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Miki T, Yamamoto S, Liu C, Torikai K, Kinoshita M, Matsumori N, Kawai T. Highly sensitive two-dimensional profiling of N-linked glycans by hydrophilic interaction liquid chromatography and dual stacking capillary gel electrophoresis. Anal Chim Acta 2024; 1320:342990. [PMID: 39142768 DOI: 10.1016/j.aca.2024.342990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 08/16/2024]
Abstract
BACKGROUND N-Glycosylation is one of the most important post-translational modifications in proteins. As the N-glycan profiles in biological samples are diverse and change according to the pathological condition, various profiling methods have been developed, such as liquid chromatography (LC), capillary electrophoresis (CE), and mass spectrometry. However, conventional analytical methods have limitations in sensitivity and/or resolution, hindering the discovery of minor but specific N-glycans that are important both in the basic glycobiology research and in the medical application as biomarkers. Therefore, a highly sensitive and high-resolution N-glycan profiling method is required. RESULTS In this study, we developed a novel two-dimensional (2D) separation system, which couples hydrophilic interaction liquid chromatography (HILIC) with capillary gel electrophoresis (CGE) via large-volume dual preconcentration by isotachophoresis and stacking (LDIS). Owing to the efficient preconcentration efficiency of LDIS, limit of detection reached 12 pM (60 amol, S/N = 3) with good calibration curve linearity (R2 > 0.999) in the 2D analysis of maltoheptaose. Finally, 2D profiling of N-glycans obtained from standard glycoproteins and cell lysates were demonstrated. High-resolution 2D profiles were successfully obtained by data alignment using triple internal standards. N-glycans were well distributed on the HILIC/CGE 2D plane based on the glycan size, number of sialic acids, linkage type, and so on. As a result, specific minor glycans were successfully identified in HepG2 and HeLa cell lysates. SIGNIFICANCE AND NOVELTY In conclusion, the HILIC/CGE 2D analysis method showed sufficient sensitivity and resolution for identifying minor but specific N-glycans from complicated cellular samples, indicating the potential as a next-generation N-glycomics tool. Our novel approach for coupling LC and CE can also dramatically improve the sensitivity in other separation modes, which can be a new standard of 2D bioanalysis applicable not only to glycans, but also to other diverse biomolecules such as metabolites, proteins, and nucleic acids.
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Affiliation(s)
- Takaya Miki
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Sachio Yamamoto
- Faculty of Pharmaceutical Sciences, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
| | - Chenchen Liu
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kohei Torikai
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan; Faculty of Chemistry, National University of Uzbekistan named after Mirzo Ulugbek, 4 University Str., Tashkent, 100174, Uzbekistan
| | - Mitsuhiro Kinoshita
- Faculty of Pharmaceutical Sciences, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takayuki Kawai
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan; RIKEN Center for Biosystems Dynamics Research, 6-2-4 Furuedai, Suita, Osaka, 565-0874, Japan.
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Godbole S, Voß H, Gocke A, Schlumbohm S, Schumann Y, Peng B, Mynarek M, Rutkowski S, Dottermusch M, Dorostkar MM, Korshunov A, Mair T, Pfister SM, Kwiatkowski M, Hotze M, Neumann P, Hartmann C, Weis J, Liesche-Starnecker F, Guan Y, Moritz M, Siebels B, Struve N, Schlüter H, Schüller U, Krisp C, Neumann JE. Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level. Nat Commun 2024; 15:6237. [PMID: 39043693 PMCID: PMC11266559 DOI: 10.1038/s41467-024-50554-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/11/2024] [Indexed: 07/25/2024] Open
Abstract
Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically heterogenous. The application of omics technologies-mainly studying nucleic acids-has significantly improved MB classification and stratification, but treatment options are still unsatisfactory. The proteome and their N-glycans hold the potential to discover clinically relevant phenotypes and targetable pathways. We compile a harmonized proteome dataset of 167 MBs and integrate findings with DNA methylome, transcriptome and N-glycome data. We show six proteome MB subtypes, that can be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pG3myc), and synapses/immunological processes (pSHHs, pG3 and pG4). Multiomic analysis reveals different conservation levels of proteome features across MB subtypes at the DNA methylome level. Aggressive pGroup3myc MBs and favorable pWNT MBs are most similar in cluster hierarchies concerning overall proteome patterns but show different protein abundances of the vincristine resistance-associated multiprotein complex TriC/CCT and of N-glycan turnover-associated factors. The N-glycome reflects proteome subtypes and complex-bisecting N-glycans characterize pGroup3myc tumors. Our results shed light on targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.
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Affiliation(s)
- Shweta Godbole
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Antonia Gocke
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Schlumbohm
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Yannis Schumann
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Bojia Peng
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Dottermusch
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mario M Dorostkar
- Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Mair
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Madlen Hotze
- Institute of Biochemistry, University of Innsbruck, Innsbruck, Austria
| | - Philipp Neumann
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Hannover Medical School (MHH), Hannover, Germany
| | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | | | - Yudong Guan
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manuela Moritz
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bente Siebels
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nina Struve
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Radiotherapy & Radiation Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Christoph Krisp
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia E Neumann
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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3
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Bladergroen MR, Pongracz T, Wang W, Nicolardi S, Arbous SM, Roukens A, Wuhrer M. Total plasma N-glycomic signature of SARS-CoV-2 infection. iScience 2024; 27:110374. [PMID: 39100929 PMCID: PMC11294702 DOI: 10.1016/j.isci.2024.110374] [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: 02/23/2024] [Revised: 04/19/2024] [Accepted: 06/21/2024] [Indexed: 08/06/2024] Open
Abstract
Total plasma protein N-glycosylation (TPNG) changes are a hallmark of many diseases. Here, we analyzed the TPNG of 169 COVID-19 patients and 12 healthy controls, using mass spectrometry, resulting in the relative quantification of 85 N-glycans. We found a COVID-19 N-glycomic signature, with 59 glycans differing between patients and controls, many of them additionally differentiating between severe and mild COVID-19. Tri- and tetra-antennary N-glycans were increased in patients, showing additionally elevated levels of antennary α2,6-sialylation. Conversely, bisection of di-antennary, core-fucosylated, nonsialylated glycans was low in COVID-19, particularly in severe cases, potentially driven by the previously observed low levels of bisection on antibodies of severely diseased COVID-19 patients. These glycomic changes point toward systemic changes in the blood glycoproteome, particularly involvement of acute-phase proteins, immunoglobulins and the complement cascade. Further research is needed to dissect glycosylation changes in a protein- and site-specific way to obtain specific functional leads.
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Affiliation(s)
- Marco R. Bladergroen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Tamas Pongracz
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Wenjun Wang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Sesmu M. Arbous
- Department of Intensive Care, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Anna Roukens
- Department of Infectious Diseases, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - BEAT-COVID group
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Intensive Care, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Infectious Diseases, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - LUMC COVID-19 group
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Intensive Care, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Infectious Diseases, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
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4
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Wang Y, Liu Y, Liu S, Cheng L, Liu X. Recent advances in N-glycan biomarker discovery among human diseases. Acta Biochim Biophys Sin (Shanghai) 2024; 56:1156-1171. [PMID: 38910518 DOI: 10.3724/abbs.2024101] [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: 06/25/2024] Open
Abstract
N-glycans play important roles in a variety of biological processes. In recent years, analytical technologies with high resolution and sensitivity have advanced exponentially, enabling analysts to investigate N-glycomic changes in different states. Specific glycan and glycosylation signatures have been identified in multiple diseases, including cancer, autoimmune diseases, nervous system disorders, and metabolic and cardiovascular diseases. These glycans demonstrate comparable or superior indicating capability in disease diagnosis and prognosis over routine biomarkers. Moreover, synchronous glycan alterations concurrent with disease initiation and progression provide novel insights into pathogenetic mechanisms and potential treatment targets. This review elucidates the biological significance of N-glycans, compares the existing glycomic technologies, and delineates the clinical performance of N-glycans across a range of diseases.
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Affiliation(s)
- Yi Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuanyuan Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Si Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xin Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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5
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Pongracz T, Mayboroda OA, Wuhrer M. The Human Blood N-Glycome: Unraveling Disease Glycosylation Patterns. JACS AU 2024; 4:1696-1708. [PMID: 38818049 PMCID: PMC11134357 DOI: 10.1021/jacsau.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 06/01/2024]
Abstract
Most of the proteins in the circulation are N-glycosylated, shaping together the total blood N-glycome (TBNG). Glycosylation is known to affect protein function, stability, and clearance. The TBNG is influenced by genetic, environmental, and metabolic factors, in part epigenetically imprinted, and responds to a variety of bioactive signals including cytokines and hormones. Accordingly, physiological and pathological events are reflected in distinct TBNG signatures. Here, we assess the specificity of the emerging disease-associated TBNG signatures with respect to a number of key glycosylation motifs including antennarity, linkage-specific sialylation, fucosylation, as well as expression of complex, hybrid-type and oligomannosidic N-glycans, and show perplexing complexity of the glycomic dimension of the studied diseases. Perspectives are given regarding the protein- and site-specific analysis of N-glycosylation, and the dissection of underlying regulatory layers and functional roles of blood protein N-glycosylation.
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Affiliation(s)
- Tamas Pongracz
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Oleg A. Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
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6
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Muchowicz A, Bartoszewicz A, Zaslona Z. The Exploitation of the Glycosylation Pattern in Asthma: How We Alter Ancestral Pathways to Develop New Treatments. Biomolecules 2024; 14:513. [PMID: 38785919 PMCID: PMC11117584 DOI: 10.3390/biom14050513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/12/2024] [Accepted: 04/21/2024] [Indexed: 05/25/2024] Open
Abstract
Asthma has reached epidemic levels, yet progress in developing specific therapies is slow. One of the main reasons for this is the fact that asthma is an umbrella term for various distinct subsets. Due to its high heterogeneity, it is difficult to establish biomarkers for each subset of asthma and to propose endotype-specific treatments. This review focuses on protein glycosylation as a process activated in asthma and ways to utilize it to develop novel biomarkers and treatments. We discuss known and relevant glycoproteins whose functions control disease development. The key role of glycoproteins in processes integral to asthma, such as inflammation, tissue remodeling, and repair, justifies our interest and research in the field of glycobiology. Altering the glycosylation states of proteins contributing to asthma can change the pathological processes that we previously failed to inhibit. Special emphasis is placed on chitotriosidase 1 (CHIT1), an enzyme capable of modifying LacNAc- and LacdiNAc-containing glycans. The expression and activity of CHIT1 are induced in human diseased lungs, and its pathological role has been demonstrated by both genetic and pharmacological approaches. We propose that studying the glycosylation pattern and enzymes involved in glycosylation in asthma can help in patient stratification and in developing personalized treatment.
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Affiliation(s)
| | | | - Zbigniew Zaslona
- Molecure S.A., Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.M.); (A.B.)
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7
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Li J, Liu D, Zhang Y, Shen J, Dan W, Chen Z, Sun S. Site-Specific Analysis of Core and Antenna Fucosylation on Serum Glycoproteins. Anal Chem 2024; 96:5741-5745. [PMID: 38573003 DOI: 10.1021/acs.analchem.4c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Fucosylation is an important structural feature of glycans and plays an essential role in the regulation of glycoprotein functions. Fucosylation can be classified into core- (CF) and antenna-fucosylation (AF, also known as (sialyl-) Lewis) based on the location on N-glycans, and they perform distinct biological functions. In this study, core- and antenna-fucosylated N-glycans on human serum glycoproteins that hold great clinical application values were systematically characterized at the site-specific level using StrucGP combined with the recently developed fucosylation assignment method. The results showed that fucosylation was widely distributed on serum glycoproteins, with 50% of fucosylated glycopeptides modified by AF N-glycans, 37% by CF N-glycans, and 13% by dual-fucosylated N-glycans. Interestingly, CF and AF N-glycans preferred to modify different groups of serum glycoproteins with different tissue origins and were involved in distinctive biological processes. Specifically, AF N-glycoproteins are mainly from the liver and participated in complement activation, blood coagulation, and endopeptidase activities, while CF N-glycoproteins originate from diverse tissues and are mainly involved in cell adhesion and signaling transduction. These data further enhanced our understanding of fucosylation on circulation glycoproteins.
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Affiliation(s)
- Jun Li
- College of Life Sciences, Northwest University, Xi'an 710069, China P.R
| | - Didi Liu
- College of Life Sciences, Northwest University, Xi'an 710069, China P.R
| | - Yingjie Zhang
- College of Life Sciences, Northwest University, Xi'an 710069, China P.R
| | - Jiechen Shen
- College of Life Sciences, Northwest University, Xi'an 710069, China P.R
| | - Wei Dan
- College of Life Sciences, Northwest University, Xi'an 710069, China P.R
| | - Zexuan Chen
- College of Life Sciences, Northwest University, Xi'an 710069, China P.R
| | - Shisheng Sun
- College of Life Sciences, Northwest University, Xi'an 710069, China P.R
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He K, Baniasad M, Kwon H, Caval T, Xu G, Lebrilla C, Hommes DW, Bertozzi C. Decoding the glycoproteome: a new frontier for biomarker discovery in cancer. J Hematol Oncol 2024; 17:12. [PMID: 38515194 PMCID: PMC10958865 DOI: 10.1186/s13045-024-01532-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024] Open
Abstract
Cancer early detection and treatment response prediction continue to pose significant challenges. Cancer liquid biopsies focusing on detecting circulating tumor cells (CTCs) and DNA (ctDNA) have shown enormous potential due to their non-invasive nature and the implications in precision cancer management. Recently, liquid biopsy has been further expanded to profile glycoproteins, which are the products of post-translational modifications of proteins and play key roles in both normal and pathological processes, including cancers. The advancements in chemical and mass spectrometry-based technologies and artificial intelligence-based platforms have enabled extensive studies of cancer and organ-specific changes in glycans and glycoproteins through glycomics and glycoproteomics. Glycoproteomic analysis has emerged as a promising tool for biomarker discovery and development in early detection of cancers and prediction of treatment efficacy including response to immunotherapies. These biomarkers could play a crucial role in aiding in early intervention and personalized therapy decisions. In this review, we summarize the significant advance in cancer glycoproteomic biomarker studies and the promise and challenges in integration into clinical practice to improve cancer patient care.
