: Yangjun Zhang, ; Weijie Qin,
| | - Weijie Qin
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
- *Correspondence: Yangjun Zhang, ; Weijie Qin,
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Rajesh C, Sagar S, Rathinavel AK, Chemparathy DT, Peng XL, Yeh JJ, Hollingsworth MA, Radhakrishnan P. Truncated O-Glycan-Bearing MUC16 Enhances Pancreatic Cancer Cells Aggressiveness via α4β1 Integrin Complexes and FAK Signaling. Int J Mol Sci 2022; 23:ijms23105459. [PMID: 35628269 PMCID: PMC9141077 DOI: 10.3390/ijms23105459] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
Elevated levels of Mucin-16 (MUC16) in conjunction with a high expression of truncated O-glycans is implicated in playing crucial roles in the malignancy of pancreatic ductal adenocarcinoma (PDAC). However, the mechanisms by which such aberrant glycoforms present on MUC16 itself promote an increased disease burden in PDAC are yet to be elucidated. This study demonstrates that the CRISPR/Cas9-mediated genetic deletion of MUC16 in PDAC cells decreases tumor cell migration. We found that MUC16 enhances tumor malignancy by activating the integrin-linked kinase and focal adhesion kinase (ILK/FAK)-signaling axis. These findings are especially noteworthy in truncated O-glycan (Tn and STn antigen)-expressing PDAC cells. Activation of these oncogenic-signaling pathways resulted in part from interactions between MUC16 and integrin complexes (α4β1), which showed a stronger association with aberrant glycoforms of MUC16. Using a monoclonal antibody to functionally hinder MUC16 significantly reduced the migratory cascades in our model. Together, these findings suggest that truncated O-glycan containing MUC16 exacerbates malignancy in PDAC by activating FAK signaling through specific interactions with α4 and β1 integrin complexes on cancer cell membranes. Targeting these aberrant glycoforms of MUC16 can aid in the development of a novel platform to study and treat metastatic pancreatic cancer.
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Affiliation(s)
- Christabelle Rajesh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (C.R.); (S.S.); (A.K.R.); (D.T.C.); (M.A.H.)
| | - Satish Sagar
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (C.R.); (S.S.); (A.K.R.); (D.T.C.); (M.A.H.)
| | - Ashok Kumar Rathinavel
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (C.R.); (S.S.); (A.K.R.); (D.T.C.); (M.A.H.)
| | - Divya Thomas Chemparathy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (C.R.); (S.S.); (A.K.R.); (D.T.C.); (M.A.H.)
| | - Xianlu Laura Peng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514-7295, USA; (X.L.P.); (J.J.Y.)
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514-7295, USA; (X.L.P.); (J.J.Y.)
| | - Michael A. Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (C.R.); (S.S.); (A.K.R.); (D.T.C.); (M.A.H.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - Prakash Radhakrishnan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (C.R.); (S.S.); (A.K.R.); (D.T.C.); (M.A.H.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
- Correspondence:
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Pellegrinelli R, Yue L, Carrascosa E, Ben Faleh A, Warnke S, Bansal P, Rizzo TR. A New Strategy Coupling Ion-Mobility-Selective CID and Cryogenic IR Spectroscopy to Identify Glycan Anomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:859-864. [PMID: 35437995 PMCID: PMC9074103 DOI: 10.1021/jasms.2c00043] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 05/26/2023]
Abstract
Determining the primary structure of glycans remains challenging due to their isomeric complexity. While high-resolution ion mobility spectrometry (IMS) has recently allowed distinguishing between many glycan isomers, the arrival-time distributions (ATDs) frequently exhibit multiple peaks, which can arise from positional isomers, reducing-end anomers, or different conformations. Here, we present the combination of ultrahigh-resolution ion mobility, collision-induced dissociation (CID), and cryogenic infrared (IR) spectroscopy as a systematic method to identify reducing-end anomers of glycans. Previous studies have suggested that high-resolution ion mobility of sodiated glycans is able to separate the two reducing-end anomers. In this case, Y-fragments generated from mobility-separated precursor species should also contain a single anomer at their reducing end. We confirm that this is the case by comparing the IR spectra of selected Y-fragments to those of anomerically pure mono- and disaccharides, allowing the assignment of the mobility-separated precursor and its IR spectrum to a single reducing-end anomer. The anomerically pure precursor glycans can henceforth be rapidly identified on the basis of their IR spectrum alone, allowing them to be distinguished from other isomeric forms.
