1
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Mach N. The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases. Vet Q 2024; 44:1-18. [PMID: 38606662 PMCID: PMC11018052 DOI: 10.1080/01652176.2024.2340003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 03/31/2024] [Indexed: 04/13/2024] Open
Abstract
Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.
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Affiliation(s)
- Núria Mach
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
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2
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Gregolin CS, do Nascimento M, de Souza SLB, Mota GAF, Luvizotto RDAM, Sugizaki MM, Bazan SGZ, de Campos DHS, Camacho CRC, Cicogna AC, do Nascimento AF. Cardiac dysfunction in sucrose-fed rats is associated with alterations of phospholamban phosphorylation and TNF-α levels. Mol Cell Endocrinol 2024; 589:112236. [PMID: 38608803 DOI: 10.1016/j.mce.2024.112236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
INTRODUCTION High sucrose intake is linked to cardiovascular disease, a major global cause of mortality worldwide. Calcium mishandling and inflammation play crucial roles in cardiac disease pathophysiology. OBJECTIVE Evaluate if sucrose-induced obesity is related to deterioration of myocardial function due to alterations in the calcium-handling proteins in association with proinflammatory cytokines. METHODS Wistar rats were divided into control and sucrose groups. Over eight weeks, Sucrose group received 30% sucrose water. Cardiac function was determined in vivo using echocardiography and in vitro using papillary muscle assay. Western blotting was used to detect calcium handling protein; ELISA assay was used to assess TNF-α and IL-6 levels. RESULTS Sucrose led to cardiac dysfunction. RYR2, SERCA2, NCX, pPBL Ser16 and L-type calcium channels were unchanged. However, pPBL-Thr17, and TNF-α levels were elevated in the S group. CONCLUSION Sucrose induced cardiac dysfunction and decreased myocardial contractility in association with altered pPBL-Thr17 and elevated cardiac pro-inflammatory TNF-α.
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Affiliation(s)
- Cristina Schmitt Gregolin
- Department of Pathology, Medical School (FMB) of São Paulo State University (Unesp), Botucatu Campus, São Paulo, Brazil
| | - Milena do Nascimento
- Institute of Health Sciences, Federal University of Mato Grosso (UFMT), Sinop, Mato Grosso, Brazil
| | | | - Gustavo Augusto Ferreira Mota
- Department of Internal Medicine, Botucatu School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | - Mário Mateus Sugizaki
- Institute of Health Sciences, Federal University of Mato Grosso (UFMT), Sinop, Mato Grosso, Brazil
| | - Silméia Garcia Zanati Bazan
- Department of Internal Medicine, Botucatu School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Dijon Henrique Salomé de Campos
- Department of Internal Medicine, Botucatu School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Camila Renata Corrêa Camacho
- Department of Pathology, Medical School (FMB) of São Paulo State University (Unesp), Botucatu Campus, São Paulo, Brazil
| | - Antonio Carlos Cicogna
- Department of Internal Medicine, Botucatu School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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3
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Usama, Khan Z, Ali A, Shah M, Imran M. Differential glycosylation in mutant vitamin D-binding protein decimates the binding stability of vitamin D. J Biomol Struct Dyn 2024; 42:5365-5375. [PMID: 37357441 DOI: 10.1080/07391102.2023.2226742] [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: 03/31/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
Abstract
Vitamin D (VD) is produced by the skin upon exposure to sunlight or is obtained from dietary sources. Several risk factors are associated with VD deficiency including mutations and post-translational modifications in its transport protein known as vitamin D binding protein (VDBP) or GC-globulin. The two common single nucleotide polymorphisms rs7041 and rs4588 create three major isoforms of VDBP, including GC-1F also called wild type, GC1S, and GC-2. The 3D models for both GC-1F and GC-2 were constructed in their glycosylated states to decipher the effect of these mutations on the overall conformational changes and VD-binding affinity. The binding affinities were estimated using the Molecular Mechanics Poison-Boltzmann surface area (MM-PBSA) method and conformational changes were investigated after free energy landscapes estimations. Total free energies suggest that GC-1F exhibits stronger affinity (ΔE = -116.09 kJ/mol) than GC-2 (ΔE = -95 kJ/mol) variant with VD. The GC-1F isoforms had more streamlined motion compared to GC-2 isoforms, predicting a trade-off between cross-talk residues that significantly impacts protein structural stability. The data suggest that glycation at Thr418 plays a vital role in the overall VDBP-VD affinity by stabilizing the N-T loop that holds the domain I (VD-pocket) and domain III intact. The loss of glycation in GC-2 has a pivotal role in the inter-domain conformational stability of VDBP, which may ultimately affect VD transportation and maturation. These findings describe a novel mechanism in how mutations distant from the VD-active site change the overall conformational of the VDBP and abrogate the VDBP-VD interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Usama
- Biochemistry Section, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Zahid Khan
- Biochemistry Section, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Aktar Ali
- Biological Screening Core, Warren Family Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana, USA
| | - Masaud Shah
- Department of Physiology, School of Medicine, Ajou University, Suwon, South Korea
| | - Muhammad Imran
- Biochemistry Section, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
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4
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Ma YH, Li B, Wang C, Yang J, Han X, Lu X. Unsaturation effects on lipid transmembrane asymmetry. J Chem Phys 2024; 160:215102. [PMID: 38842495 DOI: 10.1063/5.0209950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
Within cell plasma membranes, unsaturated lipids are asymmetrically distributed over the inner and outer leaflets, offering an attractive local structural feature. However, the mechanism to keep lipid transmembrane asymmetry and the closely related transmembrane movement (flip-flop) for unsaturated lipids remain poorly understood. Here, we applied sum frequency generation vibrational spectroscopy to investigate this lipid transmembrane asymmetry upon mimicking the cell membrane homeostatic processes. On the one hand, unsaturated lipids were found to hinder the flip-flop process and preserve lipid transmembrane asymmetry in model cell membranes, owing to the steric hindrance caused by their bent tails. On the other hand, local unsaturated lipids in the mixed unsaturated/saturated lipid bilayer were conducive to the formation of the local asymmetry. Therefore, lipid unsaturation can be recognized as an intrinsic key factor to form and maintain lipid transmembrane asymmetry in cell membranes.
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Affiliation(s)
- Yong-Hao Ma
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Bolin Li
- Anhui Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory, HFIPS, Chinese Academy of Sciences, Hefei 230031, China
| | - Chu Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jingjing Yang
- Department of Biochemistry and Molecular Biology, School of Medicine and Holistic Integrative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaofeng Han
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiaolin Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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5
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Oh S, Cao W, Song M. Twin Scholarships of Glycomedicine and Precision Medicine in Times of Single-Cell Multiomics. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024. [PMID: 38841897 DOI: 10.1089/omi.2024.0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Systems biology and multiomics research expand the prospects of planetary health innovations. In this context, this mini-review unpacks the twin scholarships of glycomedicine and precision medicine in the current era of single-cell multiomics. A significant growth in glycan research has been observed over the past decade, unveiling and establishing co- and post-translational modifications as dynamic indicators of both pathological and physiological conditions. Systems biology technologies have enabled large-scale and high-throughput glycoprofiling and access to data-intensive biological repositories for global research. These advancements have established glycans as a pivotal third code of life, alongside nucleic acids and amino acids. However, challenges persist, particularly in the simultaneous analysis of the glycome and transcriptome in single cells owing to technical limitations. In addition, holistic views of the complex molecular interactions between glycomics and other omics types remain elusive. We underscore and call for a paradigm shift toward the exploration of integrative glycan platforms and analysis methods for single-cell multiomics research and precision medicine biomarker discovery. The integration of multiple datasets from various single-cell omics levels represents a crucial application of systems biology in understanding complex cellular processes and is essential for advancing the twin scholarships of glycomedicine and precision medicine.
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Affiliation(s)
- Seungyoul Oh
- Centre for Precision Health, Edith Cowan University, Perth, Australia
| | - Weijie Cao
- Centre for Precision Health, Edith Cowan University, Perth, Australia
| | - Manshu Song
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
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6
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Baerenfaenger M, Post MA, Zijlstra F, van Gool AJ, Lefeber DJ, Wessels HJCT. Maximizing Glycoproteomics Results through an Integrated Parallel Accumulation Serial Fragmentation Workflow. Anal Chem 2024; 96:8956-8964. [PMID: 38776126 DOI: 10.1021/acs.analchem.3c05874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Glycoproteins play important roles in numerous physiological processes and are often implicated in disease. Analysis of site-specific protein glycobiology through glycoproteomics has evolved rapidly in recent years thanks to hardware and software innovations. Particularly, the introduction of parallel accumulation serial fragmentation (PASEF) on hybrid trapped ion mobility time-of-flight mass spectrometry instruments combined deep proteome sequencing with separation of (near-)isobaric precursor ions or converging isotope envelopes through ion mobility separation. However, the reported use of PASEF in integrated glycoproteomics workflows to comprehensively capture the glycoproteome is still limited. To this end, we developed an integrated methodology using timsTOF Pro 2 to enhance N-glycopeptide identifications in complex mixtures. We systematically optimized the ion optics tuning, collision energies, mobility isolation width, and the use of dopant-enriched nitrogen gas (DEN). Thus, we obtained a marked increase in unique glycopeptide identification rates compared to standard proteomics settings, showcasing our results on a large set of glycopeptides. With short liquid chromatography gradients of 30 min, we increased the number of unique N-glycopeptide identifications in human plasma samples from around 100 identifications under standard proteomics conditions to up to 1500 with our optimized glycoproteomics approach, highlighting the need for tailored optimizations to obtain comprehensive data.
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Affiliation(s)
- Melissa Baerenfaenger
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
- Division of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, Netherlands
| | - Merel A Post
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Fokje Zijlstra
- Translational Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Alain J van Gool
- Translational Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
- Translational Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
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7
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Zhang T, Wang W, Wuhrer M, de Haan N. Comprehensive O-Glycan Analysis by Porous Graphitized Carbon Nanoliquid Chromatography-Mass Spectrometry. Anal Chem 2024; 96:8942-8948. [PMID: 38758656 DOI: 10.1021/acs.analchem.3c05826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
The diverse and unpredictable structures of O-GalNAc-type protein glycosylation present a challenge for its structural and functional characterization in a biological system. Porous graphitized carbon (PGC) liquid chromatography (LC) coupled to mass spectrometry (MS) has become one of the most powerful methods for the global analysis of glycans in complex biological samples, mainly due to the extensive chromatographic separation of (isomeric) glycan structures and the information delivered by collision induced fragmentation in negative mode MS for structural elucidation. However, current PGC-based methodologies fail to detect the smaller glycan species consisting of one or two monosaccharides, such as the Tn (single GalNAc) antigen, which is broadly implicated in cancer biology. This limitation is caused by the loss of small saccharides during sample preparation and LC. Here, we improved the conventional PGC nano-LC-MS/MS-based strategy for O-glycan analysis, enabling the detection of truncated O-glycan species and improving isomer separation. This was achieved by the implementation of 2.7 μm PGC particles in both the trap and analytical LC columns, which provided an enhanced binding capacity and isomer separation for O-glycans. Furthermore, a novel mixed-mode PGC-boronic acid-solid phase extraction during sample preparation was established to purify a broad range of glycans in an unbiased manner, including the previously missed mono- and disaccharides. Taken together, the optimized PGC nano-LC-MS/MS platform presents a powerful component of the toolbox for comprehensive O-glycan characterization.