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Affiliation(s)
- Kai He
- James Comprehensive Cancer Center, The Ohio State University, Columbus, USA.
| | | | - Hyunwoo Kwon
- James Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | | | - Gege Xu
- InterVenn Biosciences, South San Francisco, USA
| | - Carlito Lebrilla
- Department of Biochemistry and Molecular Medicine, UC Davis Health, Sacramento, USA
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Liu S, Tu C, Zhang H, Huang H, Liu Y, Wang Y, Cheng L, Liu BF, Ning K, Liu X. Noninvasive serum N-glycans associated with ovarian cancer diagnosis and precancerous lesion prediction. J Ovarian Res 2024; 17:26. [PMID: 38281033 PMCID: PMC10821556 DOI: 10.1186/s13048-024-01350-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/11/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Ovarian cancer (OC) is one of the most common gynecological tumors with high morbidity and mortality. Altered serum N-glycome has been observed in many diseases, while the association between serum protein N-glycosylation and OC progression remains unclear, particularly for the onset of carcinogenesis from benign neoplasms to cancer. METHODS Herein, a mass spectrometry based high-throughput technique was applied to characterize serum N-glycome profile in individuals with healthy controls, benign neoplasms and different stages of OC. To elucidate the alterations of glycan features in OC progression, an orthogonal strategy with lectin-based ELISA was performed. RESULTS It was observed that the initiation and development of OC was associated with increased high-mannosylationand agalactosylation, concurrently with decreased total sialylation of serum, each of which gained at least moderately accurate merits. The most important individual N-glycans in each glycan group was H7N2, H3N5 and H5N4S2F1, respectively. Notably, serum N-glycome could be used to accurately discriminate OC patients from benign cohorts, with a comparable or even higher diagnostic score compared to CA125 and HE4. Furthermore, bioinformatics analysis based discriminative model verified the diagnostic performance of serum N-glycome for OC in two independent sets. CONCLUSIONS These findings demonstrated the great potential of serum N-glycome for OC diagnosis and precancerous lesion prediction, paving a new way for OC screening and monitoring.
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Affiliation(s)
- Si Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Chang Tu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Haobo Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hanhui Huang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yuanyuan Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yi Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kang Ning
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Xin Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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10
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Peng J, Yu L, Huang L, Paschoal VA, Chu H, de Souza CO, Varre JV, Oh DY, Kohler JJ, Xiao X, Xu L, Holland WL, Shaul PW, Mineo C. Hepatic sialic acid synthesis modulates glucose homeostasis in both liver and skeletal muscle. Mol Metab 2023; 78:101812. [PMID: 37777009 PMCID: PMC10583174 DOI: 10.1016/j.molmet.2023.101812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/02/2023] Open
Abstract
OBJECTIVE Sialic acid is a terminal monosaccharide of glycans in glycoproteins and glycolipids, and its derivation from glucose is regulated by the rate-limiting enzyme UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE). Although the glycans on key endogenous hepatic proteins governing glucose metabolism are sialylated, how sialic acid synthesis and sialylation in the liver influence glucose homeostasis is unknown. Studies were designed to fill this knowledge gap. METHODS To decrease the production of sialic acid and sialylation in hepatocytes, a hepatocyte-specific GNE knockdown mouse model was generated, and systemic glucose metabolism, hepatic insulin signaling and glucagon signaling were evaluated in vivo or in primary hepatocytes. Peripheral insulin sensitivity was also assessed. Furthermore, the mechanisms by which sialylation in the liver influences hepatic insulin signaling and glucagon signaling and peripheral insulin sensitivity were identified. RESULTS Liver GNE deletion in mice caused an impairment of insulin suppression of hepatic glucose production. This was due to a decrease in the sialylation of hepatic insulin receptors (IR) and a decline in IR abundance due to exaggerated degradation through the Eph receptor B4. Hepatic GNE deficiency also caused a blunting of hepatic glucagon receptor (GCGR) function which was related to a decline in its sialylation and affinity for glucagon. An accompanying upregulation of hepatic FGF21 production caused an enhancement of skeletal muscle glucose disposal that led to an overall increase in glucose tolerance and insulin sensitivity. CONCLUSION These collective observations reveal that hepatic sialic acid synthesis and sialylation modulate glucose homeostasis in both the liver and skeletal muscle. By interrogating how hepatic sialic acid synthesis influences glucose control mechanisms in the liver, a new metabolic cycle has been identified in which a key constituent of glycans generated from glucose modulates the systemic control of its precursor.
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Affiliation(s)
- Jun Peng
- Center for Pulmonary and Vascular Biology, Dept. of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
| | - Liming Yu
- Center for Pulmonary and Vascular Biology, Dept. of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Linzhang Huang
- Center for Pulmonary and Vascular Biology, Dept. of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Vivian A Paschoal
- Dept. of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Haiyan Chu
- Center for Pulmonary and Vascular Biology, Dept. of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Camila O de Souza
- Dept. of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Joseph V Varre
- Dept. of Nutrition & Integrative Physiology, University of Utah College of Health, 250 1850 E, Salt Lake City, UT, 84112, USA
| | - Da Young Oh
- Dept. of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Jennifer J Kohler
- Dept. of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Xue Xiao
- Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Lin Xu
- Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - William L Holland
- Dept. of Nutrition & Integrative Physiology, University of Utah College of Health, 250 1850 E, Salt Lake City, UT, 84112, USA
| | - Philip W Shaul
- Center for Pulmonary and Vascular Biology, Dept. of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
| | - Chieko Mineo
- Center for Pulmonary and Vascular Biology, Dept. of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA; Dept. of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
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11
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Clerc F, Reiding KR, de Haan N, Koeleman CAM, Hipgrave Ederveen AL, Manetti N, Dotz V, Annese V, Wuhrer M. Immunoglobulin A Glycosylation Differs between Crohn's Disease and Ulcerative Colitis. J Proteome Res 2023; 22:3213-3224. [PMID: 37641533 PMCID: PMC10563165 DOI: 10.1021/acs.jproteome.3c00260] [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: 05/01/2023] [Indexed: 08/31/2023]
Abstract
Inflammatory bowel diseases (IBD), such as Crohn's disease (CD) and ulcerative colitis (UC), are chronic and relapsing inflammations of the digestive tract with increasing prevalence, yet they have unknown origins or cure. CD and UC have similar symptoms but respond differently to surgery and medication. Current diagnostic tools often involve invasive procedures, while laboratory markers for patient stratification are lacking. Large glycomic studies of immunoglobulin G and total plasma glycosylation have shown biomarker potential in IBD and could help determine disease mechanisms and therapeutic treatment choice. Hitherto, the glycosylation signatures of plasma immunoglobulin A, an important immunoglobulin secreted into the intestinal mucin, have remained undetermined in the context of IBD. Our study investigated the associations of immunoglobulin A1 and A2 glycosylation with IBD in 442 IBD cases (188 CD and 254 UC) and 120 healthy controls by reversed-phase liquid chromatography electrospray-ionization mass spectrometry of tryptic glycopeptides. Differences of IgA O- and N-glycosylation (including galactosylation, bisection, sialylation, and antennarity) between patient groups were associated with the diseases, and these findings led to the construction of a statistical model to predict the disease group of the patients without the need of invasive procedures. This study expands the current knowledge about CD and UC and could help in the development of noninvasive biomarkers and better patient care.
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Affiliation(s)
- Florent Clerc
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center (LUMC), Postbus 9600, Leiden 2300 RC, The Netherlands
| | - Karli R. Reiding
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center (LUMC), Postbus 9600, Leiden 2300 RC, The Netherlands
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical
Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, Utrecht 3584 CH, The Netherlands
| | - Noortje de Haan
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center (LUMC), Postbus 9600, Leiden 2300 RC, The Netherlands
| | - Carolien A. M. Koeleman
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center (LUMC), Postbus 9600, Leiden 2300 RC, The Netherlands
| | - Agnes L. Hipgrave Ederveen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center (LUMC), Postbus 9600, Leiden 2300 RC, The Netherlands
| | - Natalia Manetti
- Unit
of Gastroenterology SOD2 (Strutture Organizzative Dipartimentali), Azienda Ospedaliero Universitaria (AOU) Careggi, Florence 50134, Italy
- Gastroenterology
Unit, San Jacopo Hospital, Pistoia 51100, Italy
| | - IBD-BIOM Consortium
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center (LUMC), Postbus 9600, Leiden 2300 RC, The Netherlands
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical
Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, Utrecht 3584 CH, The Netherlands
- Unit
of Gastroenterology SOD2 (Strutture Organizzative Dipartimentali), Azienda Ospedaliero Universitaria (AOU) Careggi, Florence 50134, Italy
- Gastroenterology
Unit, San Jacopo Hospital, Pistoia 51100, Italy
- Unit of Gastroenterology, IRCCS
(Istituto di Ricovero e Cura a Carattere Scientifico−Casa
Sollievo della Sofferenza) Hospital, San Giovanni Rotondo 71013, Italy
- Vita-Salute
San Raffaele University Faculty of Medicine and Surgery, Milano 20132, Italy
- IRCCS
Policlinico San Danato, San Donato
Milanese 20097, Italy
| | - Viktoria Dotz
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center (LUMC), Postbus 9600, Leiden 2300 RC, The Netherlands
| | - Vito Annese
- Unit
of Gastroenterology SOD2 (Strutture Organizzative Dipartimentali), Azienda Ospedaliero Universitaria (AOU) Careggi, Florence 50134, Italy
- Unit of Gastroenterology, IRCCS
(Istituto di Ricovero e Cura a Carattere Scientifico−Casa
Sollievo della Sofferenza) Hospital, San Giovanni Rotondo 71013, Italy
- Vita-Salute
San Raffaele University Faculty of Medicine and Surgery, Milano 20132, Italy
- IRCCS
Policlinico San Danato, San Donato
Milanese 20097, Italy
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center (LUMC), Postbus 9600, Leiden 2300 RC, The Netherlands
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12
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Svecla M, Nour J, Bladergroen MR, Nicolardi S, Zhang T, Beretta G, Wuhrer M, Norata GD, Falck D. Impact of Asialoglycoprotein Receptor and Mannose Receptor Deficiency on Murine Plasma N-glycome Profiles. Mol Cell Proteomics 2023; 22:100615. [PMID: 37414249 PMCID: PMC10462831 DOI: 10.1016/j.mcpro.2023.100615] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/14/2023] [Accepted: 07/02/2023] [Indexed: 07/08/2023] Open
Abstract
The asialoglycoprotein receptor (ASGPR) and the mannose receptor C-type 1 (MRC1) are well known for their selective recognition and clearance of circulating glycoproteins. Terminal galactose and N-Acetylgalactosamine are recognized by ASGPR, while terminal mannose, fucose, and N-Acetylglucosamine are recognized by MRC1. The effects of ASGPR and MRC1 deficiency on the N-glycosylation of individual circulating proteins have been studied. However, the impact on the homeostasis of the major plasma glycoproteins is debated and their glycosylation has not been mapped with high molecular resolution in this context. Therefore, we evaluated the total plasma N-glycome and plasma proteome of ASGR1 and MRC1 deficient mice. ASGPR deficiency resulted in an increase in O-acetylation of sialic acids accompanied by higher levels of apolipoprotein D, haptoglobin, and vitronectin. MRC1 deficiency decreased fucosylation without affecting the abundance of the major circulating glycoproteins. Our findings confirm that concentrations and N-glycosylation of the major plasma proteins are tightly controlled and further suggest that glycan-binding receptors have redundancy, allowing compensation for the loss of one major clearance receptor.
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Affiliation(s)
- M Svecla
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy; Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - J Nour
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - M R Bladergroen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - S Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - T Zhang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - G Beretta
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - M Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - G D Norata
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy; Centro SISA per lo studio dell'Aterosclerosi, Ospedale Bassini, Cinisello Balsamo, Italy
| | - D Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
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13
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Zhang ZJ, Wang HF, Lian TY, Zhou YP, Xu XQ, Guo F, Wei YP, Li JY, Sun K, Liu C, Pan LR, Ren M, Nie L, Dai HL, Jing ZC. Human Plasma IgG N-Glycome Profiles Reveal a Proinflammatory Phenotype in Chronic Thromboembolic Pulmonary Hypertension. Hypertension 2023; 80:1929-1939. [PMID: 37449418 DOI: 10.1161/hypertensionaha.123.21408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND The pathological mechanism of chronic thromboembolic pulmonary hypertension (CTEPH) is not fully understood, and inflammation has been reported to be one of its etiological factors. IgG regulates systemic inflammatory homeostasis, primarily through its N-glycans. Little is known about IgG N-glycosylation in CTEPH. We aimed to map the IgG N-glycome of CTEPH to provide new insights into its pathogenesis and discover novel markers and therapies. METHODS We characterized the plasma IgG N-glycome of patients with CTEPH in a discovery cohort and validated our results in an independent validation cohort using matrix-assisted laser desorption/ionization time of flight mass spectrometry. Thereafter, we correlated IgG N-glycans with clinical parameters and circulating inflammatory cytokines in patients with CTEPH. Furthermore, we determined IgG N-glycan quantitative trait loci in CTEPH to reveal partial mechanisms underlying glycan changes. RESULTS Decreased IgG galactosylation representing a proinflammatory phenotype was found in CTEPH. The distribution of IgG galactosylation showed a strong association with NT-proBNP (N-terminal pro-B-type natriuretic peptide) in CTEPH. In line with the glycomic findings, IgG pro-/anti-inflammatory N-glycans correlated well with a series of inflammatory markers and gene loci that have been reported to be involved in the regulation of these glycans or inflammatory immune responses. CONCLUSIONS This is the first study to reveal the full signature of the IgG N-glycome of a proinflammatory phenotype and the genes involved in its regulation in CTEPH. Plasma IgG galactosylation may be useful for evaluating the inflammatory state in patients with CTEPH; however, this requires further validation. This study improves our understanding of the mechanisms underlying CTEPH inflammation from the perspective of glycomics.
