1
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Lundstrøm J, Urban J, Bojar D. Decoding glycomics with a suite of methods for differential expression analysis. CELL REPORTS METHODS 2023; 3:100652. [PMID: 37992708 PMCID: PMC10753297 DOI: 10.1016/j.crmeth.2023.100652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/04/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023]
Abstract
Glycomics, the comprehensive profiling of all glycan structures in samples, is rapidly expanding to enable insights into physiology and disease mechanisms. However, glycan structure complexity and glycomics data interpretation present challenges, especially for differential expression analysis. Here, we present a framework for differential glycomics expression analysis. Our methodology encompasses specialized and domain-informed methods for data normalization and imputation, glycan motif extraction and quantification, differential expression analysis, motif enrichment analysis, time series analysis, and meta-analytic capabilities, synthesizing results across multiple studies. All methods are integrated into our open-source glycowork package, facilitating performant workflows and user-friendly access. We demonstrate these methods using dedicated simulations and glycomics datasets of N-, O-, lipid-linked, and free glycans. Differential expression tests here focus on human datasets and cancer vs. healthy tissue comparisons. Our rigorous approach allows for robust, reliable, and comprehensive differential expression analyses in glycomics, contributing to advancing glycomics research and its translation to clinical and diagnostic applications.
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Affiliation(s)
- Jon Lundstrøm
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 41390 Gothenburg, Sweden
| | - James Urban
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Daniel Bojar
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 41390 Gothenburg, Sweden.
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2
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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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3
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Han K, Yue Y, Wang W, Wang F, Chai W, Zhao S, Yu M. Lewis x-carrying O-glycans are candidate modulators for conceptus attachment in pigs†. Biol Reprod 2023; 108:292-303. [PMID: 36401880 PMCID: PMC7614189 DOI: 10.1093/biolre/ioac204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/06/2022] [Accepted: 11/02/2022] [Indexed: 11/21/2022] Open
Abstract
Successful attachment of conceptus to the uterine luminal epithelium (LE) is crucial for establishing a functional placenta in pigs. However, the underlying mechanisms are yet to be elucidated. The uterine LE-conceptus interface is enriched in various glycoconjugates essential to implantation. Using MALDI-MS profiling, we identified for the first time the O-glycan repertoire of pig endometrium during the conceptus attachment stage. The expression pattern of blood group A, O(H), Lewis x, y, a, b (Lex, Ley, Lea, and Leb), the sialylated and sulfated Lex antigens in the uterine LE-conceptus interface was assessed using immunofluorescence assays. Notably, the Lex-carrying O-glycans exhibited a temporal-spatial expression pattern. They were absent in the endometrium on estrous cycle days but strongly and spatially presented in the conceptus and uterine LE to which the conceptus apposes during the early conceptus attachment stage. In addition, Lex-carrying O-glycans were co-localized with secreted phosphoprotein 1 (SPP1), a well-characterized factor that plays a role in promoting conceptus attachment through interacting with integrin αVβ3 and integrin αVβ6. Meanwhile, the immunoprecipitation assays revealed an interaction between the Lex-carrying O-glycans and SPP1, integrin αV, and integrin β6. Furthermore, we provided evidence that the β1,4-galactosyltransferase 1 (B4GALT1) gene is a potential regulator for Lex antigen expression in the uterine LE-conceptus interface during the early conceptus attachment stage. In conclusion, our findings show that Lex-carrying O-glycans, presumably dependent on B4GALT1 gene expression, might modulate conceptus attachment by interacting with the SPP1-integrin receptor complex in pigs.
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Affiliation(s)
- Kun Han
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yulu Yue
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weiwei Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Feiyu Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wengang Chai
- Glycosciences Laboratory, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mei Yu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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4
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A Complex Connection Between the Diversity of Human Gastric Mucin O-Glycans, Helicobacter pylori Binding, Helicobacter Infection and Fucosylation. Mol Cell Proteomics 2022; 21:100421. [PMID: 36182101 PMCID: PMC9661725 DOI: 10.1016/j.mcpro.2022.100421] [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: 12/23/2020] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 01/18/2023] Open
Abstract
Helicobacter pylori colonizes the stomach of half of the human population. Most H. pylori are located in the mucus layer, which is mainly comprised by glycosylated mucins. Using mass spectrometry, we identified 631 glycans (whereof 145 were fully characterized and the remainder assigned as compositions) on mucins isolated from 14 Helicobacter spp.-infected and 14 Helicobacter spp.-noninfected stomachs. Only six identified glycans were common to all individuals, from a total of 60 to 189 glycans in each individual. An increased number of unique glycan structures together with an increased intraindividual diversity and larger interindividual variation were identified among O-glycans from Helicobacter spp.-infected stomachs compared with noninfected stomachs. H. pylori strain J99, which carries the blood group antigen-binding adhesin (BabA), the sialic acid-binding adhesin (SabA), and the LacdiNAc-binding adhesin, bound both to Lewis b (Leb)-positive and Leb-negative mucins. Among Leb-positive mucins, H. pylori J99 binding was higher to mucins from Helicobacter spp.-infected individuals than noninfected individuals. Statistical