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40
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Mastellone J, Kabir KM, Huang X, Donald WA. Separation of disaccharide epimers, anomers and connectivity isomers by high resolution differential ion mobility mass spectrometry. Anal Chim Acta 2022; 1206:339783. [DOI: 10.1016/j.aca.2022.339783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 11/15/2022]
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Li H, Wang X, Huang X, He Y, Zhang Y, Hao C, Zeng P, Zhang M, Gao Y, Yang D, Shan M, Dou H, Li X, Chang X, Tian Z, Zhang L. Circulating Glycan Monosaccharide Composite-Based Biomarker Diagnoses Colorectal Cancer at Early Stages and Predicts Prognosis. Front Oncol 2022; 12:852044. [PMID: 35574422 PMCID: PMC9099097 DOI: 10.3389/fonc.2022.852044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/06/2022] [Indexed: 12/29/2022] Open
Abstract
Introduction Early diagnosis could lead to a cure of colorectal cancer (CRC). Since CRC is related to aging and lifestyles, we tested if the environmental information-enriched monosaccharide composite (MC) of circulating glycans could serve as an early diagnostic biomarker for CRC. Meanwhile, we evaluated its role in predicting prognosis. Methods HPAEC-PAD was used to quantify glycan monosaccharide compositions from a total of 467 serum samples including CRC patients, colorectal adenoma (CRA) patients and healthy individuals. Two diagnostic model was constructed by logistic regression analysis. The diagnostic performance of the two models was verified in the retrospective validation group and the prospective validation group. The prognostic performance of the model was assessed by survival analysis. Results The concentrations of monosaccharides in serum were significantly higher in CRA and CRC patients than in healthy individuals. Two diagnostic models were constructed: MC1 was used to distinguish between healthy individuals and CRC; MC2 was used to distinguish between healthy individuals and CRA. Area under receptor operating characteristic curve (AUC) of MC2 and MC1 was 0.8025 and 0.9403 respectively. However, the AUC of CEA between healthy individuals and CRC was 0.7384. Moreover, in early stage of CRC (without lymph node metastasis), the positive rates of CEA and MC1 were 28% and 80%, respectively. The follow-up data showed that the increased MC1 value was associated with poor survival in patients with CRC (p=0.0010, HR=5.30). Discussion The MC1 model is superior to CEA in the diagnosis of CRC, especially in the early diagnosis. MC1 can be used for predicting prognosis of CRC patients, and elevated MC1 values indicate poor survival.
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Affiliation(s)
- Haoran Li
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xueling Wang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
- Center for Clinical Research, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaodan Huang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yanli He
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yiran Zhang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
- Shandong Institute of Orthopedics and Traumatology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Cui Hao
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Pengjiao Zeng
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Meng Zhang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yanyun Gao
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Dandan Yang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ming Shan
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Huaiqian Dou
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaoyu Li
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaotian Chang
- Center for Clinical Research, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Lijuan Zhang, ; Xiaotian Chang, ; Zibin Tian,
| | - Zibin Tian
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Lijuan Zhang, ; Xiaotian Chang, ; Zibin Tian,
| | - Lijuan Zhang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Lijuan Zhang, ; Xiaotian Chang, ; Zibin Tian,
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Temme JS, Gildersleeve JC. General Strategies for Glycan Microarray Data Processing and Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2460:67-87. [PMID: 34972931 DOI: 10.1007/978-1-0716-2148-6_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Glycan microarrays provide a high-throughput technology for rapidly profiling interactions between carbohydrates and glycan-binding proteins (GBPs). Use of glycan microarrays involves several general steps, including construction of the microarray, carrying out the assay, detection of binding events, and analysis of the results. While multiple platforms have been developed to construct microarrays, most utilize fluorescence for detection of binding events. This chapter describes methods to acquire and process microarray images, including generating GAL files, imaging of the slide, aligning the grid, detecting problematic spots, and evaluating the quality of the data. The chapter focuses on processing our neoglycoprotein microarrays, but many of the lessons we have learned are applicable to other array formats.
