1
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Wang G, Wang Y, Wang L, Wu S, Cao A, Pu W, Li T, Xie R, Wang H, Ding L, Ju H. Stressor-Actuated Proximity Labeling for Reporting Cellular Interaction. Anal Chem 2024; 96:20065-20073. [PMID: 39621845 DOI: 10.1021/acs.analchem.4c05008] [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: 12/18/2024]
Abstract
Cell-cell interactions determine the activation state and function of cells. When host cells are exposed to stressors such as microorganisms, immune defense machinery is activated to release H2O2, providing direct evidence of the relevant cellular physiological processes. Inspired by the fact that peroxidase can catalyze proximity labeling in the presence of exogenous H2O2, a stressor-actuated proximity labeling (SAPL) strategy is developed to report the process information on cell-cell interactions by recording stress levels. The stressors are covalently modified with horseradish peroxidase (HRP) and the H2O2 released by the host cells in response to the stressors triggers HRP-based proximity labeling. Using a fungal mimic or live fungi as stressors, the stress levels of different host cells are compared by in situ imaging of the labeling signals. The ability to accumulate stress signals allows SAPL to more sensitively differentiate between interactions involving different macrophage phenotypes. SAPL is also a powerful tool for real-time, in situ monitoring of the effects of surface modifications on cellular interactions. Thus, the SAPL strategy represents a new perspective in the monitoring of cell-cell interactions using endogenous effector molecules.
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Affiliation(s)
- Guyu Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yichun Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Lan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shijie Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ao Cao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wenyuan Pu
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Tielei Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Department of Polymer Science & Engineering, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Hongwei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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2
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Geyer PE, Hornburg D, Pernemalm M, Hauck SM, Palaniappan KK, Albrecht V, Dagley LF, Moritz RL, Yu X, Edfors F, Vandenbrouck Y, Mueller-Reif JB, Sun Z, Brun V, Ahadi S, Omenn GS, Deutsch EW, Schwenk JM. The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends. J Proteome Res 2024; 23:5279-5295. [PMID: 39479990 PMCID: PMC11629384 DOI: 10.1021/acs.jproteome.4c00586] [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: 07/09/2024] [Revised: 09/26/2024] [Accepted: 09/27/2024] [Indexed: 11/02/2024]
Abstract
Recent improvements in proteomics technologies have fundamentally altered our capacities to characterize human biology. There is an ever-growing interest in using these novel methods for studying the circulating proteome, as blood offers an accessible window into human health. However, every methodological innovation and analytical progress calls for reassessing our existing approaches and routines to ensure that the new data will add value to the greater biomedical research community and avoid previous errors. As representatives of HUPO's Human Plasma Proteome Project (HPPP), we present our 2024 survey of the current progress in our community, including the latest build of the Human Plasma Proteome PeptideAtlas that now comprises 4608 proteins detected in 113 data sets. We then discuss the updates of established proteomics methods, emerging technologies, and investigations of proteoforms, protein networks, extracellualr vesicles, circulating antibodies and microsamples. Finally, we provide a prospective view of using the current and emerging proteomics tools in studies of circulating proteins.
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Affiliation(s)
- Philipp E. Geyer
- Department
of Proteomics and Signal Transduction, Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Daniel Hornburg
- Seer,
Inc., Redwood City, California 94065, United States
- Bruker
Scientific, San Jose, California 95134, United States
| | - Maria Pernemalm
- Department
of Oncology and Pathology/Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Stefanie M. Hauck
- Metabolomics
and Proteomics Core, Helmholtz Zentrum München
GmbH, German Research Center for Environmental Health, 85764 Oberschleissheim,
Munich, Germany
| | | | - Vincent Albrecht
- Department
of Proteomics and Signal Transduction, Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Laura F. Dagley
- The
Walter and Eliza Hall Institute for Medical Research, Parkville, VIC 3052, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Robert L. Moritz
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Xiaobo Yu
- State
Key Laboratory of Medical Proteomics, Beijing
Proteome Research Center, National Center for Protein Sciences-Beijing
(PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fredrik Edfors
- Science
for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, 17121 Solna, Sweden
| | | | - Johannes B. Mueller-Reif
- Department
of Proteomics and Signal Transduction, Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Zhi Sun
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Virginie Brun
- Université Grenoble
Alpes, CEA, Leti, Clinatec, Inserm UA13
BGE, CNRS FR2048, Grenoble, France
| | - Sara Ahadi
- Alkahest, Inc., Suite
D San Carlos, California 94070, United States
| | - Gilbert S. Omenn
- Institute
for Systems Biology, Seattle, Washington 98109, United States
- Departments
of Computational Medicine & Bioinformatics, Internal Medicine,
Human Genetics and Environmental Health, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | - Eric W. Deutsch
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Jochen M. Schwenk
- Science
for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, 17121 Solna, Sweden
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3
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Gong H, Li S, Chen F, Li Y, Chen C, Cai C. High-sensitivity detection of glycoproteins by high-density boric acid modified metal-organic framework surface molecularly imprinted polymers resonant light scattering sensor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124813. [PMID: 39018673 DOI: 10.1016/j.saa.2024.124813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/19/2024]
Abstract
Glycoproteins are difficult to be detected by imprinting strategy due to their low natural abundance, high flexible conformation and large size. Herein, a high-density boric acid modified metal-organic framework (MOF) surface molecularly imprinted polymer (SMIP) resonant light scattering sensor was constructed for the high-sensitivity detection of target glycoproteins. A MOF with large specific surface area was selected as the substrate material to support the boric acid group with high loading density (4.66 %). The introduction of the boric acid group in the SMIP provided a high-affinity binding site for the recognition and binding of glycoproteins. Shallow surface cavities with rapid mass transfer (equilibrium time 20 min) were thus formed by surface imprinting. Furthermore, high sensitivity (limit of detection 15 pM) was achieved at physiological pH (7.4), which was conducive to the detection of glycoproteins with low natural abundance in complex biological samples and maintaining physiological activity.
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Affiliation(s)
- Hang Gong
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650500, China; The Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
| | - Shuting Li
- The Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Xiangtan 411105, China
| | - Feng Chen
- The Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Xiangtan 411105, China
| | - Yong Li
- Yunnan Academy of Tobacco Agricultural Science, Kunming 650021, China
| | - Chunyan Chen
- The Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
| | - Changqun Cai
- The Key Laboratory for Green Organic Synthesis and Application of Hunan Province, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
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4
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Lei C, Li X, Li W, Chen Z, Liu S, Cheng B, Hu Y, Song Q, Qiu Y, Zhou Y, Meng X, Yu H, Zhou W, Chen X, Li J. Chemical glycoproteomic profiling in rice seedlings reveals N-glycosylation in the ERAD-L machinery. Mol Cell Proteomics 2024:100883. [PMID: 39577566 DOI: 10.1016/j.mcpro.2024.100883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 11/14/2024] [Accepted: 11/15/2024] [Indexed: 11/24/2024] Open
Abstract
As a ubiquitous and essential posttranslational modification occurring in both plants and animals, protein N-linked glycosylation regulates various important biological processes. Unlike the well-studied animal N-glycoproteomes, the landscape of rice N-glycoproteome remains largely unexplored. Here, by developing a chemical glycoproteomic strategy based on metabolic glycan labeling (MGL), we report a comprehensive profiling of the N-glycoproteome in rice seedlings. The rice seedlings are incubated with N-azidoacetylgalactosamine (GalNAz) - a monosaccharide analog containing a bioorthogonal functional group - to metabolically label N-glycans, followed by conjugation with an affinity probe via click chemistry for enrichment of the N-glycoproteins. Subsequent mass spectrometry analyses identify a total of 403 N-glycosylation sites and 673 N-glycosylated proteins, which are involved in various important biological processes. In particular, the core components of the endoplasmic reticulum (ER)-associated protein degradation (ERAD) machinery are N-glycosylated, and the N-glycosylation is important for the ERAD-L function. This work not only provides an invaluable resource for studying rice N-glycosylation, but also demonstrates the applicability of MGL in glycoproteomic profiling for crop species.
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Affiliation(s)
- Cong Lei
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Yazhouwan National Laboratory, Sanya, China
| | - Xilong Li
- Yazhouwan National Laboratory, Sanya, China.
| | - Wenjia Li
- Yazhouwan National Laboratory, Sanya, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Zihan Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Simiao Liu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Yili Hu
- Yazhouwan National Laboratory, Sanya, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Qitao Song
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yahong Qiu
- Yazhouwan National Laboratory, Sanya, China
| | - Yilan Zhou
- Yazhouwan National Laboratory, Sanya, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hong Yu
- Yazhouwan National Laboratory, Sanya, China
| | - Wen Zhou
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China.
| | - Jiayang Li
- Yazhouwan National Laboratory, Sanya, China; State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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5
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Ghosh P. Deciphering the Cell Surface Sugar-Coating via Biochemical Pathways. Chemistry 2024; 30:e202401983. [PMID: 39215611 DOI: 10.1002/chem.202401983] [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: 05/21/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Cell surface components, specifically glycans, play a significant role in several biological functions like cell structure, crosstalk between cells, and eventual target recognition of the cells for therapeutics. The dense layer of glycans, i. e., glycocalyx, could differ in taxon, species, and cell type. Glycans are coupled with lipids and proteins to form glycolipids, glycoproteins, proteoglycans, and glycosylphosphatidylinositol-anchored proteins, making their study challenging. However, understanding glycosylation at the cellular level is vital for fundamental research and advancing glycan-targeted therapy. Among different pathways, metabolic glycan labelling uses the natural metabolic processes of the cell to introduce abiotic functionality into glycan residues. The Bertozzi group pioneered metabolic oligosaccharide engineering using glycan salvage pathways to convert monosaccharides with unnatural modifications. This eventually results in the probe becoming part of the complex cellular glycan structures via click chemistry using copper. On the other hand, the boronic acid-based probe can recognise carbohydrates in a single step without any chemical modification of the surface. This review discusses the significance of glycans as biomarkers for different diseases and the necessity to evaluate them in situ within the physiological environment. The review also discusses the prospect of this field and its potential applications.