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Affiliation(s)
- Tao Zhang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, Leiden 2300 RC, The Netherlands
| | - Wenjun Wang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, Leiden 2300 RC, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, Leiden 2300 RC, The Netherlands
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, Leiden 2300 RC, The Netherlands
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8
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Hansen SSK, Krautz R, Rago D, Havelund J, Stigliani A, Færgeman NJ, Prézelin A, Rivière J, Couturier-Tarrade A, Akimov V, Blagoev B, Elfving B, Neess D, Vogel U, Khodosevich K, Hougaard KS, Sandelin A. Pulmonary maternal immune activation does not cross the placenta but leads to fetal metabolic adaptation. Nat Commun 2024; 15:4711. [PMID: 38830841 PMCID: PMC11148039 DOI: 10.1038/s41467-024-48492-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Abstract
The fetal development of organs and functions is vulnerable to perturbation by maternal inflammation which may increase susceptibility to disorders after birth. Because it is not well understood how the placenta and fetus respond to acute lung- inflammation, we characterize the response to maternal pulmonary lipopolysaccharide exposure across 24 h in maternal and fetal organs using multi-omics, imaging and integrative analyses. Unlike maternal organs, which mount strong inflammatory immune responses, the placenta upregulates immuno-modulatory genes, in particular the IL-6 signaling suppressor Socs3. Similarly, we observe no immune response in the fetal liver, which instead displays metabolic changes, including increases in lipids containing docosahexaenoic acid, crucial for fetal brain development. The maternal liver and plasma display similar metabolic alterations, potentially increasing bioavailability of docosahexaenoic acid for the mother and fetus. Thus, our integrated temporal analysis shows that systemic inflammation in the mother leads to a metabolic perturbation in the fetus.
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Affiliation(s)
- Signe Schmidt Kjølner Hansen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- National Research Centre for the Working Environment, Copenhagen, Denmark.
| | - Robert Krautz
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Daria Rago
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Jesper Havelund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Arnaud Stigliani
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Audrey Prézelin
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Julie Rivière
- Paris-Saclay University, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Anne Couturier-Tarrade
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Vyacheslav Akimov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Betina Elfving
- Translational Neuropsychiatry Unit, Aarhus University, Aarhus, Denmark
| | - Ditte Neess
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Karin Sørig Hougaard
- National Research Centre for the Working Environment, Copenhagen, Denmark.
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Albin Sandelin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
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9
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Qian Z, Sun L, Wang R, Dong X, Sun J, Dong C, Qu D, Gu X, Zhao C. High-Fidelity Spatiotemporal Recognition of Golgi ALP through an Initial-Accumulation and Postactivation Strategy. Anal Chem 2024. [PMID: 38825763 DOI: 10.1021/acs.analchem.4c02202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Various signal molecules mediate complex physiological processes collectively in the Golgi. However, most currently accessible probes are questionable in illuminating the functions of these reactive species in Golgi because of the inability to irradiate these probes only at the desired Golgi location, which compromises specificity and accuracy. In this study, we rationally designed the first photocontrollable and Golgi-targeted fluorescent probe to in situ visualize the Golgi alkaline phosphatase (ALP). The designed probe with natural yellow fluorescence can provide access into Golgi and monitor the exact timing of accumulation in Golgi. On-demand photoactivation at only the desired Golgi location affords a significant emission response to ALP with illuminating red fluorescence at 710 nm. Through the photocontrollable fluorescence responsiveness to ALP, precise spatiotemporal recognition of Golgi ALP fluctuations is successfully performed. With this probe, for the first time, we revealed the Golgi ALP levels during cisplatin-induced acute kidney injury (AKI), which will further facilitate and complement the comprehensive exploration of ALP kinetics during physiological and pathological processes.
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Affiliation(s)
- Zehua Qian
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Lixin Sun
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Rongchen Wang
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xuemei Dong
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Jie Sun
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Chengjun Dong
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Dahui Qu
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xianfeng Gu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, P. R. China
| | - Chunchang Zhao
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
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10
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Sheikh SY, Hassan F, Shukla D, Bala S, Faruqui T, Akhter Y, Khan AR, Nasibullah M. A review on potential therapeutic targets for the treatment of leishmaniasis. Parasitol Int 2024; 100:102863. [PMID: 38272301 DOI: 10.1016/j.parint.2024.102863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 12/22/2023] [Accepted: 01/21/2024] [Indexed: 01/27/2024]
Abstract
Leishmania, a protozoan parasite, is responsible for the occurrence of leishmaniasis, a disease that is prevalent in tropical regions. Visceral Leishmaniasis (VL), also known as kala-azar in Asian countries, is one of the most significant forms of VL, along with Cutaneous Leishmaniasis (CL) and Mucocutaneous Leishmaniasis (ML). Management of this condition typically entails the use of chemotherapy as the sole therapeutic option. The current treatments for leishmaniasis present several drawbacks, including a multitude of side effects, prolonged treatment duration, disparate efficacy across different regions, and the emergence of resistance. To address this urgent need, it is imperative to identify alternative treatments that are both safer and more effective. The identification of appropriate pharmacological targets in conjunction with biological pathways constitutes the initial stage of drug discovery. In this review, we have addressed the key metabolic pathways that represent potential pharmacological targets as well as prominent treatment options for leishmaniasis.
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Affiliation(s)
- Sabahat Yasmeen Sheikh
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Firoj Hassan
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Deepanjali Shukla
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Shashi Bala
- Department of Chemistry, Lucknow University, Lucknow 226026, India
| | - Tabrez Faruqui
- Department of Biosciences, Integral University, Lucknow 226026, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, India
| | - Abdul Rahman Khan
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Malik Nasibullah
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India.
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11
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Crowe SA, Liu Y, Zhao X, Scheller HV, Keasling JD. Advances in Engineering Nucleotide Sugar Metabolism for Natural Product Glycosylation in Saccharomyces cerevisiae. ACS Synth Biol 2024. [PMID: 38820348 DOI: 10.1021/acssynbio.3c00737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Glycosylation is a ubiquitous modification present across all of biology, affecting many things such as physicochemical properties, cellular recognition, subcellular localization, and immunogenicity. Nucleotide sugars are important precursors needed to study glycosylation and produce glycosylated products. Saccharomyces cerevisiae is a potentially powerful platform for producing glycosylated biomolecules, but it lacks nucleotide sugar diversity. Nucleotide sugar metabolism is complex, and understanding how to engineer it will be necessary to both access and study heterologous glycosylations found across biology. This review overviews the potential challenges with engineering nucleotide sugar metabolism in yeast from the salvage pathways that convert free sugars to their associated UDP-sugars to de novo synthesis where nucleotide sugars are interconverted through a complex metabolic network with governing feedback mechanisms. Finally, recent examples of engineering complex glycosylation of small molecules in S. cerevisiae are explored and assessed.
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Affiliation(s)
- Samantha A Crowe
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Yuzhong Liu
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Xixi Zhao
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Jay D Keasling
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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12
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Pongracz T, Mayboroda OA, Wuhrer M. The Human Blood N-Glycome: Unraveling Disease Glycosylation Patterns. JACS AU 2024; 4:1696-1708. [PMID: 38818049 PMCID: PMC11134357 DOI: 10.1021/jacsau.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 06/01/2024]
Abstract
Most of the proteins in the circulation are N-glycosylated, shaping together the total blood N-glycome (TBNG). Glycosylation is known to affect protein function, stability, and clearance. The TBNG is influenced by genetic, environmental, and metabolic factors, in part epigenetically imprinted, and responds to a variety of bioactive signals including cytokines and hormones. Accordingly, physiological and pathological events are reflected in distinct TBNG signatures. Here, we assess the specificity of the emerging disease-associated TBNG signatures with respect to a number of key glycosylation motifs including antennarity, linkage-specific sialylation, fucosylation, as well as expression of complex, hybrid-type and oligomannosidic N-glycans, and show perplexing complexity of the glycomic dimension of the studied diseases. Perspectives are given regarding the protein- and site-specific analysis of N-glycosylation, and the dissection of underlying regulatory layers and functional roles of blood protein N-glycosylation.
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Affiliation(s)
- Tamas Pongracz
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Oleg A. Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
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13
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Zoneff E, Wang Y, Jackson C, Smith O, Duchi S, Onofrillo C, Farrugia B, Moulton SE, Williams R, Parish C, Nisbet DR, Caballero-Aguilar LM. Controlled oxygen delivery to power tissue regeneration. Nat Commun 2024; 15:4361. [PMID: 38778053 PMCID: PMC11111456 DOI: 10.1038/s41467-024-48719-x] [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: 11/07/2023] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Oxygen plays a crucial role in human embryogenesis, homeostasis, and tissue regeneration. Emerging engineered regenerative solutions call for novel oxygen delivery systems. To become a reality, these systems must consider physiological processes, oxygen release mechanisms and the target application. In this review, we explore the biological relevance of oxygen at both a cellular and tissue level, and the importance of its controlled delivery via engineered biomaterials and devices. Recent advances and upcoming trends in the field are also discussed with a focus on tissue-engineered constructs that could meet metabolic demands to facilitate regeneration.
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Affiliation(s)
- Elizabeth Zoneff
- The Graeme Clark Institute, The University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Yi Wang
- The Graeme Clark Institute, The University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, ACT, Australia
| | - Oliver Smith
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, ACT, Australia
| | - Serena Duchi
- Department of Surgery, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, VIC, Australia
- Aikenhead Centre for Medical Discovery, St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Carmine Onofrillo
- Department of Surgery, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, VIC, Australia
- Aikenhead Centre for Medical Discovery, St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Brooke Farrugia
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Simon E Moulton
- Aikenhead Centre for Medical Discovery, St. Vincent's Hospital, Melbourne, VIC, Australia
- Department of Engineering Technologies, Swinburne University of Technology, Melbourne, VIC, Australia
- Iverson Health Innovation Research Institute, Swinburne University of Technology, Melbourne, VIC, Australia
| | - Richard Williams
- IMPACT, School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Clare Parish
- The Florey Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - David R Nisbet
- The Graeme Clark Institute, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
- Melbourne Medical School, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, VIC, Australia.
| | - Lilith M Caballero-Aguilar
- The Graeme Clark Institute, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
- Aikenhead Centre for Medical Discovery, St. Vincent's Hospital, Melbourne, VIC, Australia.
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14
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Li GX, Chen L, Hsiao Y, Mannan R, Zhang Y, Luo J, Petralia F, Cho H, Hosseini N, Leprevost FDV, Calinawan A, Li Y, Anand S, Dagar A, Geffen Y, Kumar-Sinha C, Chugh S, Le A, Ponce S, Guo S, Zhang C, Schnaubelt M, Al Deen NN, Chen F, Caravan W, Houston A, Hopkins A, Newton CJ, Wang X, Polasky DA, Haynes S, Yu F, Jing X, Chen S, Robles AI, Mesri M, Thiagarajan M, An E, Getz GA, Linehan WM, Hostetter G, Jewell SD, Chan DW, Wang P, Omenn GS, Mehra R, Ricketts CJ, Ding L, Chinnaiyan AM, Cieslik MP, Dhanasekaran SM, Zhang H, Nesvizhskii AI. Comprehensive proteogenomic characterization of rare kidney tumors. Cell Rep Med 2024; 5:101547. [PMID: 38703764 PMCID: PMC11148773 DOI: 10.1016/j.xcrm.2024.101547] [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: 03/20/2023] [Revised: 09/29/2023] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.