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Affiliation(s)
- J Sebastian Temme
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jeffrey C Gildersleeve
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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Posttranslational Modifications in Thyroid Cancer: Implications for Pathogenesis, Diagnosis, Classification, and Treatment. Cancers (Basel) 2022; 14:cancers14071610. [PMID: 35406382 PMCID: PMC8996999 DOI: 10.3390/cancers14071610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/17/2022] Open
Abstract
There is evidence that posttranslational modifications, including phosphorylation, acetylation, methylation, ubiquitination, sumoylation, glycosylation, and succinylation, may be involved in thyroid cancer. We review recent reports supporting a role of posttranslational modifications in the tumorigenesis of thyroid cancer, sensitivity to radioiodine and other types of treatment, the identification of molecular treatment targets, and the development of molecular markers that may become useful as diagnostic tools. An increased understanding of posttranslational modifications may be an important supplement to the determination of alterations in gene expression that has gained increasing prominence in recent years.
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Rosa NMP, Ferreira FHDC, Farrell NP, Costa LAS. Substitution-inert polynuclear platinum complexes and Glycosaminoglycans: A molecular dynamics study of its non-covalent interactions. J Inorg Biochem 2022; 232:111811. [DOI: 10.1016/j.jinorgbio.2022.111811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 10/18/2022]
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Chao Q, Li T, Jia JX, Li Z, Peng P, Gao XD, Wang N. Spore-Encapsulating Glycosyltransferase Catalysis Tandem Reactions: Facile Chemoenzymatic Synthesis of Complex Human Glycans. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Qiang Chao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Tianlu Li
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan, Shandong 250012, China
| | - Ji-Xiang Jia
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Peng Peng
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan, Shandong 250012, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ning Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
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Yadav A, Vagne Q, Sens P, Iyengar G, Rao M. Glycan processing in the Golgi: optimal information coding and constraints on cisternal number and enzyme specificity. eLife 2022; 11:76757. [PMID: 35175197 PMCID: PMC9154746 DOI: 10.7554/elife.76757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Many proteins that undergo sequential enzymatic modification in the Golgi cisternae are displayed at the plasma membrane as cell identity markers. The modified proteins, called glycans, represent a molecular code. The fidelity of this glycan code is measured by how accurately the glycan synthesis machinery realises the desired target glycan distribution for a particular cell type and niche. In this paper, we construct a simplified chemical synthesis model to quantitatively analyse the tradeoffs between the number of cisternae, and the number and specificity of enzymes, required to synthesize a prescribed target glycan distribution of a certain complexity to within a given fidelity. We find that to synthesize complex distributions, such as those observed in real cells, one needs to have multiple cisternae and precise enzyme partitioning in the Golgi. Additionally, for fixed number of enzymes and cisternae, there is an optimal level of specificity (promiscuity) of enzymes that achieves the target distribution with high fidelity. The geometry of the fidelity landscape in the multidimensional space of the number and specificity of enzymes, inter-cisternal transfer rates, and number of cisternae, provides a measure for robustness and identifies stiff and sloppy directions. Our results show how the complexity of the target glycan distribution and number of glycosylation enzymes places functional constraints on the Golgi cisternal number and enzyme specificity.