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Affiliation(s)
- Pritam Ghosh
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
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6
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Mukherjee MM, Biesbrock D, Abramowitz LK, Pavan M, Kumar B, Walter PJ, Azadi P, Jacobson KA, Hanover JA. Selective bioorthogonal probe for N-glycan hybrid structures. Nat Chem Biol 2024:10.1038/s41589-024-01756-5. [PMID: 39468349 DOI: 10.1038/s41589-024-01756-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/17/2024] [Indexed: 10/30/2024]
Abstract
Metabolic incorporation of chemically tagged monosaccharides is a facile means of tagging cellular glycoproteins and glycolipids. However, since the monosaccharide precursors are often shared by several pathways, selectivity has been difficult to attain. For example, N-linked glycosylation is a chemically complex and ubiquitous posttranslational modification, with three distinct classes of GlcNAc-containing N-glycan structures: oligomannose, hybrid and complex. Here we describe the synthesis of 1,3-Pr2-6-OTs GlcNAlk (MM-JH-1) as a next-generation metabolic chemical reporter for the selective labeling of hybrid N-glycan structures. We first developed a general strategy for defining the selectivity of labeling with chemically tagged monosaccharides. We then applied this approach to establish that MM-JH-1 is selectively incorporated into hybrid N-glycans. Using this metabolic chemical reporter as a detection tool, we performed imaging and fractionation to define features of the intracellular localization and trafficking of target proteins bearing hybrid N-glycan structures.
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Affiliation(s)
- Mana Mohan Mukherjee
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Devin Biesbrock
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Lara K Abramowitz
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Matteo Pavan
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | - Bhoj Kumar
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, USA
| | - Peter J Walter
- Clinical Mass Spectrometry Core, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, USA
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | - John A Hanover
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA.
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7
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Xu L, Zhao W, Wang R, Hong M, Wang H, Sun Y, Zhong T, Hang D, Xie R, Chen L, Yao B, Ding L, Ju H. Aglycone Analysis and Quantitative Tracking of Correlated Terminal Glycan Pair on Spermatozoa. Anal Chem 2024; 96:16186-16194. [PMID: 39361617 DOI: 10.1021/acs.analchem.4c02792] [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: 10/05/2024]
Abstract
Mammalian sperm glycans directly mediate several key life events. However, previous studies have not focused on two key factors that regulate these processes, the terminal glycan pattern and the anchoring sites. Herein, we group the capping monosaccharide sialic acid (Sia) and its capping substrates galactose/N-acetylgalactosamine (Gal/GalNAc) into a "correlated terminal glycan pair" (glycopair) and, for the first time, reveal the differences in the aglycone pattern of this pair on spermatozoa using glyco-selective in situ covalent labeling techniques. Sia is mainly found in glycoproteins, whereas terminal Gal/GalNAc is mainly found in glycolipids. We quantitatively track the dynamic changes of the glycopair during sperm epididymal migration and find that the Sia capping ratio decreases with the increased expression of the glycopair; caudal upswim spermatozoa also show a lower Sia capping ratio than down spermatozoa. We thus propose two new parameters reflecting the terminal glycoforms of spermatozoa, which can well distinguish the maturity of spermatozoa. By fluorescence imaging of the glycopair in different regions of the sperm, we find that different parts of the sperm contribute differently to the overall glycan changes.
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Affiliation(s)
- Lijia Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Changshu Foreign Language School, Suzhou 215000, China
| | - Wei Zhao
- Department of Reproductive Medical Center, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China
- Center of Clinical Laboratory Science, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Ruiyuan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Min Hong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Haiqi Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yue Sun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tong Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dong Hang
- Department of Epidemiology, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer, Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Li Chen
- Department of Reproductive Medical Center, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China
| | - Bing Yao
- Department of Reproductive Medical Center, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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8
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Leslie K, Berry SS, Miller GJ, Mahon CS. Sugar-Coated: Can Multivalent Glycoconjugates Improve upon Nature's Design? J Am Chem Soc 2024; 146:27215-27232. [PMID: 39340450 PMCID: PMC11467903 DOI: 10.1021/jacs.4c08818] [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: 06/30/2024] [Revised: 09/16/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024]
Abstract
Multivalent interactions between receptors and glycans play an important role in many different biological processes, including pathogen infection, self-recognition, and the immune response. The growth in the number of tools and techniques toward the assembly of multivalent glycoconjugates means it is possible to create synthetic systems that more and more closely resemble the diversity and complexity we observe in nature. In this Perspective we present the background to the recognition and binding enabled by multivalent interactions in nature, and discuss the strategies used to construct synthetic glycoconjugate equivalents. We highlight key discoveries and the current state of the art in their applications to glycan arrays, vaccines, and other therapeutic and diagnostic tools, with an outlook toward some areas we believe are of most interest for future work in this area.
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Affiliation(s)
- Kathryn
G. Leslie
- Department
of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Sian S. Berry
- Centre
for Glycoscience and School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Gavin J. Miller
- Centre
for Glycoscience and School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Clare S. Mahon
- Department
of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
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9
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Zhu Q, Chaubard JL, Geng D, Shen J, Ban L, Cheung ST, Wei F, Liu Y, Sun H, Calderon A, Dong W, Qin W, Li T, Wen L, Wang PG, Sun S, Yi W, Hsieh-Wilson LC. Chemoenzymatic Labeling, Detection and Profiling of Core Fucosylation in Live Cells. J Am Chem Soc 2024; 146:26408-26415. [PMID: 39279393 DOI: 10.1021/jacs.4c09303] [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: 09/18/2024]
Abstract
Core fucosylation, the attachment of an α-1,6-linked-fucose to the N-glycan core pentasaccharide, is an abundant protein modification that plays critical roles in various biological processes such as cell signaling, B cell development, antibody-dependent cellular cytotoxicity, and oncogenesis. However, the tools currently used to detect core fucosylation suffer from poor specificity, exhibiting cross-reactivity against all types of fucosylation. Herein we report the development of a new chemoenzymatic strategy for the rapid and selective detection of core fucosylated glycans. This approach employs a galactosyltransferase enzyme identified fromCaenorhabditis elegansthat specifically transfers an azido-appended galactose residue onto core fucose via a β-1,4 glycosidic linkage. We demonstrate that the approach exhibits superior specificity toward core fucose on a variety of complex N-glycans. The method enables detection of core fucosylated glycoproteins from complex cell lysates, as well as on live cell surfaces, and it can be integrated into a diagnostic platform to profile protein-specific core fucosylation levels. This chemoenzymatic labeling approach offers a new strategy for the identification of disease biomarkers and will allow researchers to further characterize the fundamental role of this important glycan in normal and disease physiology.
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Affiliation(s)
- Qiang Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310012, China
| | - Jean-Luc Chaubard
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Didi Geng
- College of Life Sciences, Zhejiang University, Hangzhou 310012, China
| | - Jiechen Shen
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Lan Ban
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Sheldon T Cheung
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Fangyu Wei
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, The Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Liu
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, The Chinese Academy of Sciences, Shanghai 201203, China
| | - Haofan Sun
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing 102206, China
| | - Angie Calderon
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology Institution, Shenzhen, Guangdong 518055, China
| | - Wenbo Dong
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Weijie Qin
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing 102206, China
| | - Tiehai Li
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, The Chinese Academy of Sciences, Shanghai 201203, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, The Chinese Academy of Sciences, Shanghai 201203, China
| | - Peng George Wang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology Institution, Shenzhen, Guangdong 518055, China
| | - Shisheng Sun
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Wen Yi
- College of Life Sciences, Zhejiang University, Hangzhou 310012, China
| | - Linda C Hsieh-Wilson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
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10
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Cao Z, Zhang Z, Wang Y, Zhu Y, Li Z, Li X, Shen Y, Chen J, Liu Z. Exploring serum N-glycome patterns as candidate non-invasive biomarkers in inguinal hernia. Heliyon 2024; 10:e35908. [PMID: 39211922 PMCID: PMC11357755 DOI: 10.1016/j.heliyon.2024.e35908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 07/05/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Although inguinal hernia (IH) is prevalent in elderly males, research on its specific diagnostic biomarkers is limited. Protein N-glycosylation is one of the most important and ubiquitous post-translational modifications and often results in a remarkable heterogeneity of protein glycoforms. Protein N-glycosylation often changes in a disease and holds great potential for discovering non-invasive biomarkers. This study aimed to gain insights into total serum protein N-glycosylation of IH to identify candidate non-invasive biomarkers for diagnosis and subtype classification of IH. Methods Linkage-specific sialylation derivatization combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry detection was used to analyze serum protein N-glycosylation patterns in IH patients and healthy controls. Results IH patients had abnormal glycan fucosylation and sialylation compared to healthy controls (HC), of which two glycan traits representing linkage-specific sialylation within monoantennary glycans showed high potential as diagnostic biomarkers for IH with an area under the curve (AUC) of 0.75. Additionally, serum N-glycans were different between indirect IH and direct IH in glycosylation features, namely complexity, fucosylation, galactosylation, sialylation, and α2,6-linked sialylation. Four distinctive glycans between the two subtypes showed good performance with AUC >0.8, suggesting that these glycan traits have potential as biomarkers for subtype classification. Conclusions We first reported the serum N-glycomic features of IH patients. Furthermore, we identified several potential biomarkers for the diagnosis and subtype classification of IH. These findings can deepen the understanding of IH.
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Affiliation(s)
- Zhen Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zejian Zhang
- Institute of Clinical Medicine, State Key Laboratory of Complex Severe and Rare Diseases, National Infrastructure for Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuanyang Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yilin Zhu
- Department of Hernia and Abdominal Wall Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Zepeng Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobin Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yingmo Shen
- Department of Hernia and Abdominal Wall Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jie Chen
- Department of Hernia and Abdominal Wall Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Ziwen Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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11
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Krömer M, Poštová Slavětínská L, Hocek M. Glyco-DNA: Enzymatic Synthesis of Base-Modified and Hypermodified DNA Displaying up to Four Different Monosaccharide Units in the Major Groove. Chemistry 2024; 30:e202402318. [PMID: 38896019 DOI: 10.1002/chem.202402318] [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: 06/18/2024] [Revised: 06/19/2024] [Accepted: 06/19/2024] [Indexed: 06/21/2024]
Abstract
A portfolio of six modified 2'-deoxyribonucleoside triphosphate (dNTP) derivatives derived from 5-substituted pyrimidine or 7-substituted 7-deazapurine bearing different carbohydrate units (d-glucose, d-galactose, d-mannose, l-fucose, sialic acid and N-Ac-d-galactosamine) tethered through propargyl-glycoside linker was designed and synthesized via the Sonogashira reactions of halogenated dNTPs with the corresponding propargyl-glycosides. The nucleotides were found to be good substrates for DNA polymerases in enzymatic primer extension and PCR synthesis of modified and hypermodified DNA displaying up to four different sugars. Proof of concept binding study of sugar-modified oligonucleotides with concanavalin A showed positive effect of avidity and sugar units count.