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Affiliation(s)
- Ze-Jian Zhang
- Department of Cardiology (Z.-J.Z., T.-Y.L., Y.-P.Z., X.-Q.X., F.G., Y.-P.W., J.-Y.L., K.S., C.L., Z.-C.J.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Medical Research Center (Z.-J.Z., T.-Y.L., K.S.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui-Fang Wang
- Department of Biochemistry and Molecular Biology, the School of Basic Medicine Sciences, Hebei Medical University, Shijiazhuang, China (H.-F.W., L.N.)
| | - Tian-Yu Lian
- Department of Cardiology (Z.-J.Z., T.-Y.L., Y.-P.Z., X.-Q.X., F.G., Y.-P.W., J.-Y.L., K.S., C.L., Z.-C.J.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Medical Research Center (Z.-J.Z., T.-Y.L., K.S.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu-Ping Zhou
- Department of Cardiology (Z.-J.Z., T.-Y.L., Y.-P.Z., X.-Q.X., F.G., Y.-P.W., J.-Y.L., K.S., C.L., Z.-C.J.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xi-Qi Xu
- Department of Cardiology (Z.-J.Z., T.-Y.L., Y.-P.Z., X.-Q.X., F.G., Y.-P.W., J.-Y.L., K.S., C.L., Z.-C.J.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Guo
- Department of Cardiology (Z.-J.Z., T.-Y.L., Y.-P.Z., X.-Q.X., F.G., Y.-P.W., J.-Y.L., K.S., C.L., Z.-C.J.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yun-Peng Wei
- Department of Cardiology (Z.-J.Z., T.-Y.L., Y.-P.Z., X.-Q.X., F.G., Y.-P.W., J.-Y.L., K.S., C.L., Z.-C.J.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing-Yi Li
- Department of Cardiology (Z.-J.Z., T.-Y.L., Y.-P.Z., X.-Q.X., F.G., Y.-P.W., J.-Y.L., K.S., C.L., Z.-C.J.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kai Sun
- Department of Cardiology (Z.-J.Z., T.-Y.L., Y.-P.Z., X.-Q.X., F.G., Y.-P.W., J.-Y.L., K.S., C.L., Z.-C.J.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Medical Research Center (Z.-J.Z., T.-Y.L., K.S.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Liu
- Department of Cardiology (Z.-J.Z., T.-Y.L., Y.-P.Z., X.-Q.X., F.G., Y.-P.W., J.-Y.L., K.S., C.L., Z.-C.J.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lu-Rong Pan
- Global Health Drug Discovery Institute, Beijing, China (L.-R.P.)
| | - Ming Ren
- Department of Cardiology, Affiliated Hospital of Qinghai University, Xining, China (M.R.)
| | - Lei Nie
- Department of Biochemistry and Molecular Biology, the School of Basic Medicine Sciences, Hebei Medical University, Shijiazhuang, China (H.-F.W., L.N.)
| | - Hai-Long Dai
- Department of Cardiology, Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan'an Affiliated Hospital of Kunming Medical University, China (H.-L.D.)
| | - Zhi-Cheng Jing
- Department of Cardiology (Z.-J.Z., T.-Y.L., Y.-P.Z., X.-Q.X., F.G., Y.-P.W., J.-Y.L., K.S., C.L., Z.-C.J.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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14
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Porcino GN, Bladergroen MR, Dotz V, Nicolardi S, Memarian E, Gardinassi LG, Nery Costa CH, Pacheco de Almeida R, Ferreira de Miranda Santos IK, Wuhrer M. Total serum N-glycans mark visceral leishmaniasis in human infections with Leishmania infantum. iScience 2023; 26:107021. [PMID: 37485378 PMCID: PMC10362369 DOI: 10.1016/j.isci.2023.107021] [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: 02/08/2023] [Revised: 04/07/2023] [Accepted: 05/30/2023] [Indexed: 07/25/2023] Open
Abstract
Visceral leishmaniasis (VL) is a clinical form of leishmaniasis with high mortality rates when not treated. Diagnosis suffers from invasive techniques and sub-optimal sensitivities. The current (affordable) treatment with pentavalent antimony as advised by the WHO is possibly harmful to the patient. There is need for an improved diagnosis to prevent possibly unnecessary treatment. N-glycan analysis may aid in diagnosis. We evaluated the N-glycan profiles from active VL, asymptomatic infections (ASYMP) and controls from non-endemic (NC) and endemic (EC) areas. Active VL has a distinct N-glycome profile that associates with disease severity. Our study suggests that the observed glycan signatures could be a valuable additive to diagnosis and assist in identifying possible markers of disease and understanding the pathogenesis of VL. Further studies are warranted to assess a possible future role of blood glycome analysis in active VL diagnosis and should aim at disease specificity.
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Affiliation(s)
- Gabriane Nascimento Porcino
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Marco René Bladergroen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Viktoria Dotz
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Elham Memarian
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Luiz Gustavo Gardinassi
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia 74605-050, Brazil
| | | | - Roque Pacheco de Almeida
- Departamento de Medicina, Programa de Pós-Graduação em Ciências da Saúde – PPGCS, Universidade Federal de Sergipe, Aracajú 49060-100, Brazil
| | | | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
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15
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Mayboroda OA, Lageveen-Kammeijer GSM, Wuhrer M, Dolhain RJEM. An Integrated Glycosylation Signature of Rheumatoid Arthritis. Biomolecules 2023; 13:1106. [PMID: 37509142 PMCID: PMC10377307 DOI: 10.3390/biom13071106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Rheumatoid arthritis (RA) Is a highly prevalent autoimmune disease that affects the joints but also various other organs. The disease is characterized by autoantibodies that are often already observed pre-disease. Since the 1980s, it has been known that antibody glycosylation is different in RA as compared to control individuals. While the literature on glycosylation changes in RA is dominated by reports on serum or plasma immunoglobulin G (IgG), our recent studies have indicated that the glycosylation changes observed for immunoglobulin A (IgA) and total serum N-glycome (TSNG) may be similarly prominent, and useful in differentiating between the RA patients and controls, or as a proxy of the disease activity. In this study, we integrated and compared the RA glycosylation signatures of IgG, IgA and TSNG, all determined in the pregnancy-induced amelioration of rheumatoid arthritis (PARA) cohort. We assessed the association of the altered glycosylation patterns with the disease, autoantibody positivity and disease activity. Our analyses indicated a common, composite glycosylation signature of RA that was independent of the autoantibody status.
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Affiliation(s)
- Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Guinevere S M Lageveen-Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Analytical Biochemistry, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Radboud J E M Dolhain
- Department of Rheumatology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
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16
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Sharapov SZ, Timoshchuk AN, Aulchenko YS. Genetic control of N-glycosylation of human blood plasma proteins. Vavilovskii Zhurnal Genet Selektsii 2023; 27:224-239. [PMID: 37293449 PMCID: PMC10244589 DOI: 10.18699/vjgb-23-29] [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: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/23/2022] [Indexed: 06/10/2023] Open
Abstract
Glycosylation is an important protein modification, which influences the physical and chemical properties as well as biological function of these proteins. Large-scale population studies have shown that the levels of various plasma protein N-glycans are associated with many multifactorial human diseases. Observed associations between protein glycosylation levels and human diseases have led to the conclusion that N-glycans can be considered a potential source of biomarkers and therapeutic targets. Although biochemical pathways of glycosylation are well studied, the understanding of the mechanisms underlying general and tissue-specific regulation of these biochemical reactions in vivo is limited. This complicates both the interpretation of the observed associations between protein glycosylation levels and human diseases, and the development of glycan-based biomarkers and therapeutics. By the beginning of the 2010s, high-throughput methods of N-glycome profiling had become available, allowing research into the genetic control of N-glycosylation using quantitative genetics methods, including genome-wide association studies (GWAS). Application of these methods has made it possible to find previously unknown regulators of N-glycosylation and expanded the understanding of the role of N-glycans in the control of multifactorial diseases and human complex traits. The present review considers the current knowledge of the genetic control of variability in the levels of N-glycosylation of plasma proteins in human populations. It briefly describes the most popular physical-chemical methods of N-glycome profiling and the databases that contain genes involved in the biosynthesis of N-glycans. It also reviews the results of studies of environmental and genetic factors contributing to the variability of N-glycans as well as the mapping results of the genomic loci of N-glycans by GWAS. The results of functional in vitro and in silico studies are described. The review summarizes the current progress in human glycogenomics and suggests possible directions for further research.
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Affiliation(s)
- S Zh Sharapov
- MSU Institute for Artificial Intelligence, Lomonosov Moscow State University, Moscow, Russia
| | - A N Timoshchuk
- MSU Institute for Artificial Intelligence, Lomonosov Moscow State University, Moscow, Russia
| | - Y S Aulchenko
- MSU Institute for Artificial Intelligence, Lomonosov Moscow State University, Moscow, Russia Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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17
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Zedan H, Morimura K, Elguoshy A, Yamamoto T, Natsuka S. Microheterogeneity and Individual Differences of Human Urinary N-Glycome under Normal Physiological Conditions. Biomolecules 2023; 13:biom13050756. [PMID: 37238626 DOI: 10.3390/biom13050756] [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: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Urine is considered an outstanding biological fluid for biomarker discovery, reflecting both systemic and urogenital physiology. However, analyzing the N-glycome in urine in detail has been challenging due to the low abundance of glycans attached to glycoproteins compared to free oligosaccharides. Therefore, this study aims to thoroughly analyze urinary N-glycome using LC-MS/MS. The N-glycans were released using hydrazine and labeled with 2-aminopyridine (PA), followed by anion-exchange fractionation before LC-MS/MS analysis. A total of 109 N-glycans were identified and quantified, of which 58 were identified and quantified repeatedly in at least 80% of samples and accounted for approximately 85% of the total urinary glycome signal. Interestingly, a comparison between urine and serum N-glycome revealed that approximately 50% of the urinary glycome could originate from the kidney and urinary tract, where they were exclusively identified in urine, while the remaining 50% were common in both. Additionally, a correlation was found between age/sex and the relative abundances of urinary N-glycome, with more age-related changes observed in women than men. The results of this study provide a reference for human urine N-glycome profiling and structural annotations.
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Affiliation(s)
- Hend Zedan
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Kousuke Morimura
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Amr Elguoshy
- Biofluid Biomarker Center, Niigata University, Niigata 950-2181, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Niigata University, Niigata 950-2181, Japan
| | - Shunji Natsuka
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
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18
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Plavša B, Szavits-Nossan J, Blivajs A, Rapčan B, Radovani B, Šesto I, Štambuk K, Mustapić V, Đerek L, Rudan D, Lauc G, Gudelj I. The N-Glycosylation of Total Plasma Proteins and IgG in Atrial Fibrillation. Biomolecules 2023; 13:biom13040605. [PMID: 37189353 DOI: 10.3390/biom13040605] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/13/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Atrial fibrillation is a disease with a complex pathophysiology, whose occurrence and persistence are caused not only by aberrant electrical signaling in the heart, but by the development of a susceptible heart substrate. These changes, such as the accumulation of adipose tissue and interstitial fibrosis, are characterized by the presence of inflammation. N-glycans have shown great promise as biomarkers in different diseases, specifically those involving inflammatory changes. To assess the changes in the N-glycosylation of the plasma proteins and IgG in atrial fibrillation, we analyzed the N-glycosylation of 172 patients with atrial fibrillation, before and six months after a pulmonary vein isolation procedure, with 54 cardiovascularly healthy controls. An analysis was performed using ultra-high-performance liquid chromatography. We found one oligomannose N-glycan structure from the plasma N-glycome and six IgG N-glycans, mainly revolving around the presence of bisecting N-acetylglucosamine, that were significantly different between the case and control groups. In addition, four plasma N-glycans, mostly oligomannose structures and a derived trait that was related to them, were found to be different in the patients who experienced an atrial fibrillation recurrence during the six-month follow-up. IgG N-glycosylation was extensively associated with the CHA2DS2-VASc score, confirming its previously reported associations with the conditions that make up the score. This is the first study looking at the N-glycosylation patterns in atrial fibrillation and warrants further investigation into the prospect of glycans as biomarkers for atrial fibrillation.
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19
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Kozuch AJ, Petukhov PA, Fagyas M, Popova IA, Lindeblad MO, Bobkov AP, Kamalov AA, Toth A, Dudek SM, Danilov SM. Urinary ACE Phenotyping as a Research and Diagnostic Tool: Identification of Sex-Dependent ACE Immunoreactivity. Biomedicines 2023; 11:953. [PMID: 36979933 PMCID: PMC10045976 DOI: 10.3390/biomedicines11030953] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Angiotensin-converting enzyme (ACE) is highly expressed in renal proximal tubules, but ACE activity/levels in the urine are at least 100-fold lower than in the blood. Decreased proximal tubular ACE has been associated with renal tubular damage in both animal models and clinical studies. Because ACE is shed into urine primarily from proximal tubule epithelial cells, its urinary ACE measurement may be useful as an index of tubular damage. OBJECTIVE AND METHODOLOGY We applied our novel approach-ACE phenotyping-to characterize urinary ACE in volunteer subjects. ACE phenotyping includes (1) determination of ACE activity using two substrates (ZPHL and HHL); (2) calculation of the ratio of hydrolysis of the two substrates (ZPHL/HHL ratio); (3) quantification of ACE immunoreactive protein levels; and (4) fine mapping of local ACE conformation with mAbs to ACE. PRINCIPAL FINDINGS In normal volunteers, urinary ACE activity was 140-fold less than in corresponding plasma/serum samples and did not differ between males and females. However, urinary ACE immunoreactivity (normalized binding of 25 mAbs to different epitopes) was strongly sex-dependent for the several mAbs tested, an observation likely explained by differences in tissue ACE glycosylation/sialylation between males and females. Urinary ACE phenotyping also allowed the identification of ACE outliers. In addition, daily variability of urinary ACE has potential utility as a feedback marker for dieting individuals pursuing weight loss. CONCLUSIONS/SIGNIFICANCE Urinary ACE phenotyping is a promising new approach with potential clinical significance to advance precision medicine screening techniques.