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Affiliation(s)
- Ginny Xiaohe Li
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Yi Hsiao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Luo
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanbyul Cho
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Aniket Dagar
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seema Chugh
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anne Le
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sean Ponce
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Shenghao Guo
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Cissy Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Andrew Houston
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Alex Hopkins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Xiaoming Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaojun Jing
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Siqi Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | | | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Gad A Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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15
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Whittington C, Sharma A, Hill SG, Iavarone AT, Hoffman BM, Offenbacher AR. Impact of N-Glycosylation on Protein Structure and Dynamics Linked to Enzymatic C-H Activation in the M. oryzae Lipoxygenase. Biochemistry 2024; 63:1335-1346. [PMID: 38690768 DOI: 10.1021/acs.biochem.4c00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Lipoxygenases (LOXs) from pathogenic fungi are potential therapeutic targets for defense against plant and select human diseases. In contrast to the canonical LOXs in plants and animals, fungal LOXs are unique in having appended N-linked glycans. Such important post-translational modifications (PTMs) endow proteins with altered structure, stability, and/or function. In this study, we present the structural and functional outcomes of removing or altering these surface carbohydrates on the LOX from the devastating rice blast fungus, M. oryzae, MoLOX. Alteration of the PTMs did notinfluence the active site enzyme-substrate ground state structures as visualized by electron-nuclear double resonance (ENDOR) spectroscopy. However, removal of the eight N-linked glycans by asparagine-to-glutamine mutagenesis nonetheless led to a change in substrate selectivity and an elevated activation energy for the reaction with substrate linoleic acid, as determined by kinetic measurements. Comparative hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis of wild-type and Asn-to-Gln MoLOX variants revealed a regionally defined impact on the dynamics of the arched helix that covers the active site. Guided by these HDX results, a single glycan sequon knockout was generated at position 72, and its comparative substrate selectivity from kinetics nearly matched that of the Asn-to-Gln variant. The cumulative data from model glyco-enzyme MoLOX showcase how the presence, alteration, or removal of even a single N-linked glycan can influence the structural integrity and dynamics of the protein that are linked to an enzyme's catalytic proficiency, while indicating that extensive glycosylation protects the enzyme during pathogenesis by protecting it from protease degradation.
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Affiliation(s)
- Chris Whittington
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Ajay Sharma
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - S Gage Hill
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Adam R Offenbacher
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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16
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Qu K, Li J. Functional Interface for Glycoprotein Sensing: Focusing on Biosensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10405-10413. [PMID: 38723020 DOI: 10.1021/acs.langmuir.4c00607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Glycosylated proteins or glycoproteins make up a large family of glycoconjugates, and they participate in a variety of fundamental biological events. Glycoproteins have become important biomarkers in the diagnosis and treatment of a number of tumors. Biosensors are quite suitable for glycoprotein detection. The design and fabrication of a functional sensing interface play a crucial role in the biosensor construction to target glycoproteins. The functional interface, particularly receptors, typically determines the key characteristics of a biosensor, such as selectivity and sensitivity. Antibody, peptide, aptamer, boronic acid derivative, lectin, and molecularly imprinted polymer are all capable receptors for glycoprotein recognition, and each of these will be discussed. Most glycoproteins exist in low abundance, thus rendering signal amplification techniques indispensable. Nucleic acid-mediated and nanomaterial-mediated signal amplification for the detection of glycoproteins will be focused on herein. This review aims to highlight these different functional interfaces for glycoprotein sensing.
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Affiliation(s)
- Ke Qu
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, P. R. China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China
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17
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Shu T, Zhang Y, Sun T, Zhu Y. Polypeptide N-Acetylgalactosaminyl transferase 14 is a novel mediator in pancreatic β-cell function and growth. Mol Cell Endocrinol 2024; 591:112269. [PMID: 38763428 DOI: 10.1016/j.mce.2024.112269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024]
Abstract
Polypeptide N-Acetylgalactosaminyl transferase 14 (GALNT14) plays important roles in cancer progression and chemotherapy response. Here, we show that GALNT14 is highly expressed in pancreatic β cells and regulates β cell function and growth. We found that the expression level of Ganlt14 was significantly decreased in the primary islets from three rodent type-2 diabetic models. Single-Cell sequencing defined that Galnt14 was mainly expressed in β cells of mouse islets. Galnt14 knockout (G14KO) INS-1 cell line, constructed by using CRISPR/Cas9 technology were growth normal, but showed blunt shape, and increased basal insulin secretion. Combined proteomics and glycoproteomics demonstrated that G14KO altered cell-to-cell junctions, communication, and adhesion. Insulin receptor (IR) and IGF1-1R were indirectly confirmed for GALNT14 substrates, contributed to diminished IGF1-induced p-AKT levels and cell growth in G14KO cells. Overall, this study uncovers that GALNT14 is a novel modulator in regulating β cells biology, providing a missing link of β cells O-glycosylation to diabetes development.
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Affiliation(s)
- Tingting Shu
- Department of Central Laboratory, Geriatric Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210024, China
| | - Yan Zhang
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China; Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Tong Sun
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Yunxia Zhu
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China.
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18
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Yuasa H, Morino N, Wagatsuma T, Munekane M, Ueda S, Matsunaga M, Uchida Y, Katayama T, Katoh T, Kambe T. ZNT5-6 and ZNT7 play an integral role in protein N-glycosylation by supplying Zn 2+ to Golgi α-mannosidase II. J Biol Chem 2024:107378. [PMID: 38762179 DOI: 10.1016/j.jbc.2024.107378] [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: 02/19/2024] [Revised: 04/20/2024] [Accepted: 05/07/2024] [Indexed: 05/20/2024] Open
Abstract
The stepwise addition of monosaccharides to N-glycans attached to client proteins to generate a repertoire of mature proteins involves a concerted action of many glycosidases and glycosyltransferases. Here, we report that Golgi α-mannosidase II (GMII), a pivotal enzyme catalyzing the first step in the conversion of hybrid- to complex-type N-glycans, is activated by Zn2+ supplied by the early secretory compartment-resident ZNT5-ZNT6 heterodimers (ZNT5-6) and ZNT7 homodimers (ZNT7). Loss of ZNT5-6 and ZNT7 function results in marked accumulation of hybrid-type and complex/hybrid glycans with concomitant reduction of complex- and high-mannose-type glycans. In cells lacking the ZNT5-6 and ZNT7 functions, the GMII activity is substantially decreased. In contrast, the activity of its homolog, lysosomal mannosidase (LAMAN), is not decreased. Moreover, we show that the growth of pancreatic cancer MIA PaCa-2 cells lacking ZNT5-6 and ZNT7 is significantly decreased in a nude mouse xenograft model. Our results indicate the integral roles of ZNT5-6 and ZNT7 in N-glycosylation and highlight their potential as novel target proteins for cancer therapy.
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Affiliation(s)
- Hana Yuasa
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Naho Morino
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takumi Wagatsuma
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Masayuki Munekane
- Institute of Medical, Pharmaceutical and Health Sciences Faculty of Pharmacy, Kanazawa University, Kanazawa 920-1192, Japan
| | - Sachiko Ueda
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mayu Matsunaga
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yasuo Uchida
- Department of Molecular Systems Pharmaceutics, Graduate School of Biomedical and Health Sciences, Hiroshima University, 734-0037 Hiroshima city, Japan
| | - Takane Katayama
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Toshihiko Katoh
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Taiho Kambe
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
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19
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Shao Y, Li R, Chen G, Zhang L. Pan-Cancer Analysis of GALNT6 with Potential Implications for Prognosis and Tumor Microenvironment in Human Cancer Based on Bioinformatics and qPCR Verification. Int J Gen Med 2024; 17:2187-2201. [PMID: 38770365 PMCID: PMC11104441 DOI: 10.2147/ijgm.s459953] [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: 01/18/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024] Open
Abstract
Purpose We explored the expression and prognostic value of GALNT6 and the tumor microenvironment of pan-cancer in humans. Methods In this study, we explored the expression pattern of GALNT6 pan-cancer across multiple databases. The prognostic value of GALNT6 was evaluated using the Kaplan-Meier method. The types and numbers of GALNT6 gene alterations were exhibited using the cBio Cancer Genomics Portal. The correlations between GALNT6 expression and immune infiltration in cancers were analyzed using the database Tumor Immune Estimation Resource 2. We also used the Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology analysis to investigate the molecular mechanisms of the GALNT6 gene in tumorigenesis. The expression of GALNT6 was also further verified by qPCR in lung adenocarcinoma tissues. Results In general, compared with normal tissue, tumor tissue had a higher expression level of GALNT6. GALNT6 showed a protective effect in colon carcinoma and other cancers; however, a high expression level of GALNT6 was detrimental to survival in bladder cancer and in pheochromocytoma and paraganglioma. Mutation, amplification, and deep deletion were the three main types of GALNT6 mutations in tumors. There was a significant positive correlation between GALNT6 expression and immune infiltration of CD8+ T-cells in skin cutaneous melanoma metastasis, based on most of the algorithms used. Moreover, protein processing- and glycoprotein metabolic-associated functions were involved in the functional mechanisms of GALNT6. Conclusion This first pan-cancer study offers a relatively comprehensive understanding of the oncogenic roles of GALNT6 across different cancer types.
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Affiliation(s)
- Yue Shao
- Department of Respiratory Medicine, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116001, People’s Republic of China
| | - Rong Li
- Department of Respiratory Medicine, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116001, People’s Republic of China
| | - Guangmei Chen
- Department of Respiratory Medicine, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116001, People’s Republic of China
| | - Lichuan Zhang
- Department of Respiratory Medicine, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116001, People’s Republic of China
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20
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Kontodimas V, Yaman M, Greis K, Lettow M, Pagel K, Marianski M. Reinvestigation of the internal glycan rearrangement of Lewis a and blood group type H1 epitopes. Phys Chem Chem Phys 2024; 26:14160-14170. [PMID: 38712976 PMCID: PMC11147448 DOI: 10.1039/d3cp04491b] [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: 05/08/2024]
Abstract
Protonated ions of fucose-containing oligosaccharides are prone to undergo internal glycan rearrangement which results in chimeric fragments that obfuscate mass-spectrometric analysis. Lack of accessible tools that would facilitate systematic analysis of glycans in the gas phase limits our understanding of this phenomenon. In this work, we use density functional theory modeling to interpret cryogenic IR spectra of Lewis a and blood group type H1 trisaccharides and to establish whether these trisaccharides undergo the rearrangement during gas-phase analysis. Structurally unconstrained search reveals that none of the parent ions constitute a thermodynamic global minimum. In contrast, predicted collision cross sections and anharmonic IR spectra provide a good match to available experimental data which allowed us to conclude that fucose migration does not occur in these antigens. By comparing the predicted structures with those obtained for Lewis x and blood group type H2 epitopes, we demonstrate that the availability of the mobile proton and a large difference in the relative stability of the parent ions and rearrangement products constitute the prerequisites for the rearrangement reaction.