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Affiliation(s)
- Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
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12
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Yang SS, Jiang YH, Zhang X, Liu LH, Liu S, Zhang H. Triazine-structured covalent organic framework nanosheets with inherent hydrophilicity for the highly efficient and selective enrichment of glycosylated peptides. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5304-5310. [PMID: 39028021 DOI: 10.1039/d4ay01068j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Protein glycosylation plays a crucial role in various biological processes and is related to various diseases. Highly specific enrichment of glycopeptides before mass spectrometry detection is crucial for comprehensive glycoproteomic analysis. However, it still remains a great challenge due to the absence of affinity materials with excellent enrichment efficiency. In this work, a triazine structure linked by a -NH- bond of two-dimensional (2-D) covalent organic framework (COF) nanosheets was synthesized as an affinity adsorbent for the selective capture of glycopeptides. In particular, by introducing hydrophilic monomers via a bottom-up approach, the 2-D COF (denoted as NENP-1) nanosheets were provided with abundant amino groups and inherent hydrophilicity. Owing to the specific surface area and excessive accessible sites for hydrophilicity, the resulting NENP-1 nanosheets exhibited an outstanding glycopeptide enrichment efficiency from standard samples with a superior detection sensitivity (1 × 10-10 M), good enrichment selectivity (1 : 800, HRP tryptic digest to BSA protein), excellent binding capacity (100 mg g-1), great reusability, and recovery (60.2%). Furthermore, using the NENP-1 nanosheet adsorbent, twenty-four endogenous glycopeptides in the serum of patients with gastric cancer were successfully identified by LC-MS/MS technology, which illustrates a promising prospective of hydrophilic COF nanosheets in glycoproteomics research.
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Affiliation(s)
- Shi-Shu Yang
- Henan Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Yu-Heng Jiang
- Henan Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Xuan Zhang
- Henan Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Li-Hong Liu
- Henan Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Si Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, 350122, P. R. China
| | - Hua Zhang
- Henan Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, P. R. China.
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13
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Liang Y, Liu Z, Zuo D, Chen S, Chen J, Yan X, Liu P, Wang Q. Single cell glycan-linkages profiling for hepatocellular carcinoma early diagnosis using lanthanide encoded bacteriophage MS2 based ICP-MS. Talanta 2024; 274:126056. [PMID: 38599123 DOI: 10.1016/j.talanta.2024.126056] [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: 01/11/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Early diagnosis is paramount for enhancing survival rates and prognosis in the context of malignant diseases. Hepatocellular carcinoma (HCC), the second leading cause of cancer-related deaths worldwide, poses significant challenges for its early detection. In this study, we present an innovative approach which contributed to the early diagnosis of HCC. By lanthanide encoding signal amplification to map glycan-linkages at the single-cell level, the minute quantities of "soft" glycan-linkages on single cell surface were converted into "hard" elemental tags through the use of an MS2 signal amplifier. Harnessing the power of lanthanides encoded within MS2, we achieve nearly three orders of magnitude signal amplification. These encoded tags are subsequently quantified using single-cell inductively coupled plasma mass spectrometry (SC-ICP-MS). Linear discriminant analysis (LDA) identifies seven specific glycan-linkages (α-2,3-Sia, α-Gal, α-1,2-Fuc, α-1,6-Fuc, α-2,6-Sia, α-GalNAc, and Gal-β-1,3-GalNAc) as biomarkers. Our methodology is initially validated at the cellular level with 100% accuracy in discriminating between hepatic carcinoma HepG2 cells and their normal HL7702 cells. We apply this approach to quantify and classify glycan-linkages on the surfaces of 55 clinical surgical HCC specimens. Leveraging these seven glycan-linkages as biomarkers, we achieve precise differentiation between 8 normal hepatic specimens, 40 early HCC specimens, and 7 colorectal metastasis HCC specimens. This pioneering work represents the first instance of employing single-cell glycan-linkages as biomarkers promising for the early diagnosis of HCC with a remarkable 100% predictive accuracy rate, which holds immense potential for enhancing the feasibility and precision of HCC diagnosis in clinical practice.
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Affiliation(s)
- Yong Liang
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China.
| | - Zhen Liu
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Dongliang Zuo
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory for Chronic Liver Disease and Hepatocellular Carcinoma, Xiamen, 361004, China; The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, 445000, China
| | - Shi Chen
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jianbin Chen
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xiaowen Yan
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Pingguo Liu
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory for Chronic Liver Disease and Hepatocellular Carcinoma, Xiamen, 361004, China.
| | - Qiuquan Wang
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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14
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Tian Y, Ma S, Wen L. Towards chemoenzymatic labeling strategies for profiling protein glycosylation. Curr Opin Chem Biol 2024; 80:102460. [PMID: 38678979 DOI: 10.1016/j.cbpa.2024.102460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/31/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024]
Abstract
Protein glycosylation is one of the most common and important post-translational modifications of proteins involved in regulating glycoprotein functions. The chemoenzymatic glycan labeling strategy allows rapid, efficient, and selective interrogation of glycoproteins. Glycoproteomics identifies protein glycosylation events at a large scale, providing information such as peptide sequences, glycan structures, and glycosylated sites. This review discusses the recent development of chemoenzymatic labeling strategies for glycoprotein analysis, mainly including glycoprotein and glycosite profiling. Furthermore, we highlight the chemoenzymatic enrichment approaches in mass spectrometry analysis for three classes of glycan modifications, including N-glycosylation, O-GlcNAcylation, and mucin-type O-glycosylation. Finally, we highlight the emerging trends in new tools and cutting-edge technologies available for glycoproteomic research.
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Affiliation(s)
- Yinping Tian
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shengzhou Ma
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Liuqing Wen
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China.
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15
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Kufleitner M, Haiber LM, Li S, Surendran H, Mayer TU, Zumbusch A, Wittmann V. Next-Generation Metabolic Glycosylation Reporters Enable Detection of Protein O-GlcNAcylation in Living Cells without S-Glyco Modification. Angew Chem Int Ed Engl 2024; 63:e202320247. [PMID: 38501674 DOI: 10.1002/anie.202320247] [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: 12/30/2023] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024]
Abstract
Protein O-GlcNAcylation is a ubiquitous posttranslational modification of cytosolic and nuclear proteins involved in numerous fundamental regulation processes. Investigation of O-GlcNAcylation by metabolic glycoengineering (MGE) has been carried out for two decades with peracetylated N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine derivatives modified with varying reporter groups. Recently, it has been shown that these derivatives can result in non-specific protein labeling termed S-glyco modification. Here, we report norbornene-modified GlcNAc derivatives with a protected phosphate at the anomeric position and their application in MGE. These derivatives overcome two limitations of previously used O-GlcNAc reporters. They do not lead to detectable S-glyco modification, and they efficiently react in the inverse-electron-demand Diels-Alder (IEDDA) reaction, which can be carried out even within living cells. Using a derivative with an S-acetyl-2-thioethyl-protected phosphate, we demonstrate the protein-specific detection of O-GlcNAcylation of several proteins and the protein-specific imaging of O-GlcNAcylation inside living cells by Förster resonance energy transfer (FRET) visualized by confocal fluorescence lifetime imaging microscopy (FLIM).
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Affiliation(s)
- Markus Kufleitner
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Lisa Maria Haiber
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Shuang Li
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Harsha Surendran
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Thomas U Mayer
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Valentin Wittmann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
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16
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Li Q, Qu K. Electrochemical Impedimetric Platform Based on Con A@MIL-101 for Glycoprotein Detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7974-7981. [PMID: 38564230 DOI: 10.1021/acs.langmuir.3c03889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
An electrochemical impedimetric biosensing platform with lectin as a molecular recognition element has been established for the sensitive detection of glycoproteins, a class of important biomarkers in clinical diagnosis. One of the representative metal-organic framework materials, MIL-101(Cr)-NH2, was utilized as the supporting matrix, and its amino groups served as the anchors to immobilize the lectins of concanavalin A (Con A), constituting Con A@MIL-101(Cr)-NH2 for the determination of invertase (INV) as a model glycoprotein. The Con A concentration, immobilization time, and incubation time with INV were optimized. Under the optimal conditions, the degree of impedance increase was linearly proportional to the logarithm of INV concentration between 1.0 × 10-16 and 1.0 × 10-11 M, affording a limit of detection as low as 3.98 × 10-18 M. Good specificity, stability, reproducibility, and repeatability were demonstrated for the fabricated biosensing platform. Moreover, real mouse serum samples were spiked with different concentrations of INV. Excellent recoveries were obtained, which demonstrated the biosensing platform's capability of analyzing glycoproteins within a complex matrix.
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Affiliation(s)
- Qianlan Li
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, P. R. China
| | - Ke Qu
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, P. R. China
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17
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Milanesi F, Roelens S, Francesconi O. Towards Biomimetic Recognition of Glycans by Synthetic Receptors. Chempluschem 2024; 89:e202300598. [PMID: 37942862 DOI: 10.1002/cplu.202300598] [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: 10/19/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/10/2023]
Abstract
Carbohydrates are abundant in Nature, where they are mostly assembled within glycans as free polysaccharides or conjugated to a variety of biological molecules such as proteins and lipids. Glycans exert several functions, including protein folding, stability, solubility, resistance to proteolysis, intracellular traffic, antigenicity, and recognition by carbohydrate-binding proteins. Interestingly, misregulation of their biosynthesis that leads to changes in glycan structures is frequently recognized as a mark of a disease state. Because of glycan ubiquity, carbohydrate binding agents (CBAs) targeting glycans can lead to a deeper understanding of their function and to the development of new diagnostic and prognostic strategies. Synthetic receptors selectively recognizing specific carbohydrates of biological interest have been developed over the past three decades. In addition to the success obtained in the effective recognition of monosaccharides, synthetic receptors recognizing more complex guests have also been developed, including di- and oligosaccharide fragments of glycans, shedding light on the structural and functional requirements necessary for an effective receptor. In this review, the most relevant achievements in molecular recognition of glycans and their fragments will be summarized, highlighting potentials and future perspectives of glycan-targeting synthetic receptors.