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Affiliation(s)
- Alexander J. Kozuch
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, CSB 915, MC 719, 840 S. Wood Ave., Chicago, IL 60612, USA
| | - Pavel A. Petukhov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
| | - Miklos Fagyas
- Division of Clinical Physiology, Department of Cardiology, University of Debrecen, Nagyerdei krt. 94, 4032 Debrecen, Hungary
| | - Isolda A. Popova
- Toxicology Research Laboratory, University of Illinois at Chicago, 840 S. Wood Ave., Chicago, IL 60612, USA
| | - Matthew O. Lindeblad
- Toxicology Research Laboratory, University of Illinois at Chicago, 840 S. Wood Ave., Chicago, IL 60612, USA
| | | | | | - Attila Toth
- Division of Clinical Physiology, Department of Cardiology, University of Debrecen, Nagyerdei krt. 94, 4032 Debrecen, Hungary
| | - Steven M. Dudek
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, CSB 915, MC 719, 840 S. Wood Ave., Chicago, IL 60612, USA
| | - Sergei M. Danilov
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, CSB 915, MC 719, 840 S. Wood Ave., Chicago, IL 60612, USA
- Medical Center, Moscow University, Moscow 119435, Russia
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20
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McDowell CT, Lu X, Mehta AS, Angel PM, Drake RR. Applications and continued evolution of glycan imaging mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:674-705. [PMID: 34392557 PMCID: PMC8946722 DOI: 10.1002/mas.21725] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/16/2021] [Accepted: 08/03/2021] [Indexed: 05/03/2023]
Abstract
Glycosylation is an important posttranslational modifier of proteins and lipid conjugates critical for the stability and function of these macromolecules. Particularly important are N-linked glycans attached to asparagine residues in proteins. N-glycans have well-defined roles in protein folding, cellular trafficking and signal transduction, and alterations to them are implicated in a variety of diseases. However, the non-template driven biosynthesis of these N-glycans leads to significant structural diversity, making it challenging to identify the most biologically and clinically relevant species using conventional analyses. Advances in mass spectrometry instrumentation and data acquisition, as well as in enzymatic and chemical sample preparation strategies, have positioned mass spectrometry approaches as powerful analytical tools for the characterization of glycosylation in health and disease. Imaging mass spectrometry expands upon these strategies by capturing the spatial component of a glycan's distribution in-situ, lending additional insight into the organization and function of these molecules. Herein we review the ongoing evolution of glycan imaging mass spectrometry beginning with widely adopted tissue imaging approaches and expanding to other matrices and sample types with potential research and clinical implications. Adaptations of these techniques, along with their applications to various states of disease, are discussed. Collectively, glycan imaging mass spectrometry analyses broaden our understanding of the biological and clinical relevance of N-glycosylation to human disease.
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Affiliation(s)
- Colin T. McDowell
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Xiaowei Lu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
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21
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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22
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Integrating age, BMI, and serum N-glycans detected by MALDI mass spectrometry to classify suspicious mammogram findings as benign lesions or breast cancer. Sci Rep 2022; 12:20801. [PMID: 36460712 PMCID: PMC9718781 DOI: 10.1038/s41598-022-25401-0] [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: 09/09/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
While mammograms are the standard tool for breast cancer screening, there remains challenges for mammography to effectively distinguish benign lesions from breast cancers, leading to many unnecessary biopsy procedures. A blood-based biomarker could provide a minimally invasive supplemental assay to increase the specificity of breast cancer screening. Serum N-glycosylation alterations have associations with many cancers and several of the clinical characteristics of breast cancer. The current study utilized a high-throughput mass spectrometry workflow to identify serum N-glycans with differences in intensities between patients that had a benign lesion from patients with breast cancer. The overall N-glycan profiles of the two patient groups had no differences, but there were several individual N-glycans with significant differences in intensities between patients with benign lesions and ductal carcinoma in situ (DCIS). Many N-glycans had strong associations with age and/or body mass index, but there were several of these associations that differed between the patients with benign lesions and breast cancer. Accordingly, the samples were stratified by the patient's age and body mass index, and N-glycans with significant differences between these subsets were identified. For women aged 50-74 with a body mass index of 18.5-24.9, a model including the intensities of two N-glycans, 1850.666 m/z and 2163.743 m/z, age, and BMI were able to clearly distinguish the breast cancer patients from the patients with benign lesions with an AUROC of 0.899 and an optimal cutoff with 82% sensitivity and 84% specificity. This study indicates that serum N-glycan profiling is a promising approach for providing clarity for breast cancer screening, especially within the subset of healthy weight women in the age group recommended for mammograms.
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23
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Miller ID, Kohlhagen MC, Ladwig PM, Dasari S, Kumar S, Dispenzieri A, Willrich MAV, Murray DL. Characterizing M-protein light chain glycosylation via mass spectrometry. Clin Biochem 2022; 109-110:11-16. [PMID: 36113628 DOI: 10.1016/j.clinbiochem.2022.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/10/2022] [Accepted: 09/08/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Monoclonal gammopathy of undetermined significance (MGUS) patients with M-proteins containing n-glycosylated light chains (GLC) have an increased risk for progression to symptomatic plasma cell disorders (PCD). Large-scale research involving the determination of glycan specific moieties is understudied due to the lack of clinically viable methods. This report documents a proof-of-concept glycan characterization method for patients with M-protein GLCs. DESIGN AND METHODS Twenty-three previously characterized MGUS patients with glycosylated light chains identified by MASS-FIX were used for this study. Glycosylated light chains were enriched from patient serum using light chain (LC) specific Sepharose nanobody beads (NB), followed by glycan digestion via PNGase F. Glycan moieties were derivatized on-target using Girard's reagent T for MALDI-TOF analysis and confirmed with top-down GLC LC-ESI-Q-TOF-MS analysis. RESULTS Intact GLC LC-ESI-Q-TOF-MS and cleaved glycan MALDI-TOF MS analysis had 100% agreement for the top three intensity glycans between spectra and 88 percent agreement for all reported glycan moieties. GLC moieties among patients were similar with fucosylation being the only notable difference. Additionally, doubly glycosylated light chains were observed in two patients. CONCLUSIONS The MALDI-TOF method provides the tools to characterize and evaluate GLCs in a clinical setting as it is adaptable to our clinical MASS-Fix assay, relatively cheap, and accurate in glycan moiety assignments as confirmed by top-down GLC LC-ESI-Q-TOF-MS.
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Affiliation(s)
- Ira D Miller
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mindy C Kohlhagen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Paula M Ladwig
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Surendra Dasari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Shaji Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Angela Dispenzieri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - David L Murray
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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24
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Volkhina IV, Butolin EG. Clinical and Diagnostic Significance of Sialic Acids Determination in Biological Material. BIOCHEMISTRY (MOSCOW) SUPPLEMENT. SERIES B, BIOMEDICAL CHEMISTRY 2022; 16:165-174. [PMID: 35990315 PMCID: PMC9377294 DOI: 10.1134/s199075082203012x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/15/2023]
Abstract
Sialic acids (SA) are neuraminic acid derivatives, located at the terminal position in the chains of monosaccharide residues of various glycoconjugates. SA play a dual role: they either mask recognition sites, or, on the contrary, represent biological targets that can be recognized by receptor proteins and serve as ligands. The desialylation/sialylation processes can be considered as a dynamic modification regulated by sialyltransferases and sialidases in response to external or internal stimuli. This review describes the structural and functional diversity and the potential use of SA fractions as biomarkers for various pathological conditions. Almost any extreme impact on the body and inflammatory processes are accompanied by an increase in the level of both total and free SA in the blood and tissues. Possible reasons for the increase of sialoglycoconjugate metabolism indicators in biological material include: (i) activation of the hepatocyte synthesis and secretion of various acute-phase proteins, many of which are sialoglycoproteins, (ii) impaired membrane integrity and destruction of body cells, (iii) high activity of sialidases (neurominidases) and sialyltransferases. Most acute and chronic liver diseases are characterized by the decrease in the total level of SA in the blood serum (because many plasma proteins are synthesized and glycosylated in hepatocytes). Aberrant sialylation results in changes of sialoglycoconjugate structure, its ability to perform biological functions and sialoglycoconjugate half-life. Glycosylation is the most common post-translational modification of proteins in the virus, which not only promotes the formation of specific conformation of viral proteins, but also modulates their interaction with receptors and affects host cell recognition, viral replication and infectivity. Serum total SA concentration increases in some benign and inflammatory conditions, which indicates a lack of specificity and limits their use for early detection and screening of neoplastic diseases. Clinical and diagnostic value of determining the sialoglycoconjugate metabolic indicators, including changes in the content of both SA fractions and specific proteins in various biological fluids and tissues, consists in establishing the causes and mechanisms of biochemical changes in the body in certain diseases. In combination with the measurement of existing markers, they can be used to improve diagnosis, staging and monitoring of therapeutic response in some pathological conditions where the need for specificity is less than for specific diagnostics.
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Affiliation(s)
- I. V. Volkhina
- Saint Petersburg State Pediatric Medical University, ul. Litovskaya 2, 194100 St.Petersburg, Russia
| | - E. G. Butolin
- Izhevsk State Medical Academy, ul. Kommunarov 201, 426034 Izhevsk, Russia
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25
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Vibhute AM, Tanaka HN, Mishra SK, Osuka RF, Nagae M, Yonekawa C, Korekane H, Doerksen RJ, Ando H, Kizuka Y. Structure-based design of UDP-GlcNAc analogs as candidate GnT-V inhibitors. Biochim Biophys Acta Gen Subj 2022; 1866:130118. [PMID: 35248671 PMCID: PMC9947920 DOI: 10.1016/j.bbagen.2022.130118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 02/02/2023]
Abstract
BACKGROUND N-Glycan branching regulates various functions of glycoproteins. N-Acetylglucosaminyltransferase V (GnT-V) is a GlcNAc transferase that acts on N-glycans and the GnT-V-producing branch is highly related to cancer progression. This indicates that specific GnT-V inhibitors may be drug candidates for cancer treatment. To design novel GnT-V inhibitors, we focused on the unique and weak recognition of the donor substrate UDP-GlcNAc by GnT-V. On the basis of the catalytic pocket structure, we hypothesized that UDP-GlcNAc analogs with increasing hydrophobicity may be GnT-V inhibitors. METHODS We chemically synthesized 10 UDP-GlcNAc analogs in which one or two phosphate groups were replaced with hydrophobic groups. To test these compounds, we set up an HPLC-based enzyme assay system for all N-glycan-branching GlcNAc transferases in which GnT-I-V activity was measured using purified truncated enzymes. Using this system, we assessed the inhibitory effects of the synthesized compounds on GnT-V and their specificity. RESULTS Several UDP-GlcNAc analogs inhibited GnT-V activity, although the inhibition potency was modest. Compared with other GnTs, these compounds showed a preference for GnT-V, which suggested that GnT-V was relatively tolerant of hydrophobicity in the donor substrate. Docking models of the inhibitory compounds with GnT-V suggested the mechanisms of how these compounds interacted with GnT-V and inhibited its action. CONCLUSIONS Chemical modification of the donor substrate may be a promising strategy to develop selective inhibitors of GnT-V. GENERAL SIGNIFICANCE Our findings provide new insights into the design of GnT inhibitors and how GnTs recognize the donor substrate.
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Affiliation(s)
- Amol M Vibhute
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Hide-Nori Tanaka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan.
| | - Sushil K Mishra
- Glycoscience Center of Research Excellence, Department of BioMolecular Sciences, University of Mississippi, MS 38677, USA
| | - Reina F Osuka
- Graduate School of Natural Science and Technology, Gifu University, Gifu 501-1193, Japan
| | - Masamichi Nagae
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita 565-0871, Japan
| | - Chizuko Yonekawa
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Hiroaki Korekane
- Disease Glycomics Team, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, Wako 351-0198, Japan
| | - Robert J Doerksen
- Glycoscience Center of Research Excellence, Department of BioMolecular Sciences, University of Mississippi, MS 38677, USA
| | - Hiromune Ando
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Yasuhiko Kizuka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan.
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26
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Petrov VA, Sharapov SZ, Shagam L, Nostaeva AV, Pezer M, Li D, Hanić M, McGovern D, Louis E, Rahmouni S, Lauc G, Georges M, Aulchenko YS. Association Between Human Gut Microbiome and N-Glycan Composition of Total Plasma Proteome. Front Microbiol 2022; 13:811922. [PMID: 35572712 PMCID: PMC9100934 DOI: 10.3389/fmicb.2022.811922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Being one of the most dynamic entities in the human body, glycosylation of proteins fine-tunes the activity of the organismal machinery, including the immune system, and mediates the interaction with the human microbial consortium, typically represented by the gut microbiome. Using data from 194 healthy individuals, we conducted an associational study to uncover potential relations between the gut microbiome and the blood plasma N-glycome, including N-glycome of immunoglobulin G. While lacking strong linkages on the multivariate level, we were able to identify associations between alpha and beta microbiome diversity and the blood plasma N-glycome profile. Moreover, for two bacterial genera, namely, Bilophila and Clostridium innocuum, significant associations with specific glycans were also shown. The study’s results suggest a non-trivial, possibly weak link between the total plasma N-glycome and the gut microbiome, predominantly involving glycans related to the immune system proteins, including immunoglobulin G. Further studies of glycans linked to microbiome-related proteins in well-selected patient groups are required to conclusively establish specific associations.