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Affiliation(s)
| | - Quentin Vagne
- Laboratoire Physico Chimie Curie, Institut Curie, CNRS UMR168, Paris, France
| | - Pierre Sens
- Laboratoire Physico Chimie Curie, Institut Curie, CNRS UMR168, Paris, France
| | - Garud Iyengar
- Industrial Engineering and Operations Research, Columbia University, New York, United States
| | - Madan Rao
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, India
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Bansal P, Ben Faleh A, Warnke S, Rizzo TR. Identification of N-glycan positional isomers by combining IMS and vibrational fingerprinting of structurally determinant CID fragments. Analyst 2022; 147:704-711. [PMID: 35079754 PMCID: PMC8842669 DOI: 10.1039/d1an01861b] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
While glycans are present on the surface of cells in all living organisms and play key roles in most biological processes, their isomeric complexity makes their structural characterization challenging. Of particular importance are positional isomers, for which analytical standards are difficult to obtain. We combine ultrahigh-resolution ion-mobility spectrometry with collision-induced dissociation and cryogenic infrared spectroscopy to determine the structure of N-glycan positional isomers. This approach is based on first separating the parent molecules by SLIM-based IMS, producing diagnostic fragments specific to each positional isomer, separating the fragments by IMS, and identifying them by comparing their IR fingerprints to a previously recorded spectral database. We demonstrate this strategy using a bottom-up scheme to identify the positional isomers of the N-linked glycan G0-N, in which a terminal N-acetylglucosamine (GlcNAc) is attached to either the α-3 or α-6 branch of the common N-glycan pentasaccharide core. We then use IR fingerprints of these newly identified isomers to identify the positional isomers of G1 and G1F, which are biantennary complex-type N-glycans with a terminal galactose attached to either the α-3 or α-6 branch, and in the case of G1F a fucose attached to the reducing-end GlcNAc. Starting with just a few analytical standards, this fragment-based spectroscopy method allows us to develop a database which we can use to identify positional isomers. The generalization of this approach would greatly facilitate glycan analysis. We combine high-resolution IMS-IMS with cryogenic vibrational spectroscopy for the indentification of N-glycan positional isomers.![]()
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Affiliation(s)
- Priyanka Bansal
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
| | - Ahmed Ben Faleh
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
| | - Stephan Warnke
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland.
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Yang J, Yin M, Hou Y, Li H, Guo Y, Yu H, Zhang K, Zhang C, Jia L, Zhang F, Li X, Bian H, Li Z. Role of ammonia for brain abnormal protein glycosylation during the development of hepatitis B virus-related liver diseases. Cell Biosci 2022; 12:16. [PMID: 35164881 PMCID: PMC8842931 DOI: 10.1186/s13578-022-00751-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/29/2022] [Indexed: 11/30/2022] Open
Abstract
Background Ammonia is the most typical neurotoxin in hepatic encephalopathy (HE), but the underlying pathophysiology between ammonia and aberrant glycosylation in HE remains unknown. Results Here, we used HBV transgenic mice and astrocytes to present a systems-based study of glycosylation changes and corresponding enzymes associated with the key factors of ammonia in HE. We surveyed protein glycosylation changes associated with the brain of HBV transgenic mice by lectin microarrays. Upregulation of Galβ1-3GalNAc mediated by core 1 β1,3-galactosyltransferase (C1GALT1) was identified as a result of ammonia stimulation. Using in vitro assays, we validated that upregulation of C1GALT1 is a driver of deregulates calcium (Ca2+) homeostasis by overexpression of inositol 1,4,5-trisphosphate receptor type 1 (IP3R1) in astrocytes. Conclusions We demonstrated that silencing C1GALT1 could depress the IP3R1 expression, an effective strategy to inhibit the ammonia-induced upregulation of Ca2+ activity, thereby C1GALT1 and IP3R1 may serve as therapeutic targets in hyperammonemia of HE. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00751-4.