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Affiliation(s)
- Francesco Milanesi
- Department of Chemistry "Ugo Schiff", DICUS and INSTM, Università degli Studi di Firenze, Campus Sesto, 50019, Sesto Fiorentino, Firenze, Italy
| | - Stefano Roelens
- Department of Chemistry "Ugo Schiff", DICUS and INSTM, Università degli Studi di Firenze, Campus Sesto, 50019, Sesto Fiorentino, Firenze, Italy
| | - Oscar Francesconi
- Department of Chemistry "Ugo Schiff", DICUS and INSTM, Università degli Studi di Firenze, Campus Sesto, 50019, Sesto Fiorentino, Firenze, Italy
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18
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Chao X, Zhang B, Yang S, Liu X, Zhang J, Zang X, Chen L, Qi L, Wang X, Hu H. Enrichment methods of N-linked glycopeptides from human serum or plasma: A mini-review. Carbohydr Res 2024; 538:109094. [PMID: 38564900 DOI: 10.1016/j.carres.2024.109094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
Human diseases often correlate with changes in protein glycosylation, which can be observed in serum or plasma samples. N-glycosylation, the most common form, can provide potential biomarkers for disease prognosis and diagnosis. However, glycoproteins constitute a relatively small proportion of the total proteins in human serum and plasma compared to the non-glycosylated protein albumin, which constitutes the majority. The detection of microheterogeneity and low glycan abundance presents a challenge. Mass spectrometry facilitates glycoproteomics research, yet it faces challenges due to interference from abundant plasma proteins. Therefore, methods have emerged to enrich N-glycans and N-linked glycopeptides using glycan affinity, chemical properties, stationary phase chemical coupling, bioorthogonal techniques, and other alternatives. This review focuses on N-glycans and N-glycopeptides enrichment in human serum or plasma, emphasizing methods and applications. Although not exhaustive, it aims to elucidate principles and showcase the utility and limitations of glycoproteome characterization.
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Affiliation(s)
- Xuyuan Chao
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Baoying Zhang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Shengjie Yang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Xizi Liu
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, People's Republic of China
| | - Jingyi Zhang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Xin Zang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Lu Chen
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Lu Qi
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Xinghe Wang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China.
| | - Han Hu
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, People's Republic of China.
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19
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Zhao Y, Su Z, Zhang X, Wu D, Wu Y, Li G. Recent advances in nanopore-based analysis for carbohydrates and glycoconjugates. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1454-1467. [PMID: 38415741 DOI: 10.1039/d3ay02040a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Saccharides are not only the basic constituents and nutrients of living organisms, but also participate in various life activities, and play important roles in cell recognition, immune regulation, development, cancer, etc. The analysis of carbohydrates and glycoconjugates is a necessary means to study their transformations and physiological roles in living organisms. Existing detection techniques can hardly meet the requirements for the analysis of carbohydrates and glycoconjugates in complex matrices as they are expensive, involve complex derivatization, and are time-consuming. Nanopore sensing technology, which is amplification-free and label-free, and is a high-throughput process, provides a new solution for the identification and sequencing of carbohydrates and glycoconjugates. This review highlights recent advances in novel nanopore-based single-molecule sensing technologies for the detection of carbohydrates and glycoconjugates and discusses the advantages and challenges of nanopore sensing technologies. Finally, current issues and future perspectives are discussed with the aim of improving the performance of nanopores in complex media diagnostic applications, as well as providing a new direction for the quantification of glycan chains and the study of glycan chain properties and functions.
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Affiliation(s)
- Yan Zhao
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Zhuoqun Su
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Xue Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Yongning Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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Qiu K, Wu K, Ma H, Ao Y, Zhou W, Cai Q. A transition-metal-free azide-alkyne cycloaddition/hydroamination cascade reaction for the construction of triazole-fused piperazin-2-ones. Org Biomol Chem 2024; 22:1176-1180. [PMID: 38206312 DOI: 10.1039/d3ob01999c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
A time-dependent, divergent synthesis of highly functionalized [1,2,3]triazolo[1,5-a]pyrazin-4(5H)-one (reaction time: 12 h) or 6,7-dihydro-[1,2,3]triazolo[1,5-a]pyrazin-4(5H)-one (reaction time: 2 h) scaffolds via a cascade azide-alkyne cycloaddition/hydroamination protocol is reported. The transformation features good functional group compatibility, broad substrate scope, high atom economy and avoidance of the use of transition-metal catalysts.
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Affiliation(s)
- Kongxi Qiu
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou, 510632, China.
| | - Kaifu Wu
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou, 510632, China.
| | - Haowen Ma
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou, 510632, China.
| | - Yunlin Ao
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou, 510632, China.
| | - Wei Zhou
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou, 510632, China.
| | - Qian Cai
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou, 510632, China.
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21
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Kubota R, Hamachi I. Cell-Like Synthetic Supramolecular Soft Materials Realized in Multicomponent, Non-/Out-of-Equilibrium Dynamic Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306830. [PMID: 38018341 PMCID: PMC10885657 DOI: 10.1002/advs.202306830] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/30/2023] [Indexed: 11/30/2023]
Abstract
Living cells are complex, nonequilibrium supramolecular systems capable of independently and/or cooperatively integrating multiple bio-supramolecules to execute intricate physiological functions that cannot be accomplished by individual biomolecules. These biological design strategies offer valuable insights for the development of synthetic supramolecular systems with spatially controlled hierarchical structures, which, importantly, exhibit cell-like responses and functions. The next grand challenge in supramolecular chemistry is to control the organization of multiple types of supramolecules in a single system, thus integrating the functions of these supramolecules in an orthogonal and/or cooperative manner. In this perspective, the recent progress in constructing multicomponent supramolecular soft materials through the hybridization of supramolecules, such as self-assembled nanofibers/gels and coacervates, with other functional molecules, including polymer gels and enzymes is highlighted. Moreover, results show that these materials exhibit bioinspired responses to stimuli, such as bidirectional rheological responses of supramolecular double-network hydrogels, temporal stimulus pattern-dependent responses of synthetic coacervates, and 3D hydrogel patterning in response to reaction-diffusion processes are presented. Autonomous active soft materials with cell-like responses and spatially controlled structures hold promise for diverse applications, including soft robotics with directional motion, point-of-care disease diagnosis, and tissue regeneration.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Nishikyo-ku, Katsura, 615-8530, Japan
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22
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Mut J, Altmann S, Reising S, Meißner-Weigl J, Driessen MD, Ebert R, Seibel J. SiaNAl can be efficiently incorporated in glycoproteins of human mesenchymal stromal cells by metabolic glycoengineering. ACS Biomater Sci Eng 2024; 10:139-148. [PMID: 36946521 DOI: 10.1021/acsbiomaterials.2c01534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Metabolic glycoengineering involves the stimulation of cells with functionalized monosaccharides. Glucosamine, galactosamine, and mannosamine derivatives are commercially available, but their application may lead to undirected (i.e., chemical) incorporation into proteins. However, sialic acids are attached to the ends of complex sugar chains of glycoproteins, which might be beneficial for cell surface modification via click chemistry. Thus, we studied the incorporation of chemically synthesized unnatural alkyne modified sialic acid (SiaNAl) into glycoproteins of human telomerase-immortalized mesenchymal stromal cells (hMSC-TERT) and we show that SiaNAl can be efficiently incorporated in glycoproteins involved in signal transduction and cell junction.
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Affiliation(s)
- Jürgen Mut
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Stephan Altmann
- Department of Musculoskeletal Tissue Regeneration, University of Würzburg, Friedrich-Bergius-Ring 15, Würzburg 97076, Germany
| | - Sabine Reising
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Jutta Meißner-Weigl
- Department of Musculoskeletal Tissue Regeneration, University of Würzburg, Friedrich-Bergius-Ring 15, Würzburg 97076, Germany
| | - Marc D Driessen
- Institute for Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Regina Ebert
- Department of Musculoskeletal Tissue Regeneration, University of Würzburg, Friedrich-Bergius-Ring 15, Würzburg 97076, Germany
| | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
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23
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Lee CH, Park S, Kim S, Hyun JY, Lee HS, Shin I. Engineering of cell-surface receptors for analysis of receptor internalization and detection of receptor-specific glycosylation. Chem Sci 2024; 15:555-565. [PMID: 38179521 PMCID: PMC10762726 DOI: 10.1039/d3sc05054h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
The epidermal growth factor receptor (EGFR) is a cell-surface glycoprotein that is involved mainly in cell proliferation. Overexpression of this receptor is intimately related to the development of a broad spectrum of tumors. In addition, glycans linked to the EGFR are known to affect its EGF-induced activation. Because of the pathophysiological significance of the EGFR, we prepared a fluorescently labeled EGFR (EGFR128-AZDye 488) on the cell surface by employing the genetic code expansion technique and bioorthogonal chemistry. EGFR128-AZDye 488 was initially utilized to investigate time-dependent endocytosis of the EGFR in live cells. The results showed that an EGFR inhibitor and antibody suppress endocytosis of the EGFR promoted by the EGF, and that lectins recognizing glycans of the EGFR do not enhance EGFR internalization into cells. Observations made in studies of the effects of appended glycans on the entry of the EGFR into cells indicate that a de-sialylated or de-fucosylated EGFR is internalized into cells more efficiently than a wild-type EGFR. Furthermore, by using the FRET-based imaging method of cells which contain an EGFR linked to AZDye 488 (a FRET donor) and cellular glycans labeled with rhodamine (a FRET acceptor), sialic acid residues attached to the EGFR were specifically detected on the live cell surface. Taken together, the results suggest that a fluorescently labeled EGFR will be a valuable tool in studies aimed at gaining an understanding of cellular functions of the EGFR.
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Affiliation(s)
- Chang-Hee Lee
- Department of Chemistry, Yonsei University Seoul 03722 Republic of Korea
| | - Sookil Park
- Department of Chemistry, Yonsei University Seoul 03722 Republic of Korea
| | - Sanggil Kim
- Department of Chemistry, Sogang University Seoul 04107 Republic of Korea
| | - Ji Young Hyun
- Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology Daejeon 34114 Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University Seoul 04107 Republic of Korea
| | - Injae Shin
- Department of Chemistry, Yonsei University Seoul 03722 Republic of Korea
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24
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Yuan X, Song J, Wang H, Zhang W, Liu Y, Su P, Yang Y. Dual-functionalized two-dimensional metal-organic framework composite with highly hydrophilicity for effective enrichment of glycopeptides. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1232:123920. [PMID: 38101285 DOI: 10.1016/j.jchromb.2023.123920] [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: 08/14/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
Protein glycosylation research is currently focused on the development of various functionalized materials that can effectively enrich the levels of glycopeptides in samples. However, most of these materials possess limited glycopeptide-specific recognition sites because of large steric hindrance, unsuitable mass transfer kinetics, and relatively low surface areas. Herein, a highly hydrophilic two-dimensional (2-D) metal-organic framework (MOF) nanosheet modified with glutathione (GSH) and l-cysteine (l-Cys) (denoted as Zr-Fc MOF@Au@GC) has been synthesized for efficient glycopeptide enrichment. Using this composite material, 39 and 44 glycopeptides from horseradish peroxidase (HRP) and human serum immunoglobulin G (IgG) digests were detected, respectively, which represents a higher efficiency for glycopeptide enrichment from model glycoprotein digests than has been previously reported. The material Zr-Fc MOF@Au@GC exhibited ultra-high sensitivity (0.1 fmol/µL), excellent selectivity (weight ratio of HRP tryptic digest to bovine serum albumin (BSA) tryptic digest = 1:2000), good binding capacity (200 mg/g), satisfactory reusability, and long-term storage capacity. In addition, 655 glycopeptides corresponding to 366 glycoproteins were identified from human serum samples. To the best of our knowledge, this is the largest number of glycoproteins detected in human serum samples to date. These results indicated that Zr-Fc MOF@Au@GC has the potential to be used for the enrichment of glycopeptides in biological samples and the analysis of protein glycosylation.