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Affiliation(s)
- Vyacheslav A. Petrov
- Unit of Animal Genomics, Grappe Interdisciplinaire de Génoprotéomique Appliquée-Institute, University of Liège, Liège, Belgium
- Central Research Laboratory, Ministry of Healthcare of Russian Federation, Federal State Budget Educational Institution of Higher Education, Siberian State Medical University, Tomsk, Russia
| | - Sodbo Zh. Sharapov
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Lev Shagam
- Central Research Laboratory, Ministry of Healthcare of Russian Federation, Federal State Budget Educational Institution of Higher Education, Siberian State Medical University, Tomsk, Russia
| | - Arina V. Nostaeva
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University, Novosibirsk, Russia
| | | | - Dalin Li
- Cedars-Sinai Medical Center, The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA, United States
| | - Maja Hanić
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Dermot McGovern
- Cedars-Sinai Medical Center, The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA, United States
| | - Edouard Louis
- Laboratory of Translational Gastroenterology, Grappe Interdisciplinaire de Génoprotéomique Appliquée-Institute, University of Liège, Liège, Belgium
| | - Souad Rahmouni
- Central Research Laboratory, Ministry of Healthcare of Russian Federation, Federal State Budget Educational Institution of Higher Education, Siberian State Medical University, Tomsk, Russia
| | - Gordan Lauc
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Michel Georges
- Central Research Laboratory, Ministry of Healthcare of Russian Federation, Federal State Budget Educational Institution of Higher Education, Siberian State Medical University, Tomsk, Russia
| | - Yurii S. Aulchenko
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk, Russia
- *Correspondence: Yurii S. Aulchenko,
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27
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Trinh D, Gardner RA, Franciosi AN, McCarthy C, Keane MP, Soliman MG, O’Donnell JS, Meleady P, Spencer DIR, Monopoli MP. Nanoparticle Biomolecular Corona-Based Enrichment of Plasma Glycoproteins for N-Glycan Profiling and Application in Biomarker Discovery. ACS NANO 2022; 16:5463-5475. [PMID: 35341249 PMCID: PMC9047655 DOI: 10.1021/acsnano.1c09564] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/10/2022] [Indexed: 05/28/2023]
Abstract
Biomolecular corona formation has emerged as a recurring and important phenomenon in nanomedicine that has been investigated for potential applications in disease diagnosis. In this study, we have combined the "personalized protein corona" with the N-glycosylation profiling that has recently gained considerable interest in human plasma biomarker discovery as a powerful early warning diagnostic and patient stratification tool. We envisioned that the protein corona formation could be exploited as an enrichment step that is critically important in both proteomic and proteoglycomic workflows. By using silica nanoparticles, plasma fibrinogen was enriched to a level in which its proteomic and glycomic "fingerprints" could be traced with confidence. Despite being a more simplified glycan profile compared to full plasma, the corona glycan profile revealed a fibrinogen-derived glycan peak that was found to potentially distinguish lung cancer patients from controls in a pilot study.
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Affiliation(s)
- Duong
N. Trinh
- Department
of Chemistry, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Richard A. Gardner
- Ludger
Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14 3EB, United Kingdom
| | - Alessandro N. Franciosi
- UBC
Faculty of Medicine, Department of Respiratory Medicine, University of British Columbia, Vancouver, British Columbia V6Z 1Y6, Canada
| | - Cormac McCarthy
- Department
of Respiratory Medicine, St. Vincent’s
University Hospital, Dublin 4, Ireland
- School
of Medicine, University College Dublin, Dublin 4, Ireland
| | - Michael P. Keane
- Department
of Respiratory Medicine, St. Vincent’s
University Hospital, Dublin 4, Ireland
- School
of Medicine, University College Dublin, Dublin 4, Ireland
| | - Mahmoud G. Soliman
- Department
of Chemistry, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin 2, Ireland
- Physics Department,
Faculty of Science, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - James S. O’Donnell
- Irish
Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences,
Royal College of Surgeons in Ireland, University
of Medicine and Health Sciences, Dublin 2, Ireland
| | - Paula Meleady
- School
of
Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Daniel I. R. Spencer
- Ludger
Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14 3EB, United Kingdom
| | - Marco P. Monopoli
- Department
of Chemistry, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin 2, Ireland
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28
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Ivanov DG, Yang Y, Pawlowski JW, Carrick IJ, Kaltashov IA. Rapid Evaluation of the Extent of Haptoglobin Glycosylation Using Orthogonal Intact-Mass MS Approaches and Multivariate Analysis. Anal Chem 2022; 94:5140-5148. [PMID: 35285615 PMCID: PMC11232314 DOI: 10.1021/acs.analchem.1c05585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Intact-mass measurements are becoming increasingly popular in mass spectrometry (MS) based protein characterization, as they allow the entire complement of proteoforms to be evaluated within a relatively short time. However, applications of this approach are currently limited to systems exhibiting relatively modest degrees of structural diversity, as the high extent of heterogeneity frequently prevents straightforward MS measurements. Incorporation of limited charge reduction into electrospray ionization (ESI) MS is an elegant way to obtain meaningful information on most heterogeneous systems, yielding not only the average mass of the protein but also the mass range populated by the entire complement of proteoforms. Application of this approach to characterization of two different phenotypes of haptoglobin (1-1 and 2-1) provides evidence of a significant difference in their extent of glycosylation (with the glycan load of phenotype 2-1 being notably lighter) despite a significant overlap of their ionic signals. More detailed characterization of their glycosylation patterns is enabled by the recently introduced technique of cross-path reactive chromatography (XP-RC) with online MS detection, which combines chromatographic separation with in-line reduction of disulfide bonds to generate metastable haptoglobin subunits. Application of XP-RC to both haptoglobin phenotypes confirms that no modifications are present within their light chains and provides a wealth of information on glycosylation patterns of the heavy chains. N-Glycosylation patterns of both haptoglobin phenotypes were found to be consistent with bi- and triantennary structures of complex type that exhibit significant level of fucosylation and sialylation. However, multivariate analysis of haptoglobin 1-1 reveals higher number of the triantennary structures, in comparison to haptoglobin 2-1, as well as a higher extent of fucosylation. The glycosylation patterns deduced from the XP-RC/MS measurements are in agreement with the conclusions of the intact-mass analysis supplemented by limited charge reduction, suggesting that the latter technique can be employed in situations when fast assessment of protein heterogeneity is needed (e.g., process analytical technology applications).
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Affiliation(s)
- Daniil G Ivanov
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Yang Yang
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Jake W Pawlowski
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Ian J Carrick
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
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29
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Dumić J, Cvetko A, Abramović I, Šupraha Goreta S, Perović A, Njire Bratičević M, Kifer D, Sinčić N, Gornik O, Žarak M. Changes in Specific Biomarkers Indicate Cardiac Adaptive and Anti-inflammatory Response of Repeated Recreational SCUBA Diving. Front Cardiovasc Med 2022; 9:855682. [PMID: 35360010 PMCID: PMC8964121 DOI: 10.3389/fcvm.2022.855682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveRecreational SCUBA (rSCUBA) diving has become a highly popular and widespread sport. Yet, information on molecular events underlying (patho)physiological events that follow exposure to the specific environmental conditions (hyperbaric conditions, coldness, immersion, and elevated breathing pressure), in which rSCUBA diving is performed, remain largely unknown. Our previous study suggested that repeated rSCUBA diving triggers an adaptive response of cardiovascular and immune system. To elucidate further molecular events underlying cardiac and immune system adaptation and to exclude possible adverse effects we measured blood levels of specific cardiac and inflammation markers.MethodsThis longitudinal intervention study included fourteen recreational divers who performed five dives, one per week, on the depth 20–30 m that lasted 30 min, after the non-dive period of 5 months. Blood samples were taken immediately before and after the first, third, and fifth dives. Copeptin, immunoglobulins A, G and M, complement components C3 and C4, and differential blood count parameters, including neutrophil-to-lymphocyte ratio (NLR) were determined using standard laboratory methods. Cell-free DNA was measured by qPCR analysis and N-glycans released from IgG and total plasma proteins (TPP), were analyzed by hydrophilic interaction ultra-performance liquid chromatography.ResultsCopeptin level increased after the first dive but decreased after the third and fifth dive. Increases in immunoglobulins level after every dive and during whole studied period were observed, but no changes in C3, C4, and cfDNA level were detected. NLR increased only after the first dive. IgG and TPP N-glycosylation alterations toward anti-inflammatory status over whole studied period were manifested as an increase in monogalyctosylated and core-fucosylated IgG N-glycans and decrease in agalactosylated TPP N-glycans.ConclusionrSCUBA diving practiced on a regular basis promotes anti-inflammatory status thus contributing cardioprotection and conferring multiple health benefits.
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Affiliation(s)
- Jerka Dumić
- Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Ana Cvetko
- Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Irena Abramović
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Sandra Šupraha Goreta
- Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Antonija Perović
- Department of Laboratory Diagnostics, Dubrovnik General Hospital, Dubrovnik, Croatia
| | | | - Domagoj Kifer
- Department of Biophysics, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Nino Sinčić
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Olga Gornik
- Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Marko Žarak
- Clinical Department of Laboratory Diagnostics, Dubrava University Hospital, Zagreb, Croatia
- *Correspondence: Marko Žarak,
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30
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Volkhina IV, Butolin EG. [Clinical and diagnostic significance of sialic acids determination in biological material]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:7-17. [PMID: 35221292 DOI: 10.18097/pbmc20226801007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sialic acids (SA) are derivatives of neuraminic acid; they are located at the terminal position in the chains of monosaccharide residues of various glycoconjugates. SA play a dual role, they either mask recognition sites, or, on the contrary, represent biological targets that can be recognized by receptor proteins and serve as ligands. The desialylation/sialylation processes can be viewed as a dynamic modification regulated by sialyltransferases and sialidases in response to external or internal stimuli. This review describes the structural and functional diversity and the potential use of SA fractions as biomarkers for various pathological conditions. Almost any extreme effects on the body and inflammatory processes lead to an increase in the level of both total and free SA in the blood and tissues. Possible reasons for the increase of sialoglycoconjugate metabolism indicators in biological material include activation of the hepatocyte synthesis and secretion of various acute-phase proteins, many of which are sialoglycoproteins, violation of the membrane integrity and destruction of body cells, and also high activity of sialidases (neurominidases) and sialyltransferases. Most acute and chronic liver diseases are characterized by the decrease in the total level of SA in the blood serum (because many plasma proteins are synthesized and glycosylated in hepatocytes). Aberrant sialylation results in changes of sialoglycoconjugate structure, its ability to perform biological functions and half-life. Glycosylation is the most common post-translational modification of proteins in the virus, which not only promotes the formation of specific conformation of viral proteins, but also modulates their interaction with receptors and affects host cell recognition, viral replication and infectivity. Serum total SA concentration increases in some benign and inflammatory conditions, which indicates a lack of specificity and limits their use for early detection and screening of neoplastic diseases. Nevertheless, determining blood SA level and measuring concentration of existing biomarkers can be used to improve diagnostic indicators, to stage and monitor therapeutic response in some types of cancer, when the need for specificity is less than for diagnosis. Clinical and diagnostic value of determining the sialoglycoconjugate metabolic indicators, including changes in the content of both SA fractions and specific proteins in various biological fluids and tissues, lies in establishing the causes and mechanisms of biochemical changes in the body in certain diseases.
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Affiliation(s)
- I V Volkhina
- Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - E G Butolin
- Izhevsk State Medical Academy, Izhevsk, Russia
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31
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Understanding the structure and composition of recalcitrant oligosaccharides in hydrolysate using high-throughput biotin-based glycome profiling and mass spectrometry. Sci Rep 2022; 12:2521. [PMID: 35169269 PMCID: PMC8847591 DOI: 10.1038/s41598-022-06530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 01/24/2022] [Indexed: 11/18/2022] Open
Abstract
Novel Immunological and Mass Spectrometry Methods for Comprehensive Analysis of Recalcitrant Oligosaccharides in AFEX Pretreated Corn Stover. Lignocellulosic biomass is a sustainable alternative to fossil fuel and is extensively used for developing bio-based technologies to produce products such as food, feed, fuel, and chemicals. The key to these technologies is to develop cost competitive processes to convert complex carbohydrates present in plant cell wall to simple sugars such as glucose, xylose, and arabinose. Since lignocellulosic biomass is highly recalcitrant, it must undergo a combination of thermochemical treatment such as Ammonia Fiber Expansion (AFEX), dilute acid (DA), Ionic Liquid (IL) and biological treatment such as enzyme hydrolysis and microbial fermentation to produce desired products. However, when using commercial fungal enzymes during hydrolysis, only 75–85% of the soluble sugars generated are monomeric sugars, while the remaining 15–25% are soluble recalcitrant oligosaccharides that cannot be easily utilized by microorganisms. Previously, we successfully separated and purified the soluble recalcitrant oligosaccharides using a combination of charcoal and celite-based separation followed by size exclusion chromatography and studies their inhibitory properties on enzymes. We discovered that the oligosaccharides with higher degree of polymerization (DP) containing methylated uronic acid substitutions were more recalcitrant towards commercial enzyme mixtures than lower DP and neutral oligosaccharides. Here, we report the use of several complementary techniques that include glycome profiling using plant biomass glycan specific monoclonal antibodies (mAbs) to characterize sugar linkages in plant cell walls and enzymatic hydrolysate, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) using structurally-informative diagnostic peaks offered by negative ion post-secondary decay spectra, gas chromatography followed by mass spectrometry (GC–MS) to characterize oligosaccharide sugar linkages with and without derivatization. Since oligosaccharides (DP 4–20) are small, it is challenging to mobilize these molecules for mAbs binding and characterization. To overcome this problem, we have applied a new biotin-coupling based oligosaccharide immobilization method that successfully tagged most of the low DP soluble oligosaccharides on to a micro-plate surface followed by specific linkage analysis using mAbs in a high-throughput system. This new approach will help develop more advanced versions of future high throughput glycome profiling methods that can be used to separate and characterize oligosaccharides present in biomarkers for diagnostic applications.
