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Zhang Y, Krishnan S, Bao B, Chiang AWT, Sorrentino JT, Schinn SM, Kellman BP, Lewis NE. Preparing glycomics data for robust statistical analysis with GlyCompareCT. STAR Protoc 2023; 4:102162. [PMID: 36920914 PMCID: PMC10025275 DOI: 10.1016/j.xpro.2023.102162] [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: 09/12/2022] [Revised: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
GlyCompareCT is a portable command-line tool to facilitate downstream glycomic data analyses, by addressing data inherent sparsity and non-independence. Inputting glycan abundances, users can run GlyCompareCT with one line of code to obtain the abundances of a minimal substructure set, named glycomotif, thereby quantifying hidden biosynthetic relationships between measured glycans. Optional parameters tuning and annotation are supported for personal preference. For complete details on the use and execution of this protocol, please refer to Bao et al. (2021).1.
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Affiliation(s)
- Yujie Zhang
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
| | - Sridevi Krishnan
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
| | - Bokan Bao
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
| | - Austin W T Chiang
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
| | - James T Sorrentino
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
| | - Song-Min Schinn
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
| | - Benjamin P Kellman
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Augment Biologics, 9450 SW Gemini Dr. #46664, Beaverton, OR 97008, USA.
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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Bao B, Kellman BP, Chiang AWT, Zhang Y, Sorrentino JT, York AK, Mohammad MA, Haymond MW, Bode L, Lewis NE. Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis. Nat Commun 2021; 12:4988. [PMID: 34404781 PMCID: PMC8371009 DOI: 10.1038/s41467-021-25183-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 07/27/2021] [Indexed: 11/20/2022] Open
Abstract
Glycans are fundamental cellular building blocks, involved in many organismal functions. Advances in glycomics are elucidating the essential roles of glycans. Still, it remains challenging to properly analyze large glycomics datasets, since the abundance of each glycan is dependent on many other glycans that share many intermediate biosynthetic steps. Furthermore, the overlap of measured glycans can be low across samples. We address these challenges with GlyCompare, a glycomic data analysis approach that accounts for shared biosynthetic steps for all measured glycans to correct for sparsity and non-independence in glycomics, which enables direct comparison of different glycoprofiles and increases statistical power. Using GlyCompare, we study diverse N-glycan profiles from glycoengineered erythropoietin. We obtain biologically meaningful clustering of mutant cell glycoprofiles and identify knockout-specific effects of fucosyltransferase mutants on tetra-antennary structures. We further analyze human milk oligosaccharide profiles and find mother’s fucosyltransferase-dependent secretor-status indirectly impact the sialylation. Finally, we apply our method on mucin-type O-glycans, gangliosides, and site-specific compositional glycosylation data to reveal tissues and disease-specific glycan presentations. Our substructure-oriented approach will enable researchers to take full advantage of the growing power and size of glycomics data. Glycomics can uncover important molecular changes but measured glycans are highly interconnected and incompatible with common statistical methods, introducing pitfalls during analysis. Here, the authors develop an approach to identify glycan dependencies across samples to facilitate comparative glycomics.
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Affiliation(s)
- Bokan Bao
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin P Kellman
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Austin W T Chiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA
| | - Yujie Zhang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - James T Sorrentino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Austin K York
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Mahmoud A Mohammad
- Department of Pediatrics, Children's Nutrition Research Center, US Department of Agriculture/Agricultural Research Service, Baylor College of Medicine, Houston, TX, USA
| | - Morey W Haymond
- Department of Pediatrics, Children's Nutrition Research Center, US Department of Agriculture/Agricultural Research Service, Baylor College of Medicine, Houston, TX, USA
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA. .,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. .,The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA.
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Dissecting Total Plasma and Protein-Specific Glycosylation Profiles in Congenital Disorders of Glycosylation. Int J Mol Sci 2020; 21:ijms21207635. [PMID: 33076454 PMCID: PMC7589176 DOI: 10.3390/ijms21207635] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/16/2022] Open
Abstract
Protein N-glycosylation is a multifactorial process involved in many biological processes. A broad range of congenital disorders of glycosylation (CDGs) have been described that feature defects in protein N-glycan biosynthesis. Here, we present insights into the disrupted N-glycosylation of various CDG patients exhibiting defects in the transport of nucleotide sugars, Golgi glycosylation or Golgi trafficking. We studied enzymatically released N-glycans of total plasma proteins and affinity purified immunoglobulin G (IgG) from patients and healthy controls using mass spectrometry (MS). The applied method allowed the differentiation of sialic acid linkage isomers via their derivatization. Furthermore, protein-specific glycan profiles were quantified for transferrin and IgG Fc using electrospray ionization MS of intact proteins and glycopeptides, respectively. Next to the previously described glycomic effects, we report unprecedented sialic linkage-specific effects. Defects in proteins involved in Golgi trafficking (COG5-CDG) and CMP-sialic acid transport (SLC35A1-CDG) resulted in lower levels of sialylated structures on plasma proteins as compared to healthy controls. Findings for these specific CDGs include a more pronounced effect for α2,3-sialylation than for α2,6-sialylation. The diverse abnormalities in glycomic features described in this study reflect the broad range of biological mechanisms that influence protein glycosylation.