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Affiliation(s)
- Vasilis Kontodimas
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
| | - Murat Yaman
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Kim Greis
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Maike Lettow
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Mateusz Marianski
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
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21
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Yao G, Tian Y, Ke W, Fang J, Ma S, Li T, Cheng X, Xia B, Wen L, Gao Z. Direct Identification of Complex Glycans via a Highly Sensitive Engineered Nanopore. J Am Chem Soc 2024; 146:13356-13366. [PMID: 38602480 DOI: 10.1021/jacs.4c02081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The crucial roles that glycans play in biological systems are determined by their structures. However, the analysis of glycan structures still has numerous bottlenecks due to their inherent complexities. The nanopore technology has emerged as a powerful sensor for DNA sequencing and peptide detection. This has a significant impact on the development of a related research area. Currently, nanopores are beginning to be applied for the detection of simple glycans, but the analysis of complex glycans by this technology is still challenging. Here, we designed an engineered α-hemolysin nanopore M113R/T115A to achieve the sensing of complex glycans at micromolar concentrations and under label-free conditions. By extracting characteristic features to depict a three-dimensional (3D) scatter plot, glycans with different numbers of functional groups, various chain lengths ranging from disaccharide to decasaccharide, and distinct glycosidic linkages could be distinguished. Molecular dynamics (MD) simulations show different behaviors of glycans with β1,3- or β1,4-glycosidic bonds in nanopores. More importantly, the designed nanopore system permitted the discrimination of each glycan isomer with different lengths in a mixture with a separation ratio of over 0.9. This work represents a proof-of-concept demonstration that complex glycans can be analyzed using nanopore sequencing technology.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
| | - Yinping Tian
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Fang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shengzhou Ma
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tiehai Li
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 330106, China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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22
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Nemčić M, Shkunnikova S, Kifer D, Plavša B, Vučić Lovrenčić M, Morahan G, Duvnjak L, Pociot F, Gornik O. N-glycosylation of immunoglobulin A in children and adults with type 1 diabetes mellitus. Heliyon 2024; 10:e30529. [PMID: 38765169 PMCID: PMC11098780 DOI: 10.1016/j.heliyon.2024.e30529] [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: 04/15/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024] Open
Abstract
Aims To identify N-glycan structures on immunoglobulin A related to type 1 diabetes mellitus among children at the disease onset and adults with type 1 diabetes mellitus. Methods Human polyclonal IgA N-glycans were profiled using hydrophilic interaction ultra performance liquid chromatography in two cohorts. The first cohort consisted of 62 children at the onset of type 1 diabetes mellitus and 86 of their healthy siblings. The second cohort contained 84 adults with the disease and 84 controls. Associations between N-glycans and type 1 diabetes mellitus were tested using linear mixed model for the paediatric cohort, or general linear model for the adult cohort. False discovery rate was controlled by Benjamini-Hochberg method modified by Li and Ji. Results In children, an increase in a single oligomannose N-glycan was associated with type 1 diabetes mellitus (B = 0.529, p = 0.0067). N-glycome of the adults displayed increased branching (B = 0.466, p = 0.0052), trigalactosylation (B = 0.466, p = 0.0052), trisialylation (B = 0.629, p < 0.001), and mannosylation (B = 0.604, p < 0.001). The strongest association with the disease was a decrease in immunoglobulin A core fucosylation (B = -0.900, p < 0.001). Conclusions Changes in immunoglobulin N-glycosylation patterns in type 1 diabetes point to disruptions in immunoglobulin A catabolism and dysregulated inflammatory capabilities of the antibody, potentially impacting immune responses and inflammation.
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Affiliation(s)
- Matej Nemčić
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, Zagreb, Croatia
| | - Sofia Shkunnikova
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, Zagreb, Croatia
| | - Domagoj Kifer
- Department of Biophysics, Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, Zagreb, Croatia
| | - Branimir Plavša
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, Zagreb, Croatia
| | | | - Grant Morahan
- Centre for Diabetes Research, The Harry Perkins Institute for Medical Research, 6 Verdun St, Nedlands, WA, Australia
- Australian Centre for Accelerating Diabetes Innovations, University of Melbourne, Parkville, Victoria, 3010, VIC, Australia
| | - Lea Duvnjak
- Department of Endocrinology, Vuk Vrhovac University Clinic for Diabetes, Endocrinology and Metabolic Diseases, Merkur University Hospital, Dugi dol 4A, Zagreb, Croatia
| | - Flemming Pociot
- Department of Clinical Research, Steno Diabetes Center Copenhagen, Borgmester Ib Juuls Vej 83, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Olga Gornik
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, Zagreb, Croatia
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Santisteban Celis IC, Matoba N. Lectibodies as antivirals. Antiviral Res 2024; 227:105901. [PMID: 38734211 DOI: 10.1016/j.antiviral.2024.105901] [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: 01/18/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
Growing concerns regarding the emergence of highly transmissible viral diseases highlight the urgent need to expand the repertoire of antiviral therapeutics. For this reason, new strategies for neutralizing and inhibiting these viruses are necessary. A promising approach involves targeting the glycans present on the surfaces of enveloped viruses. Lectins, known for their ability to recognize specific carbohydrate molecules, offer the potential for glycan-targeted antiviral strategies. Indeed, numerous studies have reported the antiviral effects of various lectins of both endogenous and exogenous origins. However, many lectins in their natural forms, are not suitable for use as antiviral therapeutics due to toxicity, other unfavorable pharmacological effects, and/or unreliable manufacturing sources. Therefore, improvements are crucial for employing lectins as effective antiviral therapeutics. A novel approach to enhance lectins' suitability as pharmaceuticals could be the generation of recombinant lectin-Fc fusion proteins, termed "lectibodies." In this review, we discuss the scientific rationale behind lectin-based antiviral strategies and explore how lectibodies could facilitate the development of new antiviral therapeutics. We will also share our perspective on the potential of these molecules to transcend their potential use as antiviral agents.
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Affiliation(s)
- Ian Carlosalberto Santisteban Celis
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, USA; Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville, KY, USA
| | - Nobuyuki Matoba
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, USA; Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville, KY, USA; UofL Health - Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA.
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24
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Marie AL, Gao Y, Ivanov AR. Native N-glycome profiling of single cells and ng-level blood isolates using label-free capillary electrophoresis-mass spectrometry. Nat Commun 2024; 15:3847. [PMID: 38719792 PMCID: PMC11079027 DOI: 10.1038/s41467-024-47772-w] [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] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
The development of reliable single-cell dispensers and substantial sensitivity improvement in mass spectrometry made proteomic profiling of individual cells achievable. Yet, there are no established methods for single-cell glycome analysis due to the inability to amplify glycans and sample losses associated with sample processing and glycan labeling. In this work, we present an integrated platform coupling online in-capillary sample processing with high-sensitivity label-free capillary electrophoresis-mass spectrometry for N-glycan profiling of single mammalian cells. Direct and unbiased quantitative characterization of single-cell surface N-glycomes are demonstrated for HeLa and U87 cells, with the detection of up to 100 N-glycans per single cell. Interestingly, N-glycome alterations are unequivocally detected at the single-cell level in HeLa and U87 cells stimulated with lipopolysaccharide. The developed workflow is also applied to the profiling of ng-level amounts (5-500 ng) of blood-derived protein, extracellular vesicle, and total plasma isolates, resulting in over 170, 220, and 370 quantitated N-glycans, respectively.
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Affiliation(s)
- Anne-Lise Marie
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US
| | - Yunfan Gao
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US.
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25
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Guo L, Han Y, Yang H, Fu J, Li W, Xie R, Zhang Y, Wang K, Xia XH. Single-Molecule Discrimination of Saccharides Using Carbon Nitride Nanopores. NANO LETTERS 2024; 24:5639-5646. [PMID: 38668743 DOI: 10.1021/acs.nanolett.4c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Structural complexity brings a huge challenge to the analysis of sugar chains. As a single-molecule sensor, nanopores have the potential to provide fingerprint information on saccharides. Traditionally, direct single-molecule saccharide detection with nanopores is hampered by their small size and weak affinity. Here, a carbon nitride nanopore device is developed to discern two types of trisaccharide molecules (LeApN and SLeCpN) with minor structural differences. The resolution of LeApN and SLeCpN in the mixture reaches 0.98, which has never been achieved in solid-state nanopores so far. Monosaccharide (GlcNAcpN) and disaccharide (LacNAcpN) can also be discriminated using this system, indicating that the versatile carbon nitride nanopores possess a monosaccharide-level resolution. This study demonstrates that the carbon nitride nanopores have the potential for conducting structure analysis on single-molecule saccharides.
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Affiliation(s)
- Linru Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yida Han
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Hong Yang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Jie Fu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ran Xie
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Yuanjian Zhang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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26
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Wang S, Li W, Wang L, Tiwari SK, Bray W, Wu L, Li N, Hui H, Clark AE, Zhang Q, Zhang L, Carlin AF, Rana TM. Interferon-Inducible Guanylate-Binding Protein 5 Inhibits Replication of Multiple Viruses by Binding to the Oligosaccharyltransferase Complex and Inhibiting Glycoprotein Maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.591800. [PMID: 38746287 PMCID: PMC11092618 DOI: 10.1101/2024.05.01.591800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Viral infection induces production of type I interferons and expression of interferon-stimulated genes (ISGs) that play key roles in inhibiting viral infection. Here, we show that the ISG guanylate-binding protein 5 (GBP5) inhibits N-linked glycosylation of key proteins in multiple viruses, including SARS-CoV-2 spike protein. GBP5 binds to accessory subunits of the host oligosaccharyltransferase (OST) complex and blocks its interaction with the spike protein, which results in misfolding and retention of spike protein in the endoplasmic reticulum likely due to decreased N-glycan transfer, and reduces the assembly and release of infectious virions. Consistent with these observations, pharmacological inhibition of the OST complex with NGI-1 potently inhibits glycosylation of other viral proteins, including MERS-CoV spike protein, HIV-1 gp160, and IAV hemagglutinin, and prevents the production of infectious virions. Our results identify a novel strategy by which ISGs restrict virus infection and provide a rationale for targeting glycosylation as a broad antiviral therapeutic strategy.
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Affiliation(s)
- Shaobo Wang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
- These authors contributed equally to this work
| | - Wanyu Li
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
- These authors contributed equally to this work
| | - Lingling Wang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
| | - Shashi Kant Tiwari
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
| | - William Bray
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
| | - Lujing Wu
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
| | - Na Li
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
| | - Hui Hui
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
| | - Alex E. Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine; University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
| | - Qiong Zhang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
| | - Lingzhi Zhang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine; University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
| | - Tariq M. Rana
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA
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27
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Radziejewska I. Tumor-associated carbohydrate antigens of MUC1 - Implication in cancer development. Biomed Pharmacother 2024; 174:116619. [PMID: 38643541 DOI: 10.1016/j.biopha.2024.116619] [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: 01/29/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/23/2024] Open
Abstract
Glycosylation of cancerous epithelial MUC1 protein is specifically altered in comparison to that which is presented by healthy cells. One of such changes is appearing tumor-associated carbohydrate antigens (TACAs) which are rare in normal tissues and are highly correlated with poor clinical outcomes and cancer progression. This review summarizes and describes the role of Tn, T antigens, their sialylated forms as well as fucosylated Lewis epitopes in different aspects of tumor development, progression, and metastasis. Finally, applications of MUC1 glycan epitopes as potential targets for therapeutic strategy of cancers are notified. One of the novelties of this review is presentation of TACAs as inherently connected with MUC1 mucin.
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Affiliation(s)
- Iwona Radziejewska
- Department of Medical Chemistry, Medical University of Białystok, ul. Mickiewicza 2, Białystok 15-222, Poland.