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32
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Bertok T, Bertokova A, Jane E, Hires M, Aguedo J, Potocarova M, Lukac L, Vikartovska A, Kasak P, Borsig L, Tkac J. Identification of Whole-Serum Glycobiomarkers for Colorectal Carcinoma Using Reverse-Phase Lectin Microarray. Front Oncol 2021; 11:735338. [PMID: 34956866 PMCID: PMC8695905 DOI: 10.3389/fonc.2021.735338] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/02/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common types of cancer among men and women worldwide. Efforts are currently underway to find novel and more cancer-specific biomarkers that could be detected in a non-invasive way. The analysis of aberrant glycosylation of serum glycoproteins is a way to discover novel diagnostic and prognostic CRC biomarkers. The present study investigated a whole-serum glycome with a panel of 16 different lectins in search for age-independent and CRC-specific glycomarkers using receiver operating characteristic (ROC) curve analyses and glycan heat matrices. Glycosylation changes present in the whole serum were identified, which could lead to the discovery of novel biomarkers for CRC diagnostics. In particular, the change in the bisecting glycans (recognized by Phaseolus vulgaris erythroagglutinin) had the highest discrimination potential for CRC diagnostics in combination with human L selectin providing area under the ROC curve (AUC) of 0.989 (95% CI 0.950-1.000), specificity of 1.000, sensitivity of 0.900, and accuracy of 0.960. We also implemented novel tools for identification of lectins with strong discrimination power.
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Affiliation(s)
- Tomas Bertok
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Aniko Bertokova
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Eduard Jane
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Michal Hires
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Juvissan Aguedo
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Ludovit Lukac
- University Hospital Bratislava, Bratislava, Slovakia
| | - Alica Vikartovska
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Kasak
- Center for Advanced Materials, Qatar University, Doha, Qatar
| | - Lubor Borsig
- Department of Physiology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center, Zurich, Switzerland
| | - Jan Tkac
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
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Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, Liquet B, Liu M, Mechref Y, Meng B, Neelamegham S, Nguyen-Khuong T, Nilsson J, Pap A, Park GW, Parker BL, Pegg CL, Penninger JM, Phung TK, Pioch M, Rapp E, Sakalli E, Sanda M, Schulz BL, Scott NE, Sofronov G, Stadlmann J, Vakhrushev SY, Woo CM, Wu HY, Yang P, Ying W, Zhang H, Zhang Y, Zhao J, Zaia J, Haslam SM, Palmisano G, Yoo JS, Larson G, Khoo KH, Medzihradszky KF, Kolarich D, Packer NH, Thaysen-Andersen M. Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat Methods 2021; 18:1304-1316. [PMID: 34725484 DOI: 10.1101/2021.03.14.435332] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/22/2021] [Indexed: 05/18/2023]
Abstract
Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics.
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Affiliation(s)
- Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Anastasia Chernykh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
| | | | - Weiqian Cao
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Robert J Chalkley
- UCSF, School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco, CA, USA
| | - Kai Cheng
- State University of New York, Buffalo, NY, USA
| | - Matthew S Choo
- Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Nathan Edwards
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Radoslav Goldman
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
- Department of Oncology, Georgetown University, Washington, DC, USA
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Yingwei Hu
- Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Jin Young Kim
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
| | | | - Benoit Liquet
- Department of Mathematics and Statistics, Macquarie University, Sydney, NSW, Australia
- CNRS, Laboratoire de Mathématiques et de leurs Applications de PAU, E2S-UPPA, Pau, France
| | - Mingqi Liu
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Bo Meng
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | | | - Terry Nguyen-Khuong
- Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jonas Nilsson
- Proteomics Core Facility, Sahlgrenska academy, University of Gothenburg, Gothenburg, Sweden
| | - Adam Pap
- BRC, Laboratory of Proteomics Research, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gun Wook Park
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Benjamin L Parker
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Toan K Phung
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Markus Pioch
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- glyXera GmbH, Magdeburg, Germany
| | - Enes Sakalli
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Miloslav Sanda
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Oncology, Georgetown University, Washington, DC, USA
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Nichollas E Scott
- Deparment of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Georgy Sofronov
- Department of Mathematics and Statistics, Macquarie University, Sydney, NSW, Australia
| | - Johannes Stadlmann
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hung-Yi Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pengyuan Yang
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Yong Zhang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Joseph Zaia
- Department of Biochemistry, Boston University Medical Campus, Boston, MA, USA
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, UK
| | - Giuseppe Palmisano
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jong Shin Yoo
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Göran Larson
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kai-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Katalin F Medzihradszky
- UCSF, School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco, CA, USA
- BRC, Laboratory of Proteomics Research, Szeged, Hungary
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
| | - Nicolle H Packer
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia.
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Blaschke CRK, Hartig JP, Grimsley G, Liu L, Semmes OJ, Wu JD, Ippolito JE, Hughes-Halbert C, Nyalwidhe JO, Drake RR. Direct N-Glycosylation Profiling of Urine and Prostatic Fluid Glycoproteins and Extracellular Vesicles. Front Chem 2021; 9:734280. [PMID: 34646811 PMCID: PMC8503230 DOI: 10.3389/fchem.2021.734280] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/10/2021] [Indexed: 12/19/2022] Open
Abstract
Expressed prostatic secretions (EPS), also called post digital rectal exam urines, are proximal fluids of the prostate that are widely used for diagnostic and prognostic assays for prostate cancer. These fluids contain an abundant number of glycoproteins and extracellular vesicles secreted by the prostate gland, and the ability to detect changes in their N-glycans composition as a reflection of disease state represents potential new biomarker candidates. Methods to characterize these N-glycan constituents directly from clinical samples in a timely manner and with minimal sample processing requirements are not currently available. In this report, an approach is described to directly profile the N-glycan constituents of EPS urine samples, prostatic fluids and urine using imaging mass spectrometry for detection. An amine reactive slide is used to immobilize glycoproteins from a few microliters of spotted samples, followed by peptide N-glycosidase digestion. Over 100 N-glycan compositions can be detected with this method, and it works with urine, urine EPS, prostatic fluids, and urine EPS-derived extracellular vesicles. A comparison of the N-glycans detected from the fluids with tissue N-glycans from prostate cancer tissues was done, indicating a subset of N-glycans present in fluids derived from the gland lumens. The developed N-glycan profiling is amenable to analysis of larger clinical cohorts and adaptable to other biofluids.
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Affiliation(s)
- Calvin R K Blaschke
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Jordan P Hartig
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Grace Grimsley
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Liping Liu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - O John Semmes
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, United States.,The Leroy T. Canoles Jr., Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Jennifer D Wu
- Departments of Urology and Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Joseph E Ippolito
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Chanita Hughes-Halbert
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, United States.,Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
| | - Julius O Nyalwidhe
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, United States.,The Leroy T. Canoles Jr., Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States.,Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States
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35
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Regulation of meprin metalloproteases in mucosal homeostasis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119158. [PMID: 34626680 DOI: 10.1016/j.bbamcr.2021.119158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022]
Abstract
Mucus is covering the entire epithelium of the gastrointestinal tract (GIT), building the interface for the symbiosis between microorganisms and their host. Hence, a disrupted mucosal barrier or alterations of proper mucus composition, including the gut microbiota, can cause severe infection and inflammation. Meprin metalloproteases are well-known to cleave various pro-inflammatory molecules, contributing to the onset and progression of pathological conditions including sepsis, pulmonary hypertension or inflammatory bowel disease (IBD). Moreover, meprins have an impact on migration and infiltration of immune cells like monocytes or leukocytes during intestinal inflammation by cleaving tight junction proteins or cell adhesion molecules, thereby disrupting epithelial cell barrier and promoting transendothelial cell migration. Interestingly, both meprin α and meprin β are susceptibility genes for IBD. However, both genes are significantly downregulated in inflamed intestinal tissue in contrast to healthy donors. Therefore, a detailed understanding of the underlying molecular mechanisms is the basis for developing new and effective therapies against manifold pathologies like IBD. This review focuses on the regulation of meprin metalloproteases and its impact on physiological and pathological conditions related to mucosal homeostasis.
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36
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Memarian E, 't Hart LM, Slieker RC, Lemmers RFL, van der Heijden AA, Rutters F, Nijpels G, Schoep E, Lieverse AG, Sijbrands EJG, Wuhrer M, van Hoek M, Dotz V. Plasma protein N-glycosylation is associated with cardiovascular disease, nephropathy, and retinopathy in type 2 diabetes. BMJ Open Diabetes Res Care 2021; 9:e002345. [PMID: 34645615 PMCID: PMC8515459 DOI: 10.1136/bmjdrc-2021-002345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Although associations of total plasma N-glycome (TPNG) with type 2 diabetes have been reported, little is known on the role of TPNG in type 2 diabetes complications, a major cause of type 2 diabetes-related morbidity and mortality. Here, we assessed TPNG in relation to type 2 diabetes complications in subsamples of two Dutch cohorts using mass spectrometry (n=1815 in DiaGene and n=1518 in Hoorn Diabetes Care System). RESEARCH DESIGN AND METHODS Blood plasma samples and technical replicates were pipetted into 96-well plates in a randomized manner. Peptide:N-glycosidase F (PNGase F) was used to release N-glycans, whereafter sialic acids were derivatized for stabilization and linkage differentiation. After total area normalization, 68 individual glycan compositions were quantified in total and were used to calculate 45 derived traits which reflect structural features of glycosylation. Associations of glycan features with prevalent and incident microvascular or macrovascular complications were tested in logistic and Cox regression in both independent cohorts and the results were meta-analyzed. RESULTS Our results demonstrated similarities between incident and prevalent complications. The strongest association for prevalent cardiovascular disease was a high level of bisection on a group of diantennary glycans (A2FS0B; OR=1.38, p=1.34×10-11), while for prevalent nephropathy the increase in 2,6-sialylation on triantennary glycans was most pronounced (A3E; OR=1.28, p=9.70×10-6). Several other TPNG features, including fucosylation, galactosylation, and sialylation, firmly demonstrated associations with prevalent and incident complications of type 2 diabetes. CONCLUSIONS These findings may provide a glance on how TPNG patterns change before complications emerge, paving the way for future studies on prediction biomarkers and potentially disease mechanisms.
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Affiliation(s)
- Elham Memarian
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Leen M 't Hart
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, location VUmc, Amsterdam, The Netherlands
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, location VUmc, Amsterdam, The Netherlands
| | - Roosmarijn F L Lemmers
- Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Amber A van der Heijden
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of General Practice Medicine, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Femke Rutters
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Giel Nijpels
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of General Practice Medicine, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Emma Schoep
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Aloysius G Lieverse
- Department of Internal Medicine, Maxima Medical Center, Eindhoven, The Netherlands
| | - Eric J G Sijbrands
- Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mandy van Hoek
- Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Viktoria Dotz
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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Cvetko A, Mangino M, Tijardović M, Kifer D, Falchi M, Keser T, Perola M, Spector TD, Lauc G, Menni C, Gornik O. Plasma N-glycome shows continuous deterioration as the diagnosis of insulin resistance approaches. BMJ Open Diabetes Res Care 2021; 9:9/1/e002263. [PMID: 34518155 PMCID: PMC8438737 DOI: 10.1136/bmjdrc-2021-002263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/22/2021] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Prediction of type 2 diabetes mellitus (T2DM) and its preceding factors, such as insulin resistance (IR), is of great importance as it may allow delay or prevention of onset of the disease. Plasma protein N-glycome has emerged as a promising predictive biomarker. In a prospective longitudinal study, we included patients with a first diagnosis of impaired glucose metabolism (IR or T2DM) to investigate the N-glycosylation's predictive value years before diabetes development. RESEARCH DESIGN AND METHODS Plasma protein N-glycome was profiled by hydrophilic interaction ultra-performance liquid chromatography in 534 TwinsUK participants free from disease at baseline. This included 89 participants with incident diagnosis of IR or T2DM during the follow-up period (7.14±3.04 years) whose last sample prior to diagnosis was compared using general linear regression with 445 age-matched unrelated controls. Findings were replicated in an independent cohort. Changes in N-glycome have also been presented in connection with time to diagnosis. RESULTS Eight groups of plasma N-glycans were different between incident IR or T2DM cases and controls (p<0.05) after adjusting for multiple testing using Benjamini-Hochberg correction. These differences were noticeable up to 10 years prior to diagnosis and are changing continuously as becoming more expressed toward the diagnosis. The prediction model was built using significant glycan traits, displaying a discriminative performance with an area under the receiver operating characteristic curve of 0.77. CONCLUSIONS In addition to previous studies, we showed the diagnostic potential of plasma N-glycome in the prediction of both IR and T2DM development years before the clinical manifestation and indicated the continuous deterioration of N-glycome toward the diagnosis.