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Affiliation(s)
- Xiaoyu Yuan
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Han Wang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenkang Zhang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China.
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25
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Tian X, Zheng L, Wang C, Han Y, Li Y, Cui T, Liu J, Liu C, Jia G, Yang L, Hsu Y, Zeng C, Ding L, Wang C, Cheng B, Wang M, Xie R. Selenium-based metabolic oligosaccharide engineering strategy for quantitative glycan detection. Nat Commun 2023; 14:8281. [PMID: 38092825 PMCID: PMC10719347 DOI: 10.1038/s41467-023-44118-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: 05/20/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Metabolic oligosaccharide engineering (MOE) is a classical chemical approach to perturb, profile and perceive glycans in physiological systems, but probes upon bioorthogonal reaction require accessibility and the background signal readout makes it challenging to achieve glycan quantification. Here we develop SeMOE, a selenium-based metabolic oligosaccharide engineering strategy that concisely combines elemental analysis and MOE,enabling the mass spectrometric imaging of glycome. We also demonstrate that the new-to-nature SeMOE probes allow for detection, quantitative measurement and visualization of glycans in diverse biological contexts. We also show that chemical reporters on conventional MOE can be integrated into a bifunctional SeMOE probe to provide multimodality signal readouts. SeMOE thus provides a convenient and simplified method to explore the glyco-world.
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Affiliation(s)
- Xiao Tian
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Lingna Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Changjiang Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yida Han
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yujie Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Tongxiao Cui
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jialin Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chuanming Liu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Guogeng Jia
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Lujie Yang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yi Hsu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Chen Zeng
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Lijun Ding
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Chu Wang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Bo Cheng
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Meng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China.
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26
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Mukherjee MM, Bond MR, Abramowitz LK, Biesbrock D, Woodroofe CC, Kim EJ, Swenson RE, Hanover JA. Tools and tactics to define specificity of metabolic chemical reporters. Front Mol Biosci 2023; 10:1286690. [PMID: 38143802 PMCID: PMC10740162 DOI: 10.3389/fmolb.2023.1286690] [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: 08/31/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023] Open
Abstract
Metabolic chemical reporters (MCRs) provide easily accessible means to study glycans in their native environments. However, because monosaccharide precursors are shared by many glycosylation pathways, selective incorporation has been difficult to attain. Here, a strategy for defining the selectivity and enzymatic incorporation of an MCR is presented. Performing β-elimination to interrogate O-linked sugars and using commercially available glycosidases and glycosyltransferase inhibitors, we probed the specificity of widely used azide (Ac4GalNAz) and alkyne (Ac4GalNAlk and Ac4GlcNAlk) sugar derivatives. Following the outlined strategy, we provide a semiquantitative assessment of the specific and non-specific incorporation of this bioorthogonal sugar (Ac4GalNAz) into numerous N- and O-linked glycosylation pathways. This approach should be generally applicable to other MCRs to define the extent of incorporation into the various glycan species.
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Affiliation(s)
- Mana Mohan Mukherjee
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michelle R. Bond
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lara K. Abramowitz
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Devin Biesbrock
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Carolyn C. Woodroofe
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, MD, United States
| | - Eun Ju Kim
- Department of Chemistry Education, Daegu University, Gyeongsan-si, South Korea
| | - Rolf E. Swenson
- Department of Chemistry Education, Daegu University, Gyeongsan-si, South Korea
| | - John A. Hanover
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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27
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Wang G, Li Q, Guo Y, Chen L, Yao Y, Zhong Y, Sun J, Yan X, Wang H, Wang X, Ding L, Ju H. Interception Proximity Labeling for Interrogating Cell Efflux Microenvironment. Anal Chem 2023; 95:17798-17807. [PMID: 37976298 DOI: 10.1021/acs.analchem.3c03879] [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: 11/19/2023]
Abstract
The difficulty in elucidating the microenvironment of extracellular H2O2 efflux has led to the lack of a critical extracellular link in studies of the mechanisms of redox signaling pathways. Herein, we mounted horseradish peroxidase (HRP) to glycans expressed globally on the living cell surface and constructed an interception proximity labeling (IPL) platform for H2O2 efflux. The release of endogenous H2O2 is used as a "physiological switch" for HRP to enable proximity labeling. Using this platform, we visualize the oxidative stress state of tumor cells under the condition of nutrient withdrawal, as well as that of macrophages exposed to nonparticulate stimuli. Furthermore, in combination with a proteomics technique, we identify candidate proteins at the invasion interface between fungal mimics (zymosan) and macrophages by interception labeling of locally accumulated H2O2 and confirm that Toll-like receptor 2 binds zymosan in a glycan-dependent manner. The IPL platform has great potential to elucidate the mechanisms underlying biological processes involving redox pathways.
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Affiliation(s)
- Guyu Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qiang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuna Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Liusheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yunyan Yao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yihong Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jiahui Sun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiaomin Yan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hongwei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Xiaojian Wang
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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28
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Dong S, Chen L, Sauer A, Dittus L. LC/MS Assessment of Glycoform Clearance of A Biotherapeutic MAb in Rabbit Ocular Tissues. J Pharm Sci 2023; 112:2285-2291. [PMID: 37062414 DOI: 10.1016/j.xphs.2023.04.008] [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: 02/08/2023] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/18/2023]
Abstract
Many biotherapeutics such as monoclonal antibodies (mAbs) consist of various glycoforms, which can have different PK properties upon administration to animals and human. As a result, it is necessary to monitor the abundance of glycoforms and limit lot-to-lot variability during the manufacturing process. However, limited information is known about the clearance of mAb glycoforms from ocular space upon intravitreal injection. We present here an assessment of glycoform clearance of a biotherapeutic mAb (IgG1) from rabbit vitreous humor, aqueous humor and retina tissue using LC/MS. The results show that G0, G0F and G1F have similar T1/2, while mannose-5 has a longer T1/2 and is cleared slower in rabbit ocular space, which contradicted with what has been reported in the literature in which Mann5 was cleared faster systematically.
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Affiliation(s)
- Shiyu Dong
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc. Ridgefield, CT, USA
| | - Linzhi Chen
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc. Ridgefield, CT, USA.
| | - Achim Sauer
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG. Birkendorfer Str. 65, 88397 Biberach an der Riß, Germany
| | - Lars Dittus
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG. Birkendorfer Str. 65, 88397 Biberach an der Riß, Germany
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29
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Mukherjee MM, Abramowitz LK, Kumar B, Azadi P, Hanover JA. Selective bioorthogonal probe for N-glycan hybrid structures. RESEARCH SQUARE 2023:rs.3.rs-3093724. [PMID: 37577573 PMCID: PMC10418551 DOI: 10.21203/rs.3.rs-3093724/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Metabolic incorporation of chemically tagged monosaccharides is a facile means of labelling cellular glycoprotein and glycolipids. Yet, since the monosaccharide precursors are often shared by several pathways, selectivity has been difficult to attain. For example, N-linked glycosylation is a chemically complex, and ubiquitous post translational modification with three distinct classes of GlcNAc-containing N-glycan structures: oligomannose, hybrid, and complex. Here we describe synthesis of 1,3-Pr2-6-OTs GlcNAlk as a next generation metabolic chemical reporter (MCR) for the specific labeling of hybrid N-glycan structures. We first developed a general strategy for defining the selectivity of labelling with chemically tagged monosaccharides. We then applied this approach to establish that 1,3-Pr2-6-OTs GlcNAlk is specifically incorporated into hybrid N-glycans. Using this MCR as a detection tool, we carried out imaging experiments to define the intracellular localization and trafficking of target proteins bearing hybrid N-glycan structures.
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Affiliation(s)
- Mana Mohan Mukherjee
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD
| | - Lara K Abramowitz
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD
| | - Bhoj Kumar
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - John A Hanover
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD
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30
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Xu S, Suttapitugsakul S, Tong M, Wu R. Systematic analysis of the impact of phosphorylation and O-GlcNAcylation on protein subcellular localization. Cell Rep 2023; 42:112796. [PMID: 37453062 PMCID: PMC10530397 DOI: 10.1016/j.celrep.2023.112796] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 05/02/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
The subcellular localization of proteins is critical for their functions in eukaryotic cells and is tightly correlated with protein modifications. Here, we comprehensively investigate the nuclear-cytoplasmic distributions of the phosphorylated, O-GlcNAcylated, and non-modified forms of proteins to dissect the correlation between protein distribution and modifications. Phosphorylated and O-GlcNAcylated proteins have overall higher nuclear distributions than non-modified ones. Different distributions among the phosphorylated, O-GlcNAcylated, and non-modified forms of proteins are associated with protein size, structure, and function, as well as local environment and adjacent residues around modification sites. Moreover, we perform site-mutagenesis experiments using phosphomimetic and phospho-null mutants of two proteins to validate the proteomic results. Additionally, the effects of the OGT/OGA inhibition on glycoprotein distribution are systematically investigated, and the distribution changes of glycoproteins are related to their abundance changes under the inhibitions. Systematic investigation of the relationship between protein modification and localization advances our understanding of protein functions.
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Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ming Tong
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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31
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Zheng J, Zheng Z, Fu C, Weng Y, He A, Ye X, Gao W, Tian R. Deciphering intercellular signaling complexes by interaction-guided chemical proteomics. Nat Commun 2023; 14:4138. [PMID: 37438365 DOI: 10.1038/s41467-023-39881-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
Indirect cell-cell interactions mediated by secreted proteins and their plasma membrane receptors play essential roles for regulating intercellular signaling. However, systematic profiling of the interactions between living cell surface receptors and secretome from neighboring cells remains challenging. Here we develop a chemical proteomics approach, termed interaction-guided crosslinking (IGC), to identify ligand-receptor interactions in situ. By introducing glycan-based ligation and click chemistry, the IGC approach via glycan-to-glycan crosslinking successfully captures receptors from as few as 0.1 million living cells using only 10 ng of secreted ligand. The unparalleled sensitivity and selectivity allow systematic crosslinking and identification of ligand-receptor complexes formed between cell secretome and surfaceome in an unbiased and all-to-all manner, leading to the discovery of a ligand-receptor interaction between pancreatic cancer cell-secreted urokinase (PLAU) and neuropilin 1 (NRP1) on pancreatic cancer-associated fibroblasts. This approach is thus useful for systematic exploring new ligand-receptor pairs and discovering critical intercellular signaling events.