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28
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Yao G, Ke W, Xia B, Gao Z. Nanopore-based glycan sequencing: state of the art and future prospects. Chem Sci 2024; 15:6229-6243. [PMID: 38699252 PMCID: PMC11062086 DOI: 10.1039/d4sc01466a] [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: 03/02/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Sequencing of biomacromolecules is a crucial cornerstone in life sciences. Glycans, one of the fundamental biomolecules, derive their physiological and pathological functions from their structures. Glycan sequencing faces challenges due to its structural complexity and current detection technology limitations. As a highly sensitive sensor, nanopores can directly convert nucleic acid sequence information into electrical signals, spearheading the revolution of third-generation nucleic acid sequencing technologies. However, their potential for deciphering complex glycans remains untapped. Initial attempts demonstrated the significant sensitivity of nanopores in glycan sensing, which provided the theoretical basis and insights for the realization of nanopore-based glycan sequencing. Here, we present three potential technical routes to employ nanopore technology in glycan sequencing for the first time. The three novel technical routes include: strand sequencing, capturing glycan chains as they translocate through nanopores; sequential hydrolysis sequencing, capturing released monosaccharides one by one; splicing sequencing, mapping signals from hydrolyzed glycan fragments to an oligosaccharide database/library. Designing suitable nanopores, enzymes, and motors, and extracting characteristic signals pose major challenges, potentially aided by artificial intelligence. It would be highly desirable to design an all-in-one high-throughput glycan sequencer instrument by integrating a sample processing unit, nanopore array, and signal acquisition system into a microfluidic device. The nanopore sequencer invention calls for intensive multidisciplinary cooperation including electrochemistry, glycochemistry, engineering, materials, enzymology, etc. Advancing glycan sequencing will promote the development of basic research and facilitate the discovery of glycan-based drugs and disease markers, fostering progress in glycoscience and even life sciences.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- School of Life Science and Technology, Shanghai Tech University 201210 Shanghai China
- Lingang Laboratory 200031 Shanghai China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 528400 Zhongshan China
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Das T, Luo S, Tang H, Fang J, Mao Y, Yen HH, Dash S, Shajahan A, Pepi L, Huang S, Jones VS, Xie S, Huang GF, Lu J, Anderson B, Zhang B, Azadi P, Huang RP. N-glycosylation of the SARS-CoV-2 spike protein at Asn331 and Asn343 is involved in spike-ACE2 binding, virus entry, and regulation of IL-6. Microbiol Immunol 2024; 68:165-178. [PMID: 38444370 DOI: 10.1111/1348-0421.13121] [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: 07/31/2023] [Revised: 12/06/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is an ongoing global public health crisis. The causative agent, the SARS-CoV-2 virus, enters host cells via molecular interactions between the viral spike protein and the host cell ACE2 surface protein. The SARS-CoV-2 spike protein is extensively decorated with up to 66 N-linked glycans. Glycosylation of viral proteins is known to function in immune evasion strategies but may also function in the molecular events of viral entry into host cells. Here, we show that N-glycosylation at Asn331 and Asn343 of SARS-CoV-2 spike protein is required for it to bind to ACE2 and for the entry of pseudovirus harboring the SARS-CoV-2 spike protein into cells. Interestingly, high-content glycan binding screening data have shown that N-glycosylation of Asn331 and Asn343 of the RBD is important for binding to the specific glycan molecule G4GN (Galβ-1,4 GlcNAc), which is critical for spike-RBD-ACE2 binding. Furthermore, IL-6 was identified through antibody array analysis of conditioned media of the corresponding pseudovirus assay. Mutation of N-glycosylation of Asn331 and Asn343 sites of the spike receptor-binding domain (RBD) significantly reduced the transcriptional upregulation of pro-inflammatory signaling molecule IL-6. In addition, IL-6 levels correlated with spike protein levels in COVID-19 patients' serum. These findings establish the importance of RBD glycosylation in SARS-CoV-2 pathogenesis, which can be exploited for the development of novel therapeutics for COVID-19.
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Affiliation(s)
- Tuhin Das
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Shuhong Luo
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Hao Tang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Jianmin Fang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Yinging Mao
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Haw-Han Yen
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Sabyasachi Dash
- Department of Pathology, Center for Vascular Biology, Weill Cornell Medicine, New York, New York, USA
| | - Asif Shajahan
- Vaccine Research Center, Gaithersburg, Maryland, USA
| | - Lauren Pepi
- Vaccine Research Center, Gaithersburg, Maryland, USA
| | - Steven Huang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | | | - Shehuo Xie
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | | | - Jinqiao Lu
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | | | - Benyue Zhang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Ruo-Pan Huang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
- South China Biochip Research Center, Guangzhou, China
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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30
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Sirén H. Research of saccharides and related biocomplexes: A review with recent techniques and applications. J Sep Sci 2024; 47:e2300668. [PMID: 38699940 DOI: 10.1002/jssc.202300668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 05/05/2024]
Abstract
Saccharides and biocompounds as saccharide (sugar) complexes have various roles and biological functions in living organisms due to modifications via nucleophilic substitution, polymerization, and complex formation reactions. Mostly, mono-, di-, oligo-, and polysaccharides are stabilized to inactive glycosides, which are formed in metabolic pathways. Natural saccharides are important in food and environmental monitoring. Glycosides with various functionalities are significant in clinical and medical research. Saccharides are often studied with the chromatographic methods of hydrophilic interaction liquid chromatography and anion exchange chromatograpy, but also with capillary electrophoresis and mass spectrometry with their on-line coupling systems. Sample preparation is important in the identification of saccharide compounds. The cases discussed here focus on bioscience, clinical, and food applications.
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Affiliation(s)
- Heli Sirén
- Chemicum Building, University of Helsinki, Helsinki, Finland
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31
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Gong H, Zhu C, Han D, Liu S. Secreted Glycoproteins That Regulate Synaptic Function: the Dispatchers in the Central Nervous System. Mol Neurobiol 2024; 61:2719-2727. [PMID: 37924485 DOI: 10.1007/s12035-023-03731-y] [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: 02/07/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023]
Abstract
Glycoproteins are proteins that contain oligosaccharide chains. As widely distributed functional proteins in the body, glycoproteins are essential for cellular development, cellular function maintenance, and intercellular communication. Glycoproteins not only play a role in the cell and the membrane, but they are also secreted in the intercell. These secreted glycoproteins are critical to the central nervous system for neurodevelopment and synaptic transmission. More specifically, secreted glycoproteins play indispensable roles in neurite growth mediation, axon guiding, synaptogenesis, neuronal differentiation, the release of synaptic vesicles, subunit composition of neurotransmitter receptors, and neurotransmitter receptor trafficking among other things. Abnormal expressions of secreted glycoproteins in the central nervous system are associated with abnormal neuron development, impaired synaptic organization/transmission, and neuropsychiatric disorders. This article reviews the secreted glycoproteins that regulate neuronal development and synaptic function in the central nervous system, and the molecular mechanism of these regulations, providing reference for research about synaptic function regulation and related central nervous system diseases.
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Affiliation(s)
- Haiying Gong
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Conglei Zhu
- Department of Pharmacy, Fuyang People's Hospital, Fuyang, Anhui, China
| | - Di Han
- Department of Respiratory and Critical Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Sen Liu
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.
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32
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Fazelzadeh Haghighi M, Jafari Khamirani H, Fallahi J, Monfared AA, Ashrafi Dehkordi K, Tabei SMB. Novel insight into FCSK-congenital disorder of glycosylation through a CRISPR-generated cell model. Mol Genet Genomic Med 2024; 12:e2445. [PMID: 38722107 PMCID: PMC11080630 DOI: 10.1002/mgg3.2445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/08/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND FCSK-congenital disorder of glycosylation (FCSK-CDG) is a recently discovered rare autosomal recessive genetic disorder with defective fucosylation due to mutations in the fucokinase encoding gene, FCSK. Despite the essential role of fucokinase in the fucose salvage pathway and severe multisystem manifestations of FCSK-CDG patients, it is not elucidated which cells or which types of fucosylation are affected by its deficiency. METHODS In this study, CRISPR/Cas9 was employed to construct an FCSK-CDG cell model and explore the molecular mechanisms of the disease by lectin flow cytometry and real-time PCR analyses. RESULTS Comparison of cellular fucosylation by lectin flow cytometry in the created CRISPR/Cas9 FCSK knockout and the same unedited cell lines showed no significant change in the amount of cell surface fucosylated glycans, which is consistent with the only documented previous study on different cell types. It suggests a probable effect of this disease on secretory glycoproteins. Investigating O-fucosylation by analysis of the NOTCH3 gene expression as a potential target revealed a significant decrease in the FCSK knockout cells compared with the same unedited ones, proving the effect of fucokinase deficiency on EGF-like repeats O-fucosylation. CONCLUSION This study expands insight into the FCSK-CDG molecular mechanism; to the best of our knowledge, it is the first research conducted to reveal a gene whose expression level alters due to this disease.
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Affiliation(s)
- Maryam Fazelzadeh Haghighi
- Department of Molecular Medicine, School of Advanced TechnologiesShahrekord University of Medical SciencesShahrekordIran
| | | | - Jafar Fallahi
- Molecular Medicine Department, School of Advanced Medical Sciences and TechnologiesShiraz University of Medical SciencesShirazIran
| | - Ali Arabi Monfared
- Central Research LaboratoryShiraz University of Medical SciencesShirazIran
| | - Korosh Ashrafi Dehkordi
- Department of Molecular Medicine, School of Advanced TechnologiesShahrekord University of Medical SciencesShahrekordIran
| | - Seyed Mohammad Bagher Tabei
- Department of Medical GeneticsShiraz University of Medical SciencesShirazIran
- Maternal‐Fetal Medicine Research CenterShiraz University of Medical SciencesShirazIran
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Xu X, Yin K, Wu R. Systematic Investigation of the Trafficking of Glycoproteins on the Cell Surface. Mol Cell Proteomics 2024; 23:100761. [PMID: 38593903 PMCID: PMC11087972 DOI: 10.1016/j.mcpro.2024.100761] [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: 02/22/2024] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024] Open
Abstract
Glycoproteins located on the cell surface play a pivotal role in nearly every extracellular activity. N-glycosylation is one of the most common and important protein modifications in eukaryotic cells, and it often regulates protein folding and trafficking. Glycosylation of cell-surface proteins undergoes meticulous regulation by various enzymes in the endoplasmic reticulum (ER) and the Golgi, ensuring their proper folding and trafficking to the cell surface. However, the impacts of protein N-glycosylation, N-glycan maturity, and protein folding status on the trafficking of cell-surface glycoproteins remain to be explored. In this work, we comprehensively and site-specifically studied the trafficking of cell-surface glycoproteins in human cells. Integrating metabolic labeling, bioorthogonal chemistry, and multiplexed proteomics, we investigated 706 N-glycosylation sites on 396 cell-surface glycoproteins in monocytes, either by inhibiting protein N-glycosylation, disturbing N-glycan maturation, or perturbing protein folding in the ER. The current results reveal their distinct impacts on the trafficking of surface glycoproteins. The inhibition of protein N-glycosylation dramatically suppresses the trafficking of many cell-surface glycoproteins. The N-glycan immaturity has more substantial effects on proteins with high N-glycosylation site densities, while the perturbation of protein folding in the ER exerts a more pronounced impact on surface glycoproteins with larger sizes. Furthermore, for N-glycosylated proteins, their trafficking to the cell surface is related to the secondary structures and adjacent amino acid residues of glycosylation sites. Systematic analysis of surface glycoprotein trafficking advances our understanding of the mechanisms underlying protein secretion and surface presentation.