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Affiliation(s)
- Ana Cvetko
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Marko Tijardović
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Domagoj Kifer
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Toma Keser
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, Finland
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Gordan Lauc
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Olga Gornik
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
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38
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Naryzny SN, Legina OK. Haptoglobin as a Biomarker. BIOCHEMISTRY (MOSCOW) SUPPLEMENT. SERIES B, BIOMEDICAL CHEMISTRY 2021; 15:184-198. [PMID: 34422226 PMCID: PMC8365284 DOI: 10.1134/s1990750821030069] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022]
Abstract
Haptoglobin (Hp) is a glycoprotein that binds free hemoglobin (Hb) in plasma and plays a critical role in tissue protection and prevention of oxidative damage. Besides, it has some regulatory functions. Haptoglobin is an acute-phase protein, its concentration in plasma changes in pathology, and the test for its concentration is part of normal clinical practice. Haptoglobin is a conservative protein synthesized mainly in the liver and lungs and is the subject of research as a potential biomarker of many diseases, including various forms of malignant neoplasms. Haptoglobin has several unique biophysical characteristics. The human Нр gene is polymorphic, has three structural alleles that control the synthesis of three major phenotypes of haptoglobin: homozygous Нр1-1 and Нр2-2, and heterozygous Нр2-1, determined by a combination of allelic variants that are inherited. Numerous studies indicate that the phenotype of haptoglobin can be used to judge the individual predisposition of a person to various diseases. In addition, Hp undergoes various post-translational modifications (PTMs). These are structural transformations (removal of the signal peptide, cutting off the Pre-Hp precursor molecule into two subunits, α and β, limited proteolysis of α-chains, formation of disulfide bonds, multimerization), as well as chemical modifications of α-chains and glycosylation of the β-chain. Glycosylation of the β-chain of haptoglobin at four Asn sites is the most important variable PTM that regulates the structure and function of the glycoprotein. The study of modified oligosaccharides of the β-chain of Hp has become the main direction in the study of pathological processes, including malignant neoplasms. These characteristics indicate the possibility of the existence of Hp in the form of a multitude of proteoforms, probably performing different functions. This review is devoted to the description of the structural and functional diversity and the potential use of Hp as a biomarker of various pathologies.
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Affiliation(s)
- S. N. Naryzny
- Institute of Biomedical Chemistry, ul. Pogodinskaya 10, 119121 Moscow, Russia
- St-Petersburg Nuclear Physics Institute (PNPI) NRC Kurchatov Institute, Orlova Roshcha 1, 188300 Gatchina, Leningrad oblast Russia
| | - O. K. Legina
- St-Petersburg Nuclear Physics Institute (PNPI) NRC Kurchatov Institute, Orlova Roshcha 1, 188300 Gatchina, Leningrad oblast Russia
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39
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Zhang YY, Ghirardello M, Wang T, Lu AM, Liu L, Voglmeir J, Galan MC. Imidazolium labelling permits the sensitive mass-spectrometric detection of N-glycosides directly from serum. Chem Commun (Camb) 2021; 57:7003-7006. [PMID: 34159978 PMCID: PMC8280963 DOI: 10.1039/d1cc02100a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022]
Abstract
A novel imidazolium derivative (GITag) shows superior ionisation and consequently allows increased mass spectrometric detection capabilities of oligosaccharides and N-glycans. Here we demonstrate that human serum samples can be directly labelled by GITag on a MALDI target plate, abrogating prevalently required sample pretreatment or clean-up steps.
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Affiliation(s)
- Yao-Yao Zhang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, 210095 Nanjing, China.
| | - Mattia Ghirardello
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS Bristol, UK.
| | - Ting Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, 210095 Nanjing, China.
| | - Ai-Min Lu
- College of Sciences, Nanjing Agricultural University, 1 Weigang, 210095 Nanjing, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, 210095 Nanjing, China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, 210095 Nanjing, China.
| | - M Carmen Galan
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS Bristol, UK.
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40
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Allen JD, Chawla H, Samsudin F, Zuzic L, Shivgan AT, Watanabe Y, He WT, Callaghan S, Song G, Yong P, Brouwer PJM, Song Y, Cai Y, Duyvesteyn HME, Malinauskas T, Kint J, Pino P, Wurm MJ, Frank M, Chen B, Stuart DI, Sanders RW, Andrabi R, Burton DR, Li S, Bond PJ, Crispin M. Site-Specific Steric Control of SARS-CoV-2 Spike Glycosylation. Biochemistry 2021; 60:2153-2169. [PMID: 34213308 PMCID: PMC8262170 DOI: 10.1021/acs.biochem.1c00279] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/18/2021] [Indexed: 02/08/2023]
Abstract
A central tenet in the design of vaccines is the display of native-like antigens in the elicitation of protective immunity. The abundance of N-linked glycans across the SARS-CoV-2 spike protein is a potential source of heterogeneity among the many different vaccine candidates under investigation. Here, we investigate the glycosylation of recombinant SARS-CoV-2 spike proteins from five different laboratories and compare them against S protein from infectious virus, cultured in Vero cells. We find patterns that are conserved across all samples, and this can be associated with site-specific stalling of glycan maturation that acts as a highly sensitive reporter of protein structure. Molecular dynamics simulations of a fully glycosylated spike support a model of steric restrictions that shape enzymatic processing of the glycans. These results suggest that recombinant spike-based SARS-CoV-2 immunogen glycosylation reproducibly recapitulates signatures of viral glycosylation.
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Affiliation(s)
- Joel D. Allen
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Himanshi Chawla
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Firdaus Samsudin
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
| | - Lorena Zuzic
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
- Department
of Chemistry, Faculty of Science and Engineering, Manchester Institute
of Biotechnology, The University of Manchester, Manchester M1 7DN, U.K.
| | - Aishwary Tukaram Shivgan
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
- Department
of Biological Sciences, National University
of Singapore, Singapore 117543
| | - Yasunori Watanabe
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Wan-ting He
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Sean Callaghan
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Ge Song
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Peter Yong
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Philip J. M. Brouwer
- Department
of Medical Microbiology, Amsterdam UMC,
University of Amsterdam, Amsterdam Infection & Immunity Institute, 1007 MB Amsterdam, The Netherlands
| | - Yutong Song
- Tsinghua-Peking
Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing
Advanced Innovation Center for Structural Biology and Frontier Research
Center for Biological Structure, Beijing 100084, China
| | - Yongfei Cai
- Division
of Molecular Medicine, Boston Children’s
Hospital, 3 Blackfan
Street, Boston, Massachusetts 02115, United States
| | - Helen M. E. Duyvesteyn
- Division
of Structural Biology, University of Oxford,
The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, U.K.
| | - Tomas Malinauskas
- Division
of Structural Biology, University of Oxford,
The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, U.K.
| | - Joeri Kint
- ExcellGene SA, CH1870 Monthey, Switzerland
| | - Paco Pino
- ExcellGene SA, CH1870 Monthey, Switzerland
| | | | - Martin Frank
- Biognos AB, Generatorsgatan
1, 41705 Göteborg, Sweden
| | - Bing Chen
- Division
of Molecular Medicine, Boston Children’s
Hospital, 3 Blackfan
Street, Boston, Massachusetts 02115, United States
- Department
of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, Massachusetts 02115, United States
| | - David I. Stuart
- Division
of Structural Biology, University of Oxford,
The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, U.K.
- Diamond Light Source Ltd., Harwell Science
& Innovation Campus, Didcot OX11 0DE, U.K.
| | - Rogier W. Sanders
- Department
of Medical Microbiology, Amsterdam UMC,
University of Amsterdam, Amsterdam Infection & Immunity Institute, 1007 MB Amsterdam, The Netherlands
- Department
of Microbiology and Immunology, Weill Medical
College of Cornell University, New York, New York 10065, United States
| | - Raiees Andrabi
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dennis R. Burton
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
- Ragon Institute of Massachusetts General
Hospital, Massachusetts
Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, United States
| | - Sai Li
- Tsinghua-Peking
Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing
Advanced Innovation Center for Structural Biology and Frontier Research
Center for Biological Structure, Beijing 100084, China
| | - Peter J. Bond
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
- Department
of Biological Sciences, National University
of Singapore, Singapore 117543
| | - Max Crispin
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
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41
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Multiomics Profiling Reveals Signatures of Dysmetabolism in Urban Populations in Central India. Microorganisms 2021; 9:microorganisms9071485. [PMID: 34361920 PMCID: PMC8307859 DOI: 10.3390/microorganisms9071485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/27/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022] Open
Abstract
Background: Non-communicable diseases (NCDs) have become a major cause of morbidity and mortality in India. Perturbation of host–microbiome interactions may be a key mechanism by which lifestyle-related risk factors such as tobacco use, alcohol consumption, and physical inactivity may influence metabolic health. There is an urgent need to identify relevant dysmetabolic traits for predicting risk of metabolic disorders, such as diabetes, among susceptible Asian Indians where NCDs are a growing epidemic. Methods: Here, we report the first in-depth phenotypic study in which we prospectively enrolled 218 adults from urban and rural areas of Central India and used multiomic profiling to identify relationships between microbial taxa and circulating biomarkers of cardiometabolic risk. Assays included fecal microbiota analysis by 16S ribosomal RNA gene amplicon sequencing, quantification of serum short chain fatty acids by gas chromatography-mass spectrometry, and multiplex assaying of serum diabetic proteins, cytokines, chemokines, and multi-isotype antibodies. Sera was also analysed for N-glycans and immunoglobulin G Fc N-glycopeptides. Results: Multiple hallmarks of dysmetabolism were identified in urbanites and young overweight adults, the majority of whom did not have a known diagnosis of diabetes. Association analyses revealed several host–microbe and metabolic associations. Conclusions: Host–microbe and metabolic interactions are differentially shaped by body weight and geographic status in Central Indians. Further exploration of these links may help create a molecular-level map for estimating risk of developing metabolic disorders and designing early interventions.
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42
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Ip PP, Li Q, Lin WH, Chang CC, Fann CSJ, Chen HY, Liu FT, Lebrilla CB, Yang CC, Liao F. Analysis of site-specific glycan profiles of serum proteins in patients with multiple sclerosis or neuromyelitis optica spectrum disorder - a pilot study. Glycobiology 2021; 31:1230-1238. [PMID: 34132764 DOI: 10.1093/glycob/cwab053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/14/2022] Open
Abstract
Glycosylation is important for biological functions of proteins and greatly affected by diseases. Exploring the glycosylation profile of the protein-specific glycosylation and/or the site-specific glycosylation may help understand disease etiology, differentiate diseases, and ultimately develop therapeutics. Patients with multiple sclerosis (MS) and patients with neuromyelitis optica spectrum disorder (NMOSD) are sometimes difficult to differentiate due to the similarity in their clinical symptoms. The disease-related glycosylation profiles of MS and NMOSD have not yet been well studied. Here, we analyzed site-specific glycan profiles of serum proteins of these patients by using a recently developed mass spectrometry technique. A total of 286 glycopeptides from 49 serum glycoproteins were quantified and compared between healthy controls (n = 6), remitting MS (n = 45) and remitting NMOSD (n = 23) patients. Significant differences in the levels of site-specific N-glycans on inflammation-associated components [IgM, IgG1, IgG2, complement components 8b (CO8B), attractin], central nerve system-damage-related serum proteins [apolipoprotein D (APOD), alpha-1-antitrypsin, plasma kallikrein and ADAMTS-like protein 3] were observed among three study groups. We furthered demonstrated that site-specific N-glycans on APOD on site 98, CO8B on sites 243 and 553 are potential markers to differentiate MS from NMOSD with an area under receiver operating curve value greater than 0.75. All these observations indicate that remitting MS or NMOSD patients possess a unique disease-associated glyco-signature in their serum proteins. We conclude that monitoring one's serum protein glycan profile using this high-throughput analysis may provide an additional diagnostic criterion for differentiating diseases, monitoring disease status and estimating response-to-treatment effect.
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Affiliation(s)
- Peng Peng Ip
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
| | - Qiongyu Li
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Wei-Han Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
| | - Chien-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
| | | | - Huan-Yuan Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
| | - Fu-Tong Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Chih-Chao Yang
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Fang Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
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43
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Deriš H, Cindrić A, Lauber M, Petrović T, Bielik A, Taron CH, Wingerden M, Lauc G, Trbojević-Akmačić I. Robustness and repeatability of GlycoWorks RapiFluor-MS IgG N-glycan profiling in a long-term high-throughput glycomic study. Glycobiology 2021; 31:1062-1067. [PMID: 34132802 DOI: 10.1093/glycob/cwab050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/16/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022] Open
Abstract
Protein glycosylation is the attachment of a carbohydrate moiety to a protein backbone affecting both structure and function of the protein. Abnormal glycosylation is associated with various diseases, and some of the changes in glycosylation are detectable even before symptom development. As such, glycans have emerged as compelling new biomarker candidates. A wide range of analytical methods exist for small-scale glycan analyses. However, there is a growing need for highly robust and reproducible high-throughput techniques that allow for large-scale glycoprofiling. Here we describe the evaluation of robustness and repeatability of immunoglobulin G (IgG) N-glycan analysis using the GlycoWorks RapiFluor-MS N-Glycan Kit followed by hydrophilic interaction ultra-high-performance liquid chromatography (HILIC-UHPLC) from 335 technical replicates of human plasma randomly distributed across 67 96-well plates. The data was collected over a five-month period using multiple UHPLC systems and chromatographic columns. Following relative IgG N-glycan quantification in acquired chromatograms, data analysis showed that the most abundant peaks that together made up for three fourths of the detected IgG N-glycome all had coefficients of variation (CVs) lower than 2 percent. The highest CVs ranging from 16 to 29 percent accompanied low abundance glycan peaks with the individual relative peak area below 1 percent that together made up for less than 2 percent of the detected IgG N-glycome. These results show that the tested method is very robust and repeatable, making it suitable for the IgG N-glycan analysis of a large number of samples in a high-throughput manner over a longer period of time.