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Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Zhendong Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Changying Fu
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yicheng Weng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - An He
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xueting Ye
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Weina Gao
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
- Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, 518055, China.
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32
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Campos D, Girgis M, Yang Q, Zong G, Goldman R, Wang LX, Sanda M. "Ghost" Fragment Ions in Structure and Site-Specific Glycoproteomics Analysis. Anal Chem 2023; 95:10145-10148. [PMID: 37382290 PMCID: PMC10339278 DOI: 10.1021/acs.analchem.3c02207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/26/2023] [Indexed: 06/30/2023]
Abstract
Mass spectrometry (MS) can unlock crucial insights into the intricate world of glycosylation analysis. Despite its immense potential, the qualitative and quantitative analysis of isobaric glycopeptide structures remains one of the most daunting hurdles in the field of glycoproteomics. The ability to distinguish between these complex glycan structures poses a significant challenge, hindering our ability to accurately measure and understand the role of glycoproteins in biological systems. A few recent publications described the use of collision energy (CE) modulation to improve structural elucidation, especially for qualitative purposes. Different linkages of glycan units usually demonstrate different stabilities under CID/HCD fragmentation conditions. Fragmentation of the glycan moiety produces low molecular weight ions (oxonium ions) that can serve as a structure-specific signature for specific glycan moieties; however, the specificity of these fragments has never been examined closely. Here, we particularly focused on N-glycoproteomics analysis and investigated fragmentation specificity using synthetic stable isotope-labeled N-glycopeptide standards. These standards were isotopically labeled at the reducing terminal GlcNAc, which allowed us to resolve fragments produced by the oligomannose core moiety and fragments generated from outer antennary structures. Our research identified the potential for false-positive structure assignments due to the occurrence of "Ghost" fragments resulting from single glyco unit rearrangement or mannose core fragmentation within the collision cell. To mitigate this issue, we have established a minimal intensity threshold for these fragments to prevent misidentification of structure-specific fragments in glycoproteomics analysis. Our findings provide a crucial step forward in the quest for more accurate and reliable glycoproteomics measurements.
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Affiliation(s)
- Diana Campos
- Max-Planck-Institut
fuer Herz- und Lungenforschung, Ludwigstrasse 43, 61231 Bad Nauheim, Germany
| | - Michael Girgis
- Department
of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, Virginia 22030, United States
| | - Qiang Yang
- GlycoT
Therapeutics, College Park, Maryland 20742, United States
| | - Guanghui Zong
- Department
of Chemistry and Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Radoslav Goldman
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, D.C. 20057, United States
- Clinical
and Translational Glycoscience Research Center, Georgetown University, Washington, D.C. 20057, United States
| | - Lai-Xi Wang
- Department
of Chemistry and Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Miloslav Sanda
- Max-Planck-Institut
fuer Herz- und Lungenforschung, Ludwigstrasse 43, 61231 Bad Nauheim, Germany
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, D.C. 20057, United States
- Clinical
and Translational Glycoscience Research Center, Georgetown University, Washington, D.C. 20057, United States
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33
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Pickering C, Aiyetan P, Xu G, Mitchell A, Rice R, Najjar YG, Markowitz J, Ebert LM, Brown MP, Tapia-Rico G, Frederick D, Cong X, Serie D, Lindpaintner K, Schwarz F, Boland GM. Plasma glycoproteomic biomarkers identify metastatic melanoma patients with reduced clinical benefit from immune checkpoint inhibitor therapy. Front Immunol 2023; 14:1187332. [PMID: 37388743 PMCID: PMC10302726 DOI: 10.3389/fimmu.2023.1187332] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
The clinical success of immune-checkpoint inhibitors (ICI) in both resected and metastatic melanoma has confirmed the validity of therapeutic strategies that boost the immune system to counteract cancer. However, half of patients with metastatic disease treated with even the most aggressive regimen do not derive durable clinical benefit. Thus, there is a critical need for predictive biomarkers that can identify individuals who are unlikely to benefit with high accuracy so that these patients may be spared the toxicity of treatment without the likely benefit of response. Ideally, such an assay would have a fast turnaround time and minimal invasiveness. Here, we utilize a novel platform that combines mass spectrometry with an artificial intelligence-based data processing engine to interrogate the blood glycoproteome in melanoma patients before receiving ICI therapy. We identify 143 biomarkers that demonstrate a difference in expression between the patients who died within six months of starting ICI treatment and those who remained progression-free for three years. We then develop a glycoproteomic classifier that predicts benefit of immunotherapy (HR=2.7; p=0.026) and achieves a significant separation of patients in an independent cohort (HR=5.6; p=0.027). To understand how circulating glycoproteins may affect efficacy of treatment, we analyze the differences in glycosylation structure and discover a fucosylation signature in patients with shorter overall survival (OS). We then develop a fucosylation-based model that effectively stratifies patients (HR=3.5; p=0.0066). Together, our data demonstrate the utility of plasma glycoproteomics for biomarker discovery and prediction of ICI benefit in patients with metastatic melanoma and suggest that protein fucosylation may be a determinant of anti-tumor immunity.
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Affiliation(s)
- Chad Pickering
- InterVenn Biosciences, South San Francisco, CA, United States
| | - Paul Aiyetan
- InterVenn Biosciences, South San Francisco, CA, United States
| | - Gege Xu
- InterVenn Biosciences, South San Francisco, CA, United States
| | - Alan Mitchell
- InterVenn Biosciences, South San Francisco, CA, United States
| | - Rachel Rice
- InterVenn Biosciences, South San Francisco, CA, United States
| | - Yana G. Najjar
- Department of Medicine, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, PA, United States
| | - Joseph Markowitz
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
- Immuno-Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Lisa M. Ebert
- Centre for Cancer Biology, South Australia (SA) Pathology and University of South Australia, Adelaide, SA, Australia
- Cancer Clinical Trials Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Michael P. Brown
- Centre for Cancer Biology, South Australia (SA) Pathology and University of South Australia, Adelaide, SA, Australia
- Cancer Clinical Trials Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Gonzalo Tapia-Rico
- Cancer Clinical Trials Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Dennie Frederick
- Department of Surgery, Massachusetts General Hospital, Boston, MA, United States
| | - Xin Cong
- InterVenn Biosciences, South San Francisco, CA, United States
| | - Daniel Serie
- InterVenn Biosciences, South San Francisco, CA, United States
| | | | - Flavio Schwarz
- InterVenn Biosciences, South San Francisco, CA, United States
| | - Genevieve M. Boland
- Department of Surgery, Massachusetts General Hospital, Boston, MA, United States
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34
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Griffin ME, Thompson JW, Xiao Y, Sweredoski MJ, Aksenfeld RB, Jensen EH, Koldobskaya Y, Schacht AL, Kim TD, Choudhry P, Lomenick B, Garbis SD, Moradian A, Hsieh-Wilson LC. Functional glycoproteomics by integrated network assembly and partitioning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.541482. [PMID: 37398272 PMCID: PMC10312638 DOI: 10.1101/2023.06.13.541482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The post-translational modification (PTM) of proteins by O-linked β-N-acetyl-D-glucosamine (O-GlcNAcylation) is widespread across the proteome during the lifespan of all multicellular organisms. However, nearly all functional studies have focused on individual protein modifications, overlooking the multitude of simultaneous O-GlcNAcylation events that work together to coordinate cellular activities. Here, we describe Networking of Interactors and SubstratEs (NISE), a novel, systems-level approach to rapidly and comprehensively monitor O-GlcNAcylation across the proteome. Our method integrates affinity purification-mass spectrometry (AP-MS) and site-specific chemoproteomic technologies with network generation and unsupervised partitioning to connect potential upstream regulators with downstream targets of O-GlcNAcylation. The resulting network provides a data-rich framework that reveals both conserved activities of O-GlcNAcylation such as epigenetic regulation as well as tissue-specific functions like synaptic morphology. Beyond O-GlcNAc, this holistic and unbiased systems-level approach provides a broadly applicable framework to study PTMs and discover their diverse roles in specific cell types and biological states.
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Affiliation(s)
- Matthew E. Griffin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Co-first author
| | - John W. Thompson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Co-first author
| | - Yao Xiao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Co-first author
| | - Michael J. Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rita B. Aksenfeld
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elizabeth H. Jensen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yelena Koldobskaya
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrew L. Schacht
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Terry D. Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Priya Choudhry
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Spiros D. Garbis
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Linda C. Hsieh-Wilson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Lead contact
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35
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Geng ZQ, Zhao C, Qian HD, Li SJ, Peng H, Xu H. Cu/Ag-Mediated One-Pot Enantioselective Synthesis of Fully Decorated 1,2,3-Triazolo[1,5- a]pyrazines. Org Lett 2023. [PMID: 37294825 DOI: 10.1021/acs.orglett.3c01524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The synthesis of chiral triazole-fused pyrazine scaffolds from readily available substrates in a step-economical asymmetric catalytic way is highly appealing. We herein report that an efficient Cu/Ag relay catalyzed protocol employing cascade asymmetric propargylic amination, hydroazidation, and [3 + 2] cycloaddition reaction with high efficiency to access the target enantioenriched 1,2,3-triazolo[1,5-a]pyrazine has been accomplished by applying a novel N,N,P-ligand. The one-pot reaction of three components exhibits high functional group tolerance, excellent enantioselectivities, and a broad substrate scope with readily available starting materials.