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Affiliation(s)
- Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA.
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34
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Lee J, Boo J, Kim YH, Roh J, Ko SK, Shin I. A fluorescent probe for selective detection of lysosomal β-hexosaminidase in live cells. Talanta 2024; 271:125715. [PMID: 38280264 DOI: 10.1016/j.talanta.2024.125715] [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: 11/28/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/29/2024]
Abstract
Determining the activity of lysosomal β-hexosaminidase in cells is of great importance for understanding the roles that these enzymes play in pathophysiological events. Herein, we designed the new fluorescent probe, βGalNAc-Rhod-CM(NEt2), which consisted of a βGalNAc-linked rhodol unit serving as a β-hexosaminidase reactive fluorogenic moiety and a N,N'-diethylaminocoumarin (CM(NEt2)) group acting as a fluorescence marker for determining the degree of cell permeabilization. Treatment of βGalNAc-Rhod-CM(NEt2) with β-hexosaminidase promoted generation of Rhod-CM(NEt2), thereby leading to an increase in the intensity of fluorescence of Rhod. However, this probe did not respond to the functionally related glycosidase, O-GlcNAcase. The detection limit of βGalNAc-Rhod-CM(NEt2) for β-hexosaminidase was determined to be 0.52 nM, indicating that it has high sensitivity for this enzyme. Furthermore, the probe functioned as an excellent fluorogenic substrate for β-hexosaminidase with kcat and Km values of 17 sec-1 and 22 μM, respectively. The results of cell studies using βGalNAc-Rhod-CM(NEt2) showed that levels of β-hexosaminidase activity in cells can be determined by measuring the intensity of fluorescence arising from Rhod and that the intensity of fluorescence of CM(NEt2) can be employed to determine the degree of cell permeabilization of the probe. Utilizing the new probe, we assessed β-hexosaminidase activities in several types of cells and evaluated the effect of glucose concentrations in culture media on the activity of this enzyme.
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Affiliation(s)
- Jongwon Lee
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jihyeon Boo
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Young-Hyun Kim
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jongtae Roh
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea; Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Sung-Kyun Ko
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea; Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Injae Shin
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea.
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35
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Thomas P, Peele EE, Yopak KE, Sulikowski JA, Kinsey ST. Lectin binding to pectoral fin of neonate little skates reared under ambient and projected-end-of-century temperature regimes. J Morphol 2024; 285:e21698. [PMID: 38669130 PMCID: PMC11064730 DOI: 10.1002/jmor.21698] [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: 10/20/2023] [Revised: 04/03/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
The glycosylation of macromolecules can vary both among tissue structural components and by adverse conditions, potentially providing an alternative marker of stress in organisms. Lectins are proteins that bind carbohydrate moieties and lectin histochemistry is a common method to visualize microstructures in biological specimens and diagnose pathophysiological states in human tissues known to alter glycan profiles. However, this technique is not commonly used to assess broad-spectrum changes in cellular glycosylation in response to environmental stressors. In addition, the binding of various lectins has not been studied in elasmobranchs (sharks, skates, and rays). We surveyed the binding tissue structure specificity of 14 plant-derived lectins, using both immunoblotting and immunofluorescence, in the pectoral fins of neonate little skates (Leucoraja erinacea). Skates were reared under present-day or elevated (+5°C above ambient) temperature regimes and evaluated for lectin binding as an indicator of changing cellular glycosylation and tissue structure. Lectin labeling was highly tissue and microstructure specific. Dot blots revealed no significant changes in lectin binding between temperature regimes. In addition, lectins only detected in the elevated temperature treatment were Canavalia ensiformis lectin (Concanavalin A) in spindle cells of muscle and Ricinus communis agglutinin in muscle capillaries. These results provide a reference for lectin labeling in elasmobranch tissue that may aid future investigations.
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Affiliation(s)
- Peyton Thomas
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC, 28403, USA
| | - Emily E. Peele
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC, 28403, USA
| | - Kara E. Yopak
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC, 28403, USA
| | - James A. Sulikowski
- 2030 SE Marine Science Drive, Coastal Oregon Marine Experiment Station, Oregon State University, Corvallis, OR 97365, USA
| | - Stephen T. Kinsey
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC, 28403, USA
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36
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Arora K, Sherilraj PM, Abutwaibe KA, Dhruw B, Mudavath SL. Exploring glycans as vital biological macromolecules: A comprehensive review of advancements in biomedical frontiers. Int J Biol Macromol 2024; 268:131511. [PMID: 38615867 DOI: 10.1016/j.ijbiomac.2024.131511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
This comprehensive review delves into the intricate landscape of glycans and glycoconjugates, unraveling their multifaceted roles across diverse biological dimensions. From influencing fundamental cellular processes such as signaling, recognition, and adhesion to exerting profound effects at the molecular and genetic levels, these complex carbohydrate structures emerge as linchpins in cellular functions and interactions. The structural diversity of glycoconjugates, which can be specifically classified into glycoproteins, glycolipids, and proteoglycans, underscores their importance in shaping the architecture of cells. Beyond their structural roles, these molecules also play key functions in facilitating cellular communication and modulating recognition mechanisms. Further, glycans and glycoconjugates prove invaluable as biomarkers in disease diagnostics, particularly in cancer, where aberrant glycosylation patterns offer critical diagnostic cues. Furthermore, the review explores their promising therapeutic applications, ranging from the development of glycan-based nanomaterials for precise drug delivery to innovative interventions in cancer treatment. This review endeavors to comprehensively explore the intricate functions of glycans and glycoconjugates, with the primary goal of offering valuable insights into their extensive implications in both health and disease. Encompassing a broad spectrum of biological processes, the focus of the review aims to provide a comprehensive understanding of the significant roles played by glycans and glycoconjugates.
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Affiliation(s)
- Kanika Arora
- Infectious Disease Biology Laboratory, Institute of Nano Science & Technology (INST), Sector 81, Mohali, Punjab 140306, India
| | - P M Sherilraj
- Infectious Disease Biology Laboratory, Institute of Nano Science & Technology (INST), Sector 81, Mohali, Punjab 140306, India
| | - K A Abutwaibe
- Infectious Disease Biology Laboratory, Institute of Nano Science & Technology (INST), Sector 81, Mohali, Punjab 140306, India
| | - Bharti Dhruw
- Infectious Disease Biology Laboratory, Institute of Nano Science & Technology (INST), Sector 81, Mohali, Punjab 140306, India
| | - Shyam Lal Mudavath
- Infectious Disease Biology Laboratory, Institute of Nano Science & Technology (INST), Sector 81, Mohali, Punjab 140306, India; Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli Hyderabad 500046, Telangana, India.
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37
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Xing Y, Jian Y, Zhao X, Zhang Y, Zhang Z, Zhang X, Zhang X. Morphological determination of localization and function of Golgi proteins. BIOPHYSICS REPORTS 2024; 10:121-132. [PMID: 38774352 PMCID: PMC11103716 DOI: 10.52601/bpr.2024.240008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 05/24/2024] Open
Abstract
In animal cells, the Golgi apparatus serves as the central hub of the endomembrane secretory pathway. It is responsible for the processing, modification, and sorting of proteins and lipids. The unique stacking and ribbon-like architecture of the Golgi apparatus forms the foundation for its precise functionality. Under cellular stress or pathological conditions, the structure of the Golgi and its important glycosylation modification function may change. It is crucial to employ suitable methodologies to study the structure and function of the Golgi apparatus, particularly when assessing the involvement of a target protein in Golgi regulation. This article provides a comprehensive overview of the diverse microscopy techniques used to determine the specific location of the target protein within the Golgi apparatus. Additionally, it outlines methods for assessing changes in the Golgi structure and its glycosylation modification function following the knockout of the target gene.
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Affiliation(s)
- Yusheng Xing
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yannan Jian
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaodan Zhao
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Zhang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenqian Zhang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xing Zhang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyan Zhang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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38
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Ohashi S, Takakura D, Kobayashi N, Tokuhisa M, Ichikawa Y, Kawasaki N. Comparative Analysis of Site-Specific N-glycosylation of LAMP1 from Breast Cancer Tissues. J Biochem 2024; 175:561-572. [PMID: 38215735 DOI: 10.1093/jb/mvae001] [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: 07/14/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024] Open
Abstract
Glycosylation changes in cancer proteins have been associated with malignant transformation. However, techniques for analyzing site-specific glycosylation changes in target proteins obtained from clinical tissue samples are insufficient. To overcome these problems, we developed a targeted N-glycoproteomic approach consisting of immunoprecipitation, glycopeptide enrichment, LC/MS/MS and structural assignment using commercially available analytical software followed by manual confirmation. This approach was applied to the comparative site-specific glycosylation analysis of lysosome-associated membrane glycoprotein 1 (LAMP1) between breast cancer (BC) tumors and normal tissues adjacent to tumors. Extensive determination of glycan heterogeneity from four N-glycosylation sites (Asn84/103/249/261) in LAMP1 identified 262 glycoforms and revealed remarkable diversity in tumor glycan structures. A significant increase in N-glycoforms with multiple fucoses and sialic acids at Asn84/249 and high-mannose-type glycans at Asn103/261 were observed in the tumor. Principal component analysis revealed that tumors of different subtypes have independent distributions. This approach enables site-specific glycopeptide analysis of target glycoprotein in breast cancer tissue and become a powerful tool for characterizing tumors with different pathological features by their glycan profiles.
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Affiliation(s)
- Shoko Ohashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Daisuke Takakura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Noritoshi Kobayashi
- Department of Oncology, Yokohama City University Hospital, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Motohiko Tokuhisa
- Department of Oncology, Yokohama City University Hospital, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Yasushi Ichikawa
- Department of Oncology, Yokohama City University Hospital, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Nana Kawasaki
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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39
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Tian Y, Ma S, Wen L. Towards chemoenzymatic labeling strategies for profiling protein glycosylation. Curr Opin Chem Biol 2024; 80:102460. [PMID: 38678979 DOI: 10.1016/j.cbpa.2024.102460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/31/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024]
Abstract
Protein glycosylation is one of the most common and important post-translational modifications of proteins involved in regulating glycoprotein functions. The chemoenzymatic glycan labeling strategy allows rapid, efficient, and selective interrogation of glycoproteins. Glycoproteomics identifies protein glycosylation events at a large scale, providing information such as peptide sequences, glycan structures, and glycosylated sites. This review discusses the recent development of chemoenzymatic labeling strategies for glycoprotein analysis, mainly including glycoprotein and glycosite profiling. Furthermore, we highlight the chemoenzymatic enrichment approaches in mass spectrometry analysis for three classes of glycan modifications, including N-glycosylation, O-GlcNAcylation, and mucin-type O-glycosylation. Finally, we highlight the emerging trends in new tools and cutting-edge technologies available for glycoproteomic research.
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Affiliation(s)
- Yinping Tian
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shengzhou Ma
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Liuqing Wen
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China.