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Affiliation(s)
- Helena Deriš
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia
| | - Ana Cindrić
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia
| | - Matthew Lauber
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, United States
| | - Tea Petrović
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia
| | - Alicia Bielik
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938-2723, United States
| | - Christopher H Taron
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938-2723, United States
| | - Marleen Wingerden
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, United States
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia.,University of Zagreb, Faculty of Pharmacy and Biochemistry, 10000 Zagreb, Croatia
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Paton B, Suarez M, Herrero P, Canela N. Glycosylation Biomarkers Associated with Age-Related Diseases and Current Methods for Glycan Analysis. Int J Mol Sci 2021; 22:5788. [PMID: 34071388 PMCID: PMC8198018 DOI: 10.3390/ijms22115788] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
Ageing is a complex process which implies the accumulation of molecular, cellular and organ damage, leading to an increased vulnerability to disease. In Western societies, the increase in the elderly population, which is accompanied by ageing-associated pathologies such as cardiovascular and mental diseases, is becoming an increasing economic and social burden for governments. In order to prevent, treat and determine which subjects are more likely to develop these age-related diseases, predictive biomarkers are required. In this sense, some studies suggest that glycans have a potential role as disease biomarkers, as they modify the functions of proteins and take part in intra- and intercellular biological processes. As the glycome reflects the real-time status of these interactions, its characterisation can provide potential diagnostic and prognostic biomarkers for multifactorial diseases. This review gathers the alterations in protein glycosylation profiles that are associated with ageing and age-related diseases, such as cancer, type 2 diabetes mellitus, metabolic syndrome and several chronic inflammatory diseases. Furthermore, the review includes the available techniques for the determination and characterisation of glycans, such as liquid chromatography, electrophoresis, nuclear magnetic resonance and mass spectrometry.
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Affiliation(s)
- Beatrix Paton
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
| | - Manuel Suarez
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Pol Herrero
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
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Serum N-glycan profiles differ for various breast cancer subtypes. Glycoconj J 2021; 38:387-395. [PMID: 33877489 PMCID: PMC8116229 DOI: 10.1007/s10719-021-10001-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 12/09/2022]
Abstract
Breast cancer is the most prevalent cancer in women. Early detection of this disease improves survival and therefore population screenings, based on mammography, are performed. However, the sensitivity of this screening modality is not optimal and new screening methods, such as blood tests, are being explored. Most of the analyses that aim for early detection focus on proteins in the bloodstream. In this study, the biomarker potential of total serum N-glycosylation analysis was explored with regard to detection of breast cancer. In an age-matched case-control setup serum protein N-glycan profiles from 145 breast cancer patients were compared to those from 171 healthy individuals. N-glycans were enzymatically released, chemically derivatized to preserve linkage-specificity of sialic acids and characterized by high resolution mass spectrometry. Logistic regression analysis was used to evaluate associations of specific N-glycan structures as well as N-glycosylation traits with breast cancer. In a case-control comparison three associations were found, namely a lower level of a two triantennary glycans and a higher level of one tetraantennary glycan in cancer patients. Of note, various other N-glycomic signatures that had previously been reported were not replicated in the current cohort. It was further evaluated whether the lack of replication of breast cancer N-glycomic signatures could be partly explained by the heterogenous character of the disease since the studies performed so far were based on cohorts that included diverging subtypes in different numbers. It was found that serum N-glycan profiles differed for the various cancer subtypes that were analyzed in this study.
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Coura MDM, Barbosa EA, Brand GD, Bloch C, de Sousa JB. Identification of Differential N-Glycan Compositions in the Serum and Tissue of Colon Cancer Patients by Mass Spectrometry. BIOLOGY 2021; 10:biology10040343. [PMID: 33923867 PMCID: PMC8074232 DOI: 10.3390/biology10040343] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 01/08/2023]
Abstract
Simple Summary Incidence of colorectal cancer (CRC) has been rising in Brazil. To date, no reliable biomarker has been described in CRC for diagnosis and prognosis. Modifications in the N-glycosylation profile are usually associated with many cancers, as CRC. In turn, mass spectrometry (MS)-based methods are the most accurate technology in quantification of N-glycans. Therefore, we described a unique pattern of compositions altered in serum and tissues of stages II and III colon cancer patients, identified by MALDI-TOF/MS and LC-MS technology. N-glycans were mostly found decreased in serum whilst oligomannosidic, hypogalactosylated, and tetra-antennary forms were overexpressed in tumor tissues. Total N-glycome in serum of cancer patients was different from the profile found in serum of healthy individuals. Strikingly, no correlation between tissue N-glycosylation profile and serum profile was observed in cancer patients, posing the question where these compositions are originated from. Abstract Colorectal cancer (CRC) ranks second as the leading cause of cancer-related deaths worldwide. N-glycosylation is one of the most common posttranslational protein modifications. Therefore, we studied the total serum N-glycome (TSNG) of 13 colon cancer patients compared to healthy controls using MALDI-TOF/MS and LC-MS. N-glycosylation of cancer tumor samples from the same cohort were further quantified using a similar methodology. In total, 23 N-glycan compositions were down-regulated in the serum of colon cancer patients, mostly galactosylated forms whilst the mannose-rich HexNAc2Hex7, the fucosylated bi-antennary glycan HexNAc4Hex5Fuc1NeuAc2, and the tetra-antennary HexNAc6Hex7NeuAc3 were up-regulated in serum. Hierarchical clustering analysis of TSNG correctly singled out 85% of the patients from controls. Albeit heterogenous, N-glycosylation of tumor samples showed overrepresented oligomannosidic, bi-antennary hypogalactosylated, and branched compositions related to normal colonic tissue, in both MALDI-TOF/MS and LC-MS analysis. Moreover, compositions found upregulated in tumor tissue were mostly uncorrelated to compositions in serum of cancer patients. Mass spectrometry-based N-glycan profiling in serum shows potential in the discrimination of patients from healthy controls. However, the compositions profile in serum showed no parallel with N-glycans in tumor microenvironment, which suggests a different origin of compositions found in serum of cancer patients.
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Affiliation(s)
- Marcelo de M.A. Coura
- Division of Colorectal Surgery, University Hospital of Brasilia, School of Medicine, University of Brasilia, SGAN 605, Brasilia-DF 70840-901, Brazil;
- Correspondence:
| | - Eder A. Barbosa
- Laboratory of Mass Spectrometry, EMBRAPA Genetic Resources and Biotechnology, Parque Estação Biológica, PqEB, Av. W5 Norte, Brasilia-DF 70770-917, Brazil; (E.A.B.); (C.B.J.)
- Laboratory for the Synthesis and Analysis of Biomolecules, Institute of Chemistry, Campus Universitario Darcy Ribeiro, University of Brasilia, Brasilia-DF 70910-900, Brazil;
| | - Guilherme D. Brand
- Laboratory for the Synthesis and Analysis of Biomolecules, Institute of Chemistry, Campus Universitario Darcy Ribeiro, University of Brasilia, Brasilia-DF 70910-900, Brazil;
| | - Carlos Bloch
- Laboratory of Mass Spectrometry, EMBRAPA Genetic Resources and Biotechnology, Parque Estação Biológica, PqEB, Av. W5 Norte, Brasilia-DF 70770-917, Brazil; (E.A.B.); (C.B.J.)
| | - Joao B. de Sousa
- Division of Colorectal Surgery, University Hospital of Brasilia, School of Medicine, University of Brasilia, SGAN 605, Brasilia-DF 70840-901, Brazil;
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Abstract
Haptoglobin (Hp) is a blood plasma glycoprotein that binds free hemoglobin (Hb) and plays a critical role in tissue protection and the prevention of oxidative damage. In addition, it has a number of regulatory functions. Haptoglobin is an acute phase protein, its concentration in plasma changes in pathology, and the test for its concentration is part of normal clinical practice. Haptoglobin is a conservative protein synthesized mainly in the liver and lungs and is the subject of research as a potential biomarker of many diseases, including various forms of malignant neoplasms. Haptoglobin has several unique biophysical characteristics. Only in humans, the Hp gene is polymorphic, has three structural alleles that control the synthesis of three major phenotypes of Hp, homozygous Hp1-1 and Hp2-2, and heterozygous Hp2-1, determined by a combination of allelic variants that are inherited. Numerous studies indicate that the phenotype of haptoglobin can be used to judge the individual's predisposition to various diseases. In addition, Hp undergoes various post-translational modifications (PTMs). These are structural transformations (removal of the signal peptide, cutting of the Pre-Hp precursor molecule into two subunits, α and β, limited proteolysis of α-chains, formation of disulfide bonds, multimerization), as well as chemical modifications of α-chains and glycosylation of the β-chain. Glycosylation of the β-chain of haptoglobin at four Asn sites is the most important variable PTM that regulates the structure and function of the glycoprotein. The study of modified oligosaccharides of the Hp β-chain has become the main direction in the study of pathological processes, including malignant neoplasms. Many studies are focused on the identification of PTM and changes in the level of the α2-chain of this protein in pathology. These characteristics of Hp indicate the possibility of the existence of this protein as different proteoforms, probably with different functions. This review is devoted to the description of the structural and functional diversity of Hp and its potential use as a biomarker of various pathologies.
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Affiliation(s)
- S N Naryzhny
- Institute of Biomedical Chemistry, Moscow, Russia; Petersburg Institute of Nuclear Physics B.P. Konstantinova National Research Center "Kurchatov Institute", Gatchina, Russia
| | - O K Legina
- Petersburg Institute of Nuclear Physics B.P. Konstantinova National Research Center "Kurchatov Institute", Gatchina, Russia
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Aberrant sialylation in a patient with a HNF1α variant and liver adenomatosis. iScience 2021; 24:102323. [PMID: 33889819 PMCID: PMC8050382 DOI: 10.1016/j.isci.2021.102323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/18/2021] [Accepted: 03/15/2021] [Indexed: 11/30/2022] Open
Abstract
Glycosylation is a fundamental post-translational modification of proteins that boosts their structural diversity providing subtle and specialized biological properties and functions. All those genetic diseases due to a defective glycan biosynthesis and attachment to the nascent glycoproteins fall within the wide area of congenital disorders of glycosylation (CDG), mostly causing multisystem involvement. In the present paper, we detailed the unique serum N-glycosylation of a CDG-candidate patient with an unexplained neurological phenotype and liver adenomatosis harboring a recurrent pathogenic HNF1α variant. Serum transferrin isoelectric focusing showed a surprising N-glycosylation pattern consisting on hyposialylation, as well as remarkable hypersialylation. Mass spectrometry-based glycomic analyses of individual serum glycoproteins enabled to unveil hypersialylated complex N-glycans comprising up to two sialic acids per antenna. Further advanced MS analysis showed the additional sialic acid is bonded through an α2-6 linkage to the peripheral N-acetylglucosamine residue. Serum N-glycome is altered in a boy with neurological syndrome and HNF1α mutated HCA Glycomics reveals unique hypersialylated N-glycans with two NeuAc per antenna In-depth MS studies show the additional NeuAc is α2-6 linked to an outer arm GlcNAc
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Allen JD, Chawla H, Samsudin F, Zuzic L, Shivgan AT, Watanabe Y, He WT, Callaghan S, Song G, Yong P, Brouwer PJM, Song Y, Cai Y, Duyvesteyn HME, Malinauskas T, Kint J, Pino P, Wurm MJ, Frank M, Chen B, Stuart DI, Sanders RW, Andrabi R, Burton DR, Li S, Bond PJ, Crispin M. Site-specific steric control of SARS-CoV-2 spike glycosylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.08.433764. [PMID: 33758835 PMCID: PMC7986994 DOI: 10.1101/2021.03.08.433764] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
A central tenet in the design of vaccines is the display of native-like antigens in the elicitation of protective immunity. The abundance of N-linked glycans across the SARS-CoV-2 spike protein is a potential source of heterogeneity between the many different vaccine candidates under investigation. Here, we investigate the glycosylation of recombinant SARS-CoV-2 spike proteins from five different laboratories and compare them against infectious virus S protein. We find patterns which are conserved across all samples and this can be associated with site-specific stalling of glycan maturation which act as a highly sensitive reporter of protein structure. Molecular dynamics (MD) simulations of a fully glycosylated spike support s a model of steric restrictions that shape enzymatic processing of the glycans. These results suggest that recombinant spike-based SARS-CoV-2 immunogen glycosylation reproducibly recapitulates signatures of viral glycosylation.
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Serum N-Glycomics Stratifies Bacteremic Patients Infected with Different Pathogens. J Clin Med 2021; 10:jcm10030516. [PMID: 33535571 PMCID: PMC7867038 DOI: 10.3390/jcm10030516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 01/08/2023] Open
Abstract
Bacteremia—i.e., the presence of pathogens in the blood stream—is associated with long-term morbidity and is a potential precursor condition to life-threatening sepsis. Timely detection of bacteremia is therefore critical to reduce patient mortality, but existing methods lack precision, speed, and sensitivity to effectively stratify bacteremic patients. Herein, we tested the potential of quantitative serum N-glycomics performed using porous graphitized carbon liquid chromatography tandem mass spectrometry to stratify bacteremic patients infected with Escherichia coli (n = 11), Staphylococcus aureus (n = 11), Pseudomonas aeruginosa (n = 5), and Streptococcus viridans (n = 5) from healthy donors (n = 39). In total, 62 N-glycan isomers spanning 41 glycan compositions primarily comprising complex-type core fucosylated, bisecting N-acetylglucosamine (GlcNAc), and α2,3-/α2,6-sialylated structures were profiled across all samples using label-free quantitation. Excitingly, unsupervised hierarchical clustering and principal component analysis of the serum N-glycome data accurately separated the patient groups. P. aeruginosa-infected patients displayed prominent N-glycome aberrations involving elevated levels of fucosylation and bisecting GlcNAcylation and reduced sialylation relative to other bacteremic patients. Notably, receiver operating characteristic analyses demonstrated that a single N-glycan isomer could effectively stratify each of the four bacteremic patient groups from the healthy donors (area under the curve 0.93–1.00). Thus, the serum N-glycome represents a new hitherto unexplored class of potential diagnostic markers for bloodstream infections.
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