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Affiliation(s)
- Zi-Qi Geng
- CCNU-uOttawa Joint Research Centre, Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, P. R. China
| | - Chunhui Zhao
- CCNU-uOttawa Joint Research Centre, Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, P. R. China
| | - Hao-Dong Qian
- CCNU-uOttawa Joint Research Centre, Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, P. R. China
| | - Si-Jia Li
- CCNU-uOttawa Joint Research Centre, Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, P. R. China
| | - Hao Peng
- CCNU-uOttawa Joint Research Centre, Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, P. R. China
| | - Hao Xu
- CCNU-uOttawa Joint Research Centre, Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, P. R. China
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36
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Campos D, Girgis M, Yang Q, Zong G, Goldman R, Wang LX, Sanda M. "Ghost" fragment ions in structure and site-specific glycoproteomics analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541150. [PMID: 37292769 PMCID: PMC10245710 DOI: 10.1101/2023.05.17.541150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mass spectrometry (MS) can unlock crucial insights into the intricate world of glycosylation analysis. Despite its immense potential, the qualitative and quantitative analysis of isobaric glycopeptide structures remains one of the most daunting hurdles in the field of glycoproteomics. The ability to distinguish between these complex glycan structures poses a significant challenge, hindering our ability to accurately measure and understand the role of glycoproteins in biological systems. A few recent publications described the use of collision energy (CE) modulation to improve structural elucidation, especially for qualitative purposes. Different linkages of glycan units usually demonstrate different stabilities under CID/HCD fragmentation conditions. Fragmentation of the glycan moiety produces low molecular weight ions (oxonium ions) that can serve as a structure-specific signature for specific glycan moieties, however, specificity of these fragments has never been examined closely. Here, we investigated fragmentation specificity using synthetic stable isotope-labelled glycopeptide standards. These standards were isotopically labelled at the reducing terminal GlcNAc, which allowed us to resolve fragments produced by oligomannose core moiety and fragments generated from outer antennary structures. Our research identified the potential for false positive structure assignments due to the occurrence of "Ghost" fragments resulting from single glyco unit rearrangement or mannose core fragmentation within the collision cell. To mitigate this issue, we have established a minimal intensity threshold for these fragments to prevent the misidentification of structure-specific fragments in glycoproteomics analysis. Our findings provide a crucial step forward in the quest for more accurate and reliable glycoproteomics measurements. Graphical abstract
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37
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Galicová T, Hasoň S, Ostatná V. Interaction of lectin Sambucus nigra with sialylated trisaccharides in the presence of osmolytes. Chronopotentiometric sensing. Bioelectrochemistry 2023; 152:108457. [PMID: 37196453 DOI: 10.1016/j.bioelechem.2023.108457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023]
Abstract
Trisaccharides bind to their interaction partners-lectins relatively weakly, which makes detection of their complexes challenging. In this work, we show that an osmolyte presence improves the distinguishing complexes of lectin Sambucus nigra with trisialyllactoses with various binding affinities. The addition of osmolyte, non-binding sugar mannose significantly improved the precision of binding experiments performed using chronopotentiometric stripping at the electrode surface and fluorescence analysis in solution. Osmolytes minimized nonspecific interactions between binding sugar and lectin. Obtained findings can be utilized in any in vitro methods studying interactions of carbohydrates, respectively their conjugates with proteins. The study of carbohydrate interactions appears important since they play essential roles in a variety of biological processes including carcinogenesis.
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Affiliation(s)
- Tatiana Galicová
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic; Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Stanislav Hasoň
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic.
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38
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Ji Y, Li H, Dong J, Lin J, Lin Z. Super-hydrophilic sulfonate-modified covalent organic framework nanosheets for efficient separation and enrichment of glycopeptides. J Chromatogr A 2023; 1699:464020. [PMID: 37104947 DOI: 10.1016/j.chroma.2023.464020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 04/29/2023]
Abstract
Highly efficient extraction of glycopeptides prior to mass spectrometry detection is extremely crucial for glycoproteomic research, especially in disease biomarker research. Reported here is the first time by applying two-dimensional (2D) covalent organic framework (COFs) nanosheets for highly efficient enrichment of glycopeptides. Particularly, by incorporating hydrophilic monomers through a bottom-up strategy, the 2D COF nanosheets (denoted as NUS-9) displayed an ultra-high graft density of sulfonic groups and super-hydrophilicity. In addition, because of the large surface area, low steric hindrance, high chemical stability, and abundant accessibility sites of 2D COF nanosheets, NUS-9 exhibited remarkable efficiency for glycopeptide enrichment, involving excellent detection sensitivity (0.01 fmol μL-1), outstanding enrichment capability, and good enrichment selectivity (1:1500, horseradish peroxidase (HRP) tryptic digest to bovine serum albumin (BSA) tryptic digest), and recovery (92.2 ± 2.0%). Moreover, the NUS-9 was able to unambiguously detect 631 endogenous glycopeptides from human saliva, demonstrating an unparalleled high efficiency in glycopeptide enrichment. Gene ontology analyses of proteins from human saliva enriched by NUS-9 demonstrated its potential for comprehensive glycoproteome analysis.
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Affiliation(s)
- Yin Ji
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Heming Li
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Jinghan Dong
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Jiashi Lin
- College of Physical Education, Jimei University, Xiamen, Fujian, 361021, China.
| | - Zian Lin
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China.
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39
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Čaval T, Alisson-Silva F, Schwarz F. Roles of glycosylation at the cancer cell surface: opportunities for large scale glycoproteomics. Theranostics 2023; 13:2605-2615. [PMID: 37215580 PMCID: PMC10196828 DOI: 10.7150/thno.81760] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Cell surface glycosylation has a variety of functions, and its dysregulation in cancer contributes to impaired signaling, metastasis and the evasion of the immune responses. Recently, a number of glycosyltransferases that lead to altered glycosylation have been linked to reduced anti-tumor immune responses: B3GNT3, which is implicated in PD-L1 glycosylation in triple negative breast cancer, FUT8, through fucosylation of B7H3, and B3GNT2, which confers cancer resistance to T cell cytotoxicity. Given the increased appreciation of the relevance of protein glycosylation, there is a critical need for the development of methods that allow for an unbiased interrogation of cell surface glycosylation status. Here we provide an overview of the broad changes in glycosylation at the surface of cancer cell and describe selected examples of receptors with aberrant glycosylation leading to functional changes, with emphasis on immune checkpoint inhibitors, growth-promoting and growth-arresting receptors. Finally, we posit that the field of glycoproteomics has matured to an extent where large-scale profiling of intact glycopeptides from the cell surface is feasible and is poised for discovery of new actionable targets against cancer.
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40
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Naba A. 10 years of extracellular matrix proteomics: Accomplishments, challenges, and future perspectives. Mol Cell Proteomics 2023; 22:100528. [PMID: 36918099 PMCID: PMC10152135 DOI: 10.1016/j.mcpro.2023.100528] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
The extracellular matrix (ECM) is a complex assembly of hundreds of proteins forming the architectural scaffold of multicellular organisms. In addition to its structural role, the ECM conveys signals orchestrating cellular phenotypes. Alterations of ECM composition, abundance, structure, or mechanics, have been linked to diseases and disorders affecting all physiological systems, including fibrosis and cancer. Deciphering the protein composition of the ECM and how it changes in pathophysiological contexts is thus the first step toward understanding the roles of the ECM in health and disease and toward the development of therapeutic strategies to correct disease-causing ECM alterations. Potentially, the ECM also represents a vast, yet untapped reservoir of disease biomarkers. ECM proteins are characterized by unique biochemical properties that have hindered their study: they are large, heavily and uniquely post-translationally modified, and highly insoluble. Overcoming these challenges, we and others have devised mass-spectrometry-based proteomic approaches to define the ECM composition, or "matrisome", of tissues. This review provides a historical overview of ECM proteomics research and presents the latest advances that now allow the profiling of the ECM of healthy and diseased tissues. The second part highlights recent examples illustrating how ECM proteomics has emerged as a powerful discovery pipeline to identify prognostic cancer biomarkers. The third part discusses remaining challenges limiting our ability to translate findings to clinical application and proposes approaches to overcome them. Last, the review introduces readers to resources available to facilitate the interpretation of ECM proteomics datasets. The ECM was once thought to be impenetrable. MS-based proteomics has proven to be a powerful tool to decode the ECM. In light of the progress made over the past decade, there are reasons to believe that the in-depth exploration of the matrisome is within reach and that we may soon witness the first translational application of ECM proteomics.
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Affiliation(s)
- Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, Chicago, IL 60612, USA.
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41
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Kufleitner M, Haiber LM, Wittmann V. Metabolic glycoengineering - exploring glycosylation with bioorthogonal chemistry. Chem Soc Rev 2023; 52:510-535. [PMID: 36537135 DOI: 10.1039/d2cs00764a] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Glycans are involved in numerous biological recognition events. Being secondary gene products, their labeling by genetic methods - comparable to GFP labeling of proteins - is not possible. To overcome this limitation, metabolic glycoengineering (MGE, also known as metabolic oligosaccharide engineering, MOE) has been developed. In this approach, cells or organisms are treated with synthetic carbohydrate derivatives that are modified with a chemical reporter group. In the cytosol, the compounds are metabolized and incorporated into newly synthesized glycoconjugates. Subsequently, the reporter groups can be further derivatized in a bioorthogonal ligation reaction. In this way, glycans can be visualized or isolated. Furthermore, diverse targeting strategies have been developed to direct drugs, nanoparticles, or whole cells to a desired location. This review summarizes research in the field of MGE carried out in recent years. After an introduction to the bioorthogonal ligation reactions that have been used in in connection with MGE, an overview on carbohydrate derivatives for MGE is given. The last part of the review focuses on the many applications of MGE starting from mammalian cells to experiments with animals and other organisms.
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Affiliation(s)
- Markus Kufleitner
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Lisa Maria Haiber
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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42
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Resveratrol-loaded macrophage exosomes alleviate multiple sclerosis through targeting microglia. J Control Release 2023; 353:675-684. [PMID: 36521687 DOI: 10.1016/j.jconrel.2022.12.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 11/01/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]
Abstract
Despite exosome promise as endogenous drug delivery vehicles, the current understanding of exosome may be insufficient to develop their various applications. Here we synthesized five sialic acid analogues with different length N-acyl side chains and screened out the optimal metabolic precursor for exosome labeling via bio-orthogonal click chemistry. In proof-of-principle labeling experiments, exosomes derived from macrophages (RAW-Exo) strongly co-localized with central nervous system (CNS) microglia. Inspired by this discovery, we developed a resveratrol-loaded RAW-Exo formulation (RSV&Exo) for multiple sclerosis (MS) treatment. Intranasal administration of RSV&Exo significantly inhibited inflammatory responses in the CNS and peripheral system in a mouse model of MS and effectively improved the clinical evolution of MS in vivo. These findings suggested the feasibility and efficacy of engineered RSV&Exo administration for MS, providing a potential therapeutic strategy for CNS diseases.