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40
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Liu K, Wu C, Zhu M, Xu J, Lin B, Lin H, Liu Z, Li M. Structural characteristics of alpha-fetoprotein, including N-glycosylation, metal ion and fatty acid binding sites. Commun Biol 2024; 7:505. [PMID: 38678117 PMCID: PMC11055904 DOI: 10.1038/s42003-024-06219-0] [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: 10/09/2023] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
Alpha-fetoprotein (AFP), a serum glycoprotein, is expressed during embryonic development and the pathogenesis of liver cancer. It serves as a clinical tumor marker, function as a carcinogen, immune suppressor, and transport vehicle; but the detailed AFP structural information has not yet been reported. In this study, we used single-particle cryo-electron microscopy(cryo-EM) to analyze the structure of the recombinant AFP obtained a 3.31 Å cryo-EM structure and built an atomic model of AFP. We observed and identified certain structural features of AFP, including N-glycosylation at Asn251, four natural fatty acids bound to distinct domains, and the coordination of metal ions by residues His22, His264, His268, and Asp280. Furthermore, we compared the structural similarities and differences between AFP and human serum albumin. The elucidation of AFP's structural characteristics not only contributes to a deeper understanding of its functional mechanisms, but also provides a structural basis for developing AFP-based drug vehicles.
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Affiliation(s)
- Kun Liu
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, 571199, Hainan, PR China
| | - Cang Wu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, PR China
| | - Mingyue Zhu
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, 571199, Hainan, PR China
| | - Junnv Xu
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, 571199, Hainan, PR China
- Department of Medical Oncology, Second Affiliated Hospital, Hainan Medical College, Haikou, 570023, Hainan, PR China
| | - Bo Lin
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, 571199, Hainan, PR China
| | - Haifeng Lin
- Department of Medical Oncology, Second Affiliated Hospital, Hainan Medical College, Haikou, 570023, Hainan, PR China
| | - Zhongmin Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, PR China.
| | - Mengsen Li
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, 571199, Hainan, PR China.
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, PR China.
- Institution of Tumor, Hainan Medical College, Haikou, 570102, Hainan, PR China.
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41
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Zhao C, Wang X, Wu J, Hu Y, Zhang Q, Zheng Q. Analysis of O-acetylated sialic acids by 3-nitrophenylhydrazine derivatization combined with LC-MS/MS. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:2472-2477. [PMID: 38606501 DOI: 10.1039/d4ay00330f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Sialic acids are a family of monosaccharides that share a nine-carbon backbone and a carboxyl group. A recent derivatization method based on 3-nitrophenylhydrazine (3-NPH) provides a mild chemical labeling technique for biomolecules containing carbonyl or carboxyl groups. In this study, we utilized 3-NPH to label sialic acids via a two-step derivatization process. The derivatized species can produce a common reporter ion corresponding to C1-C3 with two labels, and a fragment differentiating between Neu5Ac, Neu5Gc, and KDN. This method is compatible with O-acetylated sialic acids and provides high sensitivity to Neu5Gc and KDN, and since the utilization of dual labeling significantly enhances the hydrophobicity of derivatives, it can effectively mitigate matrix effects when combined with parallel reaction monitoring technology. Negative-ion tandem mass spectrometry (MS/MS) analysis reveals a distinctive fragmentation profile for the 4-O-acetylated species, while the other sialic acids yield similar MS/MS spectra with a high abundance of reporter ions. Using the reporter ion as a transition, this analytical strategy is effective for analyzing complex biological samples. For example, it was successfully employed to quantify sialic acids in the intestinal tissues of several carp species, demonstrating its potential in sialylation research.
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Affiliation(s)
- Chenhao Zhao
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, Hubei, China.
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, Hubei, China
| | - Xingdan Wang
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, Hubei, China.
| | - Jing Wu
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, Hubei, China.
| | - Yeli Hu
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, Hubei, China
| | - Qiwei Zhang
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, Hubei, China.
| | - Qi Zheng
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, Hubei, China.
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42
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Muchowicz A, Bartoszewicz A, Zaslona Z. The Exploitation of the Glycosylation Pattern in Asthma: How We Alter Ancestral Pathways to Develop New Treatments. Biomolecules 2024; 14:513. [PMID: 38785919 PMCID: PMC11117584 DOI: 10.3390/biom14050513] [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: 03/21/2024] [Revised: 04/12/2024] [Accepted: 04/21/2024] [Indexed: 05/25/2024] Open
Abstract
Asthma has reached epidemic levels, yet progress in developing specific therapies is slow. One of the main reasons for this is the fact that asthma is an umbrella term for various distinct subsets. Due to its high heterogeneity, it is difficult to establish biomarkers for each subset of asthma and to propose endotype-specific treatments. This review focuses on protein glycosylation as a process activated in asthma and ways to utilize it to develop novel biomarkers and treatments. We discuss known and relevant glycoproteins whose functions control disease development. The key role of glycoproteins in processes integral to asthma, such as inflammation, tissue remodeling, and repair, justifies our interest and research in the field of glycobiology. Altering the glycosylation states of proteins contributing to asthma can change the pathological processes that we previously failed to inhibit. Special emphasis is placed on chitotriosidase 1 (CHIT1), an enzyme capable of modifying LacNAc- and LacdiNAc-containing glycans. The expression and activity of CHIT1 are induced in human diseased lungs, and its pathological role has been demonstrated by both genetic and pharmacological approaches. We propose that studying the glycosylation pattern and enzymes involved in glycosylation in asthma can help in patient stratification and in developing personalized treatment.
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Affiliation(s)
| | | | - Zbigniew Zaslona
- Molecure S.A., Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.M.); (A.B.)
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43
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Miljuš G, Penezić A, Pažitná L, Gligorijević N, Baralić M, Vilotić A, Šunderić M, Robajac D, Dobrijević Z, Katrlík J, Nedić O. Glycosylation and Characterization of Human Transferrin in an End-Stage Kidney Disease. Int J Mol Sci 2024; 25:4625. [PMID: 38731843 PMCID: PMC11083005 DOI: 10.3390/ijms25094625] [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: 03/04/2024] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024] Open
Abstract
Chronic kidney disease (CKD) is a global health concern affecting approximately one billion individuals worldwide. End-stage kidney disease (ESKD), the most severe form of CKD, is often accompanied by anemia. Peritoneal dialysis (PD), a common treatment for ESKD, utilizes the peritoneum for solute transfer but is associated with complications including protein loss, including transferrin (Tf) a key protein involved in iron transport. This study investigated Tf characteristics in ESKD patients compared to healthy individuals using lectin microarray, spectroscopic techniques and immunocytochemical analysis to assess Tf interaction with transferrin receptors (TfRs). ESKD patients exhibited altered Tf glycosylation patterns, evidenced by significant changes in lectin reactivity compared to healthy controls. However, structural analyses revealed no significant differences in the Tf secondary or tertiary structures between the two groups. A functional analysis demonstrated comparable Tf-TfR interaction in both PD and healthy samples. Despite significant alterations in Tf glycosylation, structural integrity and Tf-TfR interaction remained preserved in PD patients. These findings suggest that while glycosylation changes may influence iron metabolism, they do not impair Tf function. The study highlights the importance of a glucose-free dialysis solutions in managing anemia exacerbation in PD patients with poorly controlled anemia, potentially offering a targeted therapeutic approach to improve patient outcomes.
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Affiliation(s)
- Goran Miljuš
- Institute for the Application of Nuclear Energy (INEP), Department for Metabolism, University of Belgrade, 11000 Belgrade, Serbia
| | - Ana Penezić
- Institute for the Application of Nuclear Energy (INEP), Department for Metabolism, University of Belgrade, 11000 Belgrade, Serbia
| | - Lucia Pažitná
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
| | - Nikola Gligorijević
- Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, University of Belgrade, 11000 Belgrade, Serbia
| | - Marko Baralić
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Clinic of Nephrology, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Aleksandra Vilotić
- Institute for the Application of Nuclear Energy (INEP), Department for Biology of Reproduction, University of Belgrade, 11000 Belgrade, Serbia
| | - Miloš Šunderić
- Institute for the Application of Nuclear Energy (INEP), Department for Metabolism, University of Belgrade, 11000 Belgrade, Serbia
| | - Dragana Robajac
- Institute for the Application of Nuclear Energy (INEP), Department for Metabolism, University of Belgrade, 11000 Belgrade, Serbia
| | - Zorana Dobrijević
- Institute for the Application of Nuclear Energy (INEP), Department for Metabolism, University of Belgrade, 11000 Belgrade, Serbia
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
| | - Olgica Nedić
- Institute for the Application of Nuclear Energy (INEP), Department for Metabolism, University of Belgrade, 11000 Belgrade, Serbia
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44
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Mubaid S, Sanchez BJ, Algehani RA, Skopenkova V, Adjibade P, Hall DT, Busque S, Lian XJ, Ashour K, Tremblay AMK, Carlile G, Gagné JP, Diaz-Gaxiola A, Khattak S, Di Marco S, Thomas DY, Poirier GG, Gallouzi IE. Tankyrase-1 regulates RBP-mediated mRNA turnover to promote muscle fiber formation. Nucleic Acids Res 2024; 52:4002-4020. [PMID: 38321934 DOI: 10.1093/nar/gkae059] [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: 12/15/2022] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
Poly(ADP-ribosylation) (PARylation) is a post-translational modification mediated by a subset of ADP-ribosyl transferases (ARTs). Although PARylation-inhibition based therapies are considered as an avenue to combat debilitating diseases such as cancer and myopathies, the role of this modification in physiological processes such as cell differentiation remains unclear. Here, we show that Tankyrase1 (TNKS1), a PARylating ART, plays a major role in myogenesis, a vital process known to drive muscle fiber formation and regeneration. Although all bona fide PARPs are expressed in muscle cells, experiments using siRNA-mediated knockdown or pharmacological inhibition show that TNKS1 is the enzyme responsible of catalyzing PARylation during myogenesis. Via this activity, TNKS1 controls the turnover of mRNAs encoding myogenic regulatory factors such as nucleophosmin (NPM) and myogenin. TNKS1 mediates these effects by targeting RNA-binding proteins such as Human Antigen R (HuR). HuR harbors a conserved TNKS-binding motif (TBM), the mutation of which not only prevents the association of HuR with TNKS1 and its PARylation, but also precludes HuR from regulating the turnover of NPM and myogenin mRNAs as well as from promoting myogenesis. Therefore, our data uncover a new role for TNKS1 as a key modulator of RBP-mediated post-transcriptional events required for vital processes such as myogenesis.
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Affiliation(s)
- Souad Mubaid
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Brenda Janice Sanchez
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Rinad A Algehani
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Viktoriia Skopenkova
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Pauline Adjibade
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Derek T Hall
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Sandrine Busque
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Xian Jin Lian
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Kholoud Ashour
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Anne-Marie K Tremblay
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Graeme Carlile
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Jean-Philippe Gagné
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec G1V 4G2, Canada
| | - Andrea Diaz-Gaxiola
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Shahryar Khattak
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Sergio Di Marco
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - David Y Thomas
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Guy G Poirier
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec G1V 4G2, Canada
| | - Imed-Eddine Gallouzi
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
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45
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Sun W, You X, Zhao X, Zhang X, Yang C, Zhang F, Yu J, Yang K, Wang J, Xu F, Chang Y, Qu B, Zhao X, He Y, Wang Q, Chen J, Qing G. Precise Capture and Dynamic Release of Circulating Liver Cancer Cells with Dual-Histidine-Based Cell Imprinted Hydrogels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2402379. [PMID: 38655900 DOI: 10.1002/adma.202402379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/22/2024] [Indexed: 04/26/2024]
Abstract
Circulating tumor cells (CTCs) detection presents significant advantages in diagnosing liver cancer due to its noninvasiveness, real-time monitoring, and dynamic tracking. However, the clinical application of CTCs-based diagnosis is largely limited by the challenges of capturing low-abundance CTCs within a complex blood environment while ensuring them alive. Here, an ultrastrong ligand, l-histidine-l-histidine (HH), specifically targeting sialylated glycans on the surface of CTCs, is designed. Furthermore, HH is integrated into a cell-imprinted polymer, constructing a hydrogel with precise CTCs imprinting, high elasticity, satisfactory blood compatibility, and robust anti-interference capacities. These features endow the hydrogel with excellent capture efficiency (>95%) for CTCs in peripheral blood, as well as the ability to release CTCs controllably and alive. Clinical tests substantiate the accurate differentiation between liver cancer, cirrhosis, and healthy groups using this method. The remarkable diagnostic accuracy (94%), lossless release of CTCs, material reversibility, and cost-effectiveness ($6.68 per sample) make the HH-based hydrogel a potentially revolutionary technology for liver cancer diagnosis and single-cell analysis.