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Zhang T, Madunić K, Holst S, Zhang J, Jin C, Ten Dijke P, Karlsson NG, Stavenhagen K, Wuhrer M. Development of a 96-well plate sample preparation method for integrated N- and O-glycomics using porous graphitized carbon liquid chromatography-mass spectrometry. Mol Omics 2020; 16:355-363. [PMID: 32281997 DOI: 10.1039/c9mo00180h] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Changes in glycosylation signatures of cells have been associated with pathological processes in cancer as well as infectious and autoimmune diseases. The current protocols for comprehensive analysis of N-glycomics and O-glycomics derived from cells and tissues often require a large amount of biological material. They also only allow the processing of very limited numbers of samples at a time. Here we established a workflow for sequential release of N-glycans and O-glycans based on PVDF membrane immobilization in 96-well format from 5 × 105 cells. Released glycans are reduced, desalted, purified, and reconstituted, all in 96-well format plates, without additional staining or derivatization. Glycans are then analyzed with porous graphitized carbon nano-liquid chromatography coupled to tandem mass spectrometry using negative-mode electrospray ionization, enabling the chromatographic resolution and structural elucidation of glycan species including many compositional isomers. The approach was demonstrated using glycoprotein standards and further applied to analyze the glycosylation of the murine mammary gland NMuMG cell line. The developed protocol allows the analysis of N- and O-glycans from relatively large numbers of samples in a less time consuming way with high repeatability. Inter- and intraday repeatability of the fetuin N-glycan analysis showed two median intraday coefficients of variations (CVs) of 7.6% and 8.0%, and a median interday CV of 9.8%. Median CVs of 7.9% and 8.7% for the main peaks of N- and O-glycans released from the NMuMG cell line indicate a very good repeatability. The method is applicable to purified glycoproteins as well as to biofluids and cell- or tissue-based samples.
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Affiliation(s)
- Tao Zhang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
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Franceschi C, Garagnani P, Parini P, Giuliani C, Santoro A. Inflammaging: a new immune-metabolic viewpoint for age-related diseases. Nat Rev Endocrinol 2018; 14:576-590. [PMID: 30046148 DOI: 10.1038/s41574-018-0059-4] [Citation(s) in RCA: 1490] [Impact Index Per Article: 248.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ageing and age-related diseases share some basic mechanistic pillars that largely converge on inflammation. During ageing, chronic, sterile, low-grade inflammation - called inflammaging - develops, which contributes to the pathogenesis of age-related diseases. From an evolutionary perspective, a variety of stimuli sustain inflammaging, including pathogens (non-self), endogenous cell debris and misplaced molecules (self) and nutrients and gut microbiota (quasi-self). A limited number of receptors, whose degeneracy allows them to recognize many signals and to activate the innate immune responses, sense these stimuli. In this situation, metaflammation (the metabolic inflammation accompanying metabolic diseases) is thought to be the form of chronic inflammation that is driven by nutrient excess or overnutrition; metaflammation is characterized by the same mechanisms underpinning inflammaging. The gut microbiota has a central role in both metaflammation and inflammaging owing to its ability to release inflammatory products, contribute to circadian rhythms and crosstalk with other organs and systems. We argue that chronic diseases are not only the result of ageing and inflammaging; these diseases also accelerate the ageing process and can be considered a manifestation of accelerated ageing. Finally, we propose the use of new biomarkers (DNA methylation, glycomics, metabolomics and lipidomics) that are capable of assessing biological versus chronological age in metabolic diseases.
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Affiliation(s)
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
- Laboratory of Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy
- CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy
| | - Paolo Parini
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy.
- Interdepartmental Centre 'L. Galvani' (CIG), University of Bologna, Bologna, Italy.
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Interdepartmental Centre 'L. Galvani' (CIG), University of Bologna, Bologna, Italy
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Badr HA, AlSadek DMM, El-Houseini ME, Saeui CT, Mathew MP, Yarema KJ, Ahmed H. Harnessing cancer cell metabolism for theranostic applications using metabolic glycoengineering of sialic acid in breast cancer as a pioneering example. Biomaterials 2017; 116:158-173. [PMID: 27926828 PMCID: PMC5193387 DOI: 10.1016/j.biomaterials.2016.11.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/14/2016] [Accepted: 11/24/2016] [Indexed: 12/18/2022]
Abstract
Abnormal cell surface display of sialic acids - a family of unusual 9-carbon sugars - is widely recognized as distinguishing feature of many types of cancer. Sialoglycans, however, typically cannot be identified with sufficiently high reproducibility and sensitivity to serve as clinically accepted biomarkers and similarly, almost all efforts to exploit cancer-specific differences in sialylation signatures for therapy remain in early stage development. In this report we provide an overview of important facets of glycosylation that contribute to cancer in general with a focus on breast cancer as an example of malignant disease characterized by aberrant sialylation. We then describe how cancer cells experience nutrient deprivation during oncogenesis and discuss how the resulting metabolic reprogramming, which endows breast cancer cells with the ability to obtain nutrients during scarcity, constitutes an "Achilles' heel" that we believe can be exploited by metabolic glycoengineering (MGE) strategies to develop new diagnostic methods and therapeutic approaches. In particular, we hypothesize that adaptations made by breast cancer cells that allow them to efficiently scavenge sialic acid during times of nutrient deprivation renders them vulnerable to MGE, which refers to the use of exogenously-supplied, non-natural monosaccharide analogues to modulate targeted aspects of glycosylation in living cells and animals. In specific, once non-natural sialosides are incorporated into the cancer "sialome" they can be exploited as epitopes for immunotherapy or as chemical tags for targeted delivery of imaging or therapeutic agents selectively to tumors.
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Affiliation(s)
- Haitham A Badr
- Department of Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Dina M M AlSadek
- Department of Histology and Cytology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Motawa E El-Houseini
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Christopher T Saeui
- Department of Biomedical Engineering and Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD 21231, USA
| | - Mohit P Mathew
- Department of Biomedical Engineering and Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD 21231, USA
| | - Kevin J Yarema
- Department of Biomedical Engineering and Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD 21231, USA.
| | - Hafiz Ahmed
- GlycoMantra, Inc., Baltimore, MD 21227, USA.
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