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43
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Burns MWN, Kohler JJ. Engineering Glyco‐Enzymes for Substrate Identification and Targeting. Isr J Chem 2022. [DOI: 10.1002/ijch.202200093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mary W. N. Burns
- Department of Biochemistry UT Southwestern Medical Center Dallas TX 75390 USA
| | - Jennifer J. Kohler
- Department of Biochemistry UT Southwestern Medical Center Dallas TX 75390 USA
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44
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Li S, Wei Y, Wang Y, Liang H. Advances in hydrophilic metal-organic frameworks for N-linked glycopeptide enrichment. Front Chem 2022; 10:1091243. [PMID: 36531319 PMCID: PMC9751774 DOI: 10.3389/fchem.2022.1091243] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/21/2022] [Indexed: 02/06/2024] Open
Abstract
The comprehensive profiling of glycoproteins is of great significance for the timely clinical diagnosis and therapy. However, inherent obstacles hamper their direct analysis from biological samples, and specific enrichment prior to analysis is indispensable. Among the various approaches for glycopeptide enrichment, hydrophilic interaction liquid chromatography (HILIC) has attracted special focus, especially for the development of novel hydrophilic materials, which is the key of HILIC. Metal-organic frameworks (MOFs) are a type of porous materials constructed from the self-assembly of metal and organic linkers. Advantages such as high surface area, flexible pore size, and easy modification render hydrophilic MOFs as ideal candidates for HILIC, which has inspired many studies over the past years. In this review, advances in hydrophilic MOFs for N-linked glycopeptide enrichment are summarized. According to the synthesis strategies, those materials are categorized into three classes, namely pristine MOFs, MOFs with chemical modifications, and MOFs-derived composite. In each categorization, the preparation and the function of different moieties are covered, as well as the enrichment performances of sensitivity, selectivity, and practical application. Finally, a summary and future perspective on the applications of hydrophilic MOFs for N-linked glycopeptide enrichment are briefly discussed. This review is expected to raise awareness of the properties of hydrophilic MOFs and offer some valuable information to further research in glycoproteomics.
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Affiliation(s)
| | | | | | - Haoran Liang
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing, China
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Chen D, Lin Y, Li A, Luo X, Yang C, Gao J, Lin H. Bio-orthogonal Metabolic Fluorine Labeling Enables Deep-Tissue Visualization of Tumor Cells In Vivo by 19F Magnetic Resonance Imaging. Anal Chem 2022; 94:16614-16621. [DOI: 10.1021/acs.analchem.2c02443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Dongxia Chen
- Fujian Provincial Key Laboratory of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yaying Lin
- Fujian Provincial Key Laboratory of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ao Li
- Fujian Provincial Key Laboratory of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiangjie Luo
- Fujian Provincial Key Laboratory of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- Fujian Provincial Key Laboratory of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jinhao Gao
- Fujian Provincial Key Laboratory of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hongyu Lin
- Fujian Provincial Key Laboratory of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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Ko J, Wilkovitsch M, Oh J, Kohler RH, Bolli E, Pittet MJ, Vinegoni C, Sykes DB, Mikula H, Weissleder R, Carlson JCT. Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes. Nat Biotechnol 2022; 40:1654-1662. [PMID: 35654978 PMCID: PMC9669087 DOI: 10.1038/s41587-022-01339-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/28/2022] [Indexed: 02/07/2023]
Abstract
Cells in complex organisms undergo frequent functional changes, but few methods allow comprehensive longitudinal profiling of living cells. Here we introduce scission-accelerated fluorophore exchange (SAFE), a method for multiplexed temporospatial imaging of living cells with immunofluorescence. SAFE uses a rapid bioorthogonal click chemistry to remove immunofluorescent signals from the surface of labeled cells, cycling the nanomolar-concentration reagents in seconds and enabling multiple rounds of staining of the same samples. It is non-toxic and functional in both dispersed cells and intact living tissues. We demonstrate multiparameter (n ≥ 14), non-disruptive imaging of murine peripheral blood mononuclear and bone marrow cells to profile cellular differentiation. We also show longitudinal multiplexed imaging of bone marrow progenitor cells as they develop into neutrophils over 6 days and real-time multiplexed cycling of living mouse hepatic tissues. We anticipate that SAFE will find broad utility for investigating physiologic dynamics in living systems.
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Affiliation(s)
- Jina Ko
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Juhyun Oh
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Rainer H Kohler
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Evangelia Bolli
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Mikael J Pittet
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Zurich, Switzerland
- AGORA Cancer Center, Lausanne, Switzerland
| | - Claudio Vinegoni
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannes Mikula
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Jonathan C T Carlson
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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47
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Speciale I, Notaro A, Abergel C, Lanzetta R, Lowary TL, Molinaro A, Tonetti M, Van Etten JL, De Castro C. The Astounding World of Glycans from Giant Viruses. Chem Rev 2022; 122:15717-15766. [PMID: 35820164 PMCID: PMC9614988 DOI: 10.1021/acs.chemrev.2c00118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Indexed: 12/12/2022]
Abstract
Viruses are a heterogeneous ensemble of entities, all sharing the need for a suitable host to replicate. They are extremely diverse, varying in morphology, size, nature, and complexity of their genomic content. Typically, viruses use host-encoded glycosyltransferases and glycosidases to add and remove sugar residues from their glycoproteins. Thus, the structure of the glycans on the viral proteins have, to date, typically been considered to mimick those of the host. However, the more recently discovered large and giant viruses differ from this paradigm. At least some of these viruses code for an (almost) autonomous glycosylation pathway. These viral genes include those that encode the production of activated sugars, glycosyltransferases, and other enzymes able to manipulate sugars at various levels. This review focuses on large and giant viruses that produce carbohydrate-processing enzymes. A brief description of those harboring these features at the genomic level will be discussed, followed by the achievements reached with regard to the elucidation of the glycan structures, the activity of the proteins able to manipulate sugars, and the organic synthesis of some of these virus-encoded glycans. During this progression, we will also comment on many of the challenging questions on this subject that remain to be addressed.
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Affiliation(s)
- Immacolata Speciale
- Department
of Agricultural Sciences, University of
Napoli, Via Università
100, 80055 Portici, Italy
| | - Anna Notaro
- Department
of Agricultural Sciences, University of
Napoli, Via Università
100, 80055 Portici, Italy
- Centre
National de la Recherche Scientifique, Information Génomique
& Structurale, Aix-Marseille University, Unité Mixte de Recherche
7256, IMM, IM2B, 13288 Marseille, Cedex 9, France
| | - Chantal Abergel
- Centre
National de la Recherche Scientifique, Information Génomique
& Structurale, Aix-Marseille University, Unité Mixte de Recherche
7256, IMM, IM2B, 13288 Marseille, Cedex 9, France
| | - Rosa Lanzetta
- Department
of Chemical Sciences, University of Napoli, Via Cintia 4, 80126 Napoli, Italy
| | - Todd L. Lowary
- Institute
of Biological Chemistry, Academia Sinica, Academia Road, Section 2, Nangang 11529, Taipei, Taiwan
| | - Antonio Molinaro
- Department
of Chemical Sciences, University of Napoli, Via Cintia 4, 80126 Napoli, Italy
| | - Michela Tonetti
- Department
of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy
| | - James L. Van Etten
- Nebraska
Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900, United States
- Department
of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, United States
| | - Cristina De Castro
- Department
of Agricultural Sciences, University of
Napoli, Via Università
100, 80055 Portici, Italy
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Riley NM, Wen RM, Bertozzi CR, Brooks JD, Pitteri SJ. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Adv Cancer Res 2022; 157:83-121. [PMID: 36725114 PMCID: PMC10582998 DOI: 10.1016/bs.acr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mucin-domain glycoproteins are highly O-glycosylated cell surface and secreted proteins that serve as both biochemical and biophysical modulators. Aberrant expression and glycosylation of mucins are known hallmarks in numerous malignancies, yet mucin-domain glycoproteins remain enigmatic in the broad landscape of cancer glycobiology. Here we review the multifaceted roles of mucins in cancer through the lens of the analytical and biochemical methods used to study them. We also describe a collection of emerging tools that are specifically equipped to characterize mucin-domain glycoproteins in complex biological backgrounds. These approaches are poised to further elucidate how mucin biology can be understood and subsequently targeted for the next generation of cancer therapeutics.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States.
| | - Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, Stanford, CA, United States
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States.
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Liu L, Chen X, Sun B. Construction of a Recyclable DNAzyme Motor for MUC1-Specific Glycoform In Situ Quantification. Anal Chem 2022; 94:13745-13752. [PMID: 36161871 DOI: 10.1021/acs.analchem.2c01961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Changes in the glycosylation content, especially in specific proteins, are of great importance for interpreting the mechanisms and development of certain diseases. However, current detection techniques are limited by the weak ionization efficiency of glycosyls and poor anti-interference of fluorescence signals. Herein, we present a general in situ quantification strategy for protein-specific glycoforms by constructing a recyclable DNAzyme motor for mass spectrometric detection using MUC1-specific sialic acid (Sia) as a model. This approach relies on a DNAzyme-based recycling strategy and two well-designed probes: a protein and a glycan probe. The protein probe consists of an aptamer and a DNAzyme. The glycan probe contains three functional domains: a DNAzyme complementary sequence, a substrate peptide segment, and a dibenzocyclooctyne tag. First, these two probes bind to their corresponding targets and trigger hybridization between adjacent probes on the same protein. With the help of the metal cofactor, the DNAzyme of the protein probe hydrolyzes the double-stranded glycan probe. The protein probe then reverts to a single-stranded state and remains intact for the next round of hybridization and cleavage. In this way, the recyclable DNAzyme motor can hydrolyze all glycan probes bound to the target protein. Finally, the reporter peptide released from the hydrolyzed glycan probes can be quantified by mass spectrometry, thereby converting the signal of the protein-specific glycoform to that of mass spectrometry. This strategy has been successfully used for in situ quantification of MUC1-specific Sia in different breast cancer cell lines. It provides a promising platform for protein-specific glycoform quantification.
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Affiliation(s)
- Liang Liu
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xiuyu Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Bo Sun
- Department of Pharmacy, The First People's Hospital of Lianyungang, Lianyungang 222000, China
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Zhao Y. Molecularly imprinted materials for glycan recognition and processing. J Mater Chem B 2022; 10:6607-6617. [PMID: 35481837 PMCID: PMC9476894 DOI: 10.1039/d2tb00164k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/24/2022] [Indexed: 11/21/2022]
Abstract
Carbohydrates are the most abundant organic molecules on Earth and glycosylation is the most common posttranslational modification of proteins. Glycans are involved in a plethora of biological processes including cell adhesion, bacterial and viral infection, inflammation, and cancer development. Coincidently, glycosides were some of the earliest molecules imprinted and have been instrumental in the development of covalent molecular imprinting technology. This perspective illustrates recently developed molecularly imprinted materials for glycan binding and processing. Novel imprinting techniques and postmodification led to development of synthetic glycan-binding materials capable of competing with natural lectins in affinity and artificial glycosidases for selective hydrolysis of complex glycans. These materials are expected to significantly advance glycochemistry, glycobiology, and related areas such as biomass conversion.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA.
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