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Affiliation(s)
- Wenjing Sun
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, P. R. China
- State Key Laboratory of Medical Proteomics, National Chromatographic R&A Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Xin You
- Department of Respiratory Medicine, The Second Hospital of Dalian Medical University, Dalian, 116023, P. R. China
| | - Xinjia Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R&A Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Xiaoyu Zhang
- State Key Laboratory of Medical Proteomics, National Chromatographic R&A Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Chunhui Yang
- Department of Respiratory Medicine, The Second Hospital of Dalian Medical University, Dalian, 116023, P. R. China
| | - Fusheng Zhang
- State Key Laboratory of Medical Proteomics, National Chromatographic R&A Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
- College of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan, 430200, P. R. China
| | - Jiaqi Yu
- College of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan, 430200, P. R. China
| | - Kaiguang Yang
- State Key Laboratory of Medical Proteomics, National Chromatographic R&A Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Jixia Wang
- Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, P. R. China
| | - Fangfang Xu
- Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, P. R. China
| | - Yongxin Chang
- State Key Laboratory of Medical Proteomics, National Chromatographic R&A Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Boxin Qu
- Department of Respiratory Medicine, The Second Hospital of Dalian Medical University, Dalian, 116023, P. R. China
| | - Xinmiao Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, P. R. China
| | - Yuxuan He
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, P. R. China
| | - Qi Wang
- Department of Respiratory Medicine, The Second Hospital of Dalian Medical University, Dalian, 116023, P. R. China
| | - Jinghua Chen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, P. R. China
| | - Guangyan Qing
- State Key Laboratory of Medical Proteomics, National Chromatographic R&A Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
- College of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan, 430200, P. R. China
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46
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Amorós-Pérez B, Rivas-Pardo B, Gómez del Moral M, Subiza JL, Martínez-Naves E. State of the Art in CAR-T Cell Therapy for Solid Tumors: Is There a Sweeter Future? Cells 2024; 13:725. [PMID: 38727261 PMCID: PMC11083689 DOI: 10.3390/cells13090725] [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] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024] Open
Abstract
Chimeric antigen receptor (CAR)-T cell therapy has proven to be a powerful treatment for hematological malignancies. The situation is very different in the case of solid tumors, for which no CAR-T-based therapy has yet been approved. There are many factors contributing to the absence of response in solid tumors to CAR-T cells, such as the immunosuppressive tumor microenvironment (TME), T cell exhaustion, or the lack of suitable antigen targets, which should have a stable and specific expression on tumor cells. Strategies being developed to improve CAR-T-based therapy for solid tumors include the use of new-generation CARs such as TRUCKs or bi-specific CARs, the combination of CAR therapy with chemo- or radiotherapy, the use of checkpoint inhibitors, and the use of oncolytic viruses. Furthermore, despite the scarcity of targets, a growing number of phase I/II clinical trials are exploring new solid-tumor-associated antigens. Most of these antigens are of a protein nature; however, there is a clear potential in identifying carbohydrate-type antigens associated with tumors, or carbohydrate and proteoglycan antigens that emerge because of aberrant glycosylations occurring in the context of tumor transformation.
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Affiliation(s)
- Beatriz Amorós-Pérez
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), 28040 Madrid, Spain; (B.A.-P.); (B.R.-P.)
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Inmunotek S.L., 28805 Madrid, Spain;
| | - Benigno Rivas-Pardo
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), 28040 Madrid, Spain; (B.A.-P.); (B.R.-P.)
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Manuel Gómez del Moral
- Department of Cellular Biology, School of Medicine, Universidad Complutense of Madrid (UCM), 28040 Madrid, Spain;
| | | | - Eduardo Martínez-Naves
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), 28040 Madrid, Spain; (B.A.-P.); (B.R.-P.)
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
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47
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Deng P, Dong X, Wu Z, Hou X, Mao L, Guo J, Zhao W, Peng C, Zhang Z, Peng L. Development of Glycosylation-Modified DPPA-1 Compounds as Innovative PD-1/PD-L1 Blockers: Design, Synthesis, and Biological Evaluation. Molecules 2024; 29:1898. [PMID: 38675717 PMCID: PMC11054459 DOI: 10.3390/molecules29081898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
In the context of peptide drug development, glycosylation plays a pivotal role. Accordingly, L-type peptides were synthesized predicated upon the PD-1/PD-L1 blocker DPPA-1. Subsequent glycosylation resulted in the production of two distinct glycopeptides, D-glu-LPPA-1 and D-gal-LPPA-1, by using D-glucose (D-glu) and D-galactose (D-gal), respectively, during glycosylation. Both glycopeptides significantly inhibited the interaction between PD-1 and PD-L1, and the measured half maximal inhibitory concentrations (IC50s) were 75.5 μM and 101.9 μM for D-glu-LPPA-1 and D-gal-LPPA-1, respectively. Furthermore, D-gal-LPPA-1 displayed a pronounced ability to restore T-cell functionality. In an MC38 tumor-bearing mouse model, D-gal-LPPA-1 demonstrated a significant inhibitory effect. Notably, D-gal-LPPA-1 substantially augmented the abundance and functionality of CD8+ T cells in the tumor microenvironment. Additionally, in the lymph nodes and spleens, D-gal-LPPA-1 significantly increased the proportion of CD8+ T cells secreting interferon-gamma (IFN-γ). These strong findings position D-gal-LPPA-1 as a potent enhancer of the antitumor immune response in MC38 tumor-bearing mice, underscoring its potential as a formidable PD-1/PD-L1 blocking agent.
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Affiliation(s)
- Peng Deng
- Key Laboratory of Novel Food Resources Processing Ministry of Agriculture, Key Laboratory of Agro-Products Processing Technology of Shandong Province, Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaodan Dong
- Key Laboratory of Novel Food Resources Processing Ministry of Agriculture, Key Laboratory of Agro-Products Processing Technology of Shandong Province, Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ziyuan Wu
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, 263 Kaiyuan Road, Luoyang 471003, China
| | - Xixi Hou
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Longfei Mao
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, 263 Kaiyuan Road, Luoyang 471003, China
| | - Jingjing Guo
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China;
| | - Wenshan Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China;
| | - Chune Peng
- Key Laboratory of Novel Food Resources Processing Ministry of Agriculture, Key Laboratory of Agro-Products Processing Technology of Shandong Province, Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhe Zhang
- School of Sciences, Henan University of Technology, Zhengzhou 450001, China
| | - Lizeng Peng
- Key Laboratory of Novel Food Resources Processing Ministry of Agriculture, Key Laboratory of Agro-Products Processing Technology of Shandong Province, Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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48
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Zhao J, Sun H, Wang C, Shang D. Breast cancer therapy: from the perspective of glucose metabolism and glycosylation. Mol Biol Rep 2024; 51:546. [PMID: 38642246 DOI: 10.1007/s11033-024-09466-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/22/2024] [Indexed: 04/22/2024]
Abstract
Breast cancer is a leading cause of mortality and the most prevalent form of malignant tumor among women worldwide. Breast cancer cells exhibit an elevated glycolysis and altered glucose metabolism. Moreover, these cells display abnormal glycosylation patterns, influencing invasion, proliferation, metastasis, and drug resistance. Consequently, targeting glycolysis and mitigating abnormal glycosylation represent key therapeutic strategies for breast cancer. This review underscores the importance of protein glycosylation and glucose metabolism alterations in breast cancer. The current research efforts in developing effective interventions targeting glycolysis and glycosylation are further discussed.
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Affiliation(s)
- Jiaqi Zhao
- Department of Pharmacy, School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China
| | - Haiting Sun
- Department of Pharmacy, School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China
| | - Che Wang
- Department of Pharmacy, School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China.
- Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, School of Life Science, Liaoning Normal University, Dalian, 116081, China.
| | - Dejing Shang
- Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, School of Life Science, Liaoning Normal University, Dalian, 116081, China.
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Fujinami D, Mizui A, Miyata A, Ito S. In Vitro Characterization of an O-Specific Glycosyltransferase Involved in Flagellin Glycosylation. ACS Chem Biol 2024; 19:992-998. [PMID: 38562012 DOI: 10.1021/acschembio.4c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Glycosyltransferases play a fundamental role in the biosynthesis of glycoproteins and glycotherapeutics. In this study, we investigated protein glycosyltransferase FlgGT1, belonging to the GT2 family. The GT2 family includes cysteine S-glycosyltransferases involved in antimicrobial peptide biosyntheses, sharing conserved catalytic domains while exhibiting diverse C-terminal domains. Our in vitro studies revealed that FlgGT1 recognizes structural motifs rather than specific amino acid sequences when glycosylating the flagellin protein Hag. Notably, FlgGT1 is selective for serine or threonine O-glycosylation over cysteine S-glycosylation. Molecular dynamics simulations provided insights into the structural basis of FlgGT1's ability to accommodate various sugar nucleotides as donor substrates. Mutagenesis experiments on FlgGT1 demonstrated that truncating the relatively large C-terminal domain resulted in a loss of flagellin glycosylation activity. Our classification based on sequence similarity network analysis and AlphaFold2 structural predictions suggests that the acquisition of the C-terminal domain is a key evolutionary adaptation conferring distinct substrate specificities on glycosyltransferases within the GT2 family.
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Affiliation(s)
- Daisuke Fujinami
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Ayumi Mizui
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Azusa Miyata
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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Bennett AR, Bojar D. Syntactic sugars: crafting a regular expression framework for glycan structures. BIOINFORMATICS ADVANCES 2024; 4:vbae059. [PMID: 38708029 PMCID: PMC11069104 DOI: 10.1093/bioadv/vbae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/15/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024]
Abstract
Motivation Structural analysis of glycans poses significant challenges in glycobiology due to their complex sequences. Research questions such as analyzing the sequence content of the α1-6 branch in N-glycans, are biologically meaningful yet can be hard to automate. Results Here, we introduce a regular expression system, designed for glycans, feature-complete, and closely aligned with regular expression formatting. We use this to annotate glycan motifs of arbitrary complexity, perform differential expression analysis on designated sequence stretches, or elucidate branch-specific binding specificities of lectins in an automated manner. We are confident that glycan regular expressions will empower computational analyses of these sequences. Availability and implementation Our regular expression framework for glycans is implemented in Python and is incorporated into the open-source glycowork package (version 1.1+). Code and documentation are available at https://github.com/BojarLab/glycowork/blob/master/glycowork/motif/regex.py.
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Affiliation(s)
- Alexander R Bennett
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Daniel Bojar
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 41390 Gothenburg, Sweden
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