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Affiliation(s)
- Jiajun Yang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Mengqi Yin
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yao Hou
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Hao Li
- Cell Engineering Research Centre and Department of Cell Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Yonghong Guo
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
| | - Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Kun Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Chen Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Liyuan Jia
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Fan Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xia Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Huijie Bian
- Cell Engineering Research Centre and Department of Cell Biology, Fourth Military Medical University, Xi'an, 710032, China.
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China.
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Changes in Serum N-Glycome for Risk Drinkers: A Comparison with Standard Markers for Alcohol Abuse in Men and Women. Biomolecules 2022; 12:biom12020241. [PMID: 35204742 PMCID: PMC8961540 DOI: 10.3390/biom12020241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 01/11/2023] Open
Abstract
Background and aim: Glycomic alterations serve as biomarker tools for different diseases. The present study aims to evaluate the diagnostic capability of serum N-glycosylation to identify alcohol risk drinking in comparison with standard markers. Methods: We included 1516 adult individuals (age range 18–91 years; 55.3% women), randomly selected from a general population. A total of 143 (21.0%) men and 50 (5.9%) women were classified as risk drinkers after quantification of daily alcohol consumption and the Alcohol Use Disorders Identification Test (AUDIT). Hydrophilic interaction ultra-performance liquid chromatography (HILIC-UPLC) was used for the quantification of 46 serum N-glycan peaks. Serum gamma-glutamyltransferase (GGT), carbohydrate-deficient transferrin (CDT), and red blood cell mean corpuscular volume (MCV) were measured by standard clinical laboratory methods. Results: Variations in serum N-glycome associated risk drinking were more prominent in men compared to women. A unique combination of N-glycan peaks selected by the selbal algorithm shows good discrimination between risk-drinkers and non-risk drinkers for men and women. Receiver operating characteristics (ROC) curves show accuracy for the diagnosis of risk drinking, which is comparable to that of the golden standards, GGT, MCV and CDT markers for men and women. Additionally, the inclusion of N-glycan peaks improves the diagnostic accuracy of the standard markers, although it remains relatively low, due to low sensitivity. For men, the area under the ROC curve using N-glycome data is 0.75, 0.76, and 0.77 when combined with GGT, MCV, and CDT, respectively. In women, the areas were 0.76, 0.73, and 0.73, respectively. Conclusion: Risk drinking is associated with significant variations in the serum N-glycome, which highlights its potential diagnostic utility.
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Enrichment of IgG and HRP glycoprotein by dipeptide-based polymeric material. Talanta 2022; 241:123223. [PMID: 35030500 DOI: 10.1016/j.talanta.2022.123223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 12/30/2022]
Abstract
Separation, purification, and identification of glycoproteins are essential for understanding their vital roles in biological and pathological processes. However, glycoproteins are difficult to be captured due to their low abundance, strong interference from non-glycosylated proteins. Here, we report a promising dipeptide-based saccharide recognition platform to selectively enrich two typical glycoproteins, named immunoglobin G (IgG) and horseradish peroxidase (HRP). Different from the conventional glycoprotein enrichment method based on boronic acid affinity or hydrophilic interaction with glycans, the present method was established based on affinity between Pro-Glu (PE) dipeptide and mannose, which is a key unit in the pentasaccharide core of the IgG and HRP glycans. The prepared PE homopolymer surface was proved to selectively bind IgG and HRP superior to that of bovine serum albumin (BSA). Benefiting from this feature, selective enrichment of IgG and HRP was achieved from a protein mixture containing 200-fold BSA interference by using polyPE@SiO2 under a dispersive solid-phase extraction (dSPE) mode. High adsorption capacity, controllable and selective adsorption behaviors, as well as satisfactory recovery demonstrated the high potential of the dipeptide-based polymeric material in IgG and HRP enrichment. This study might provide a new insight to solve the challenging problem of glycoprotein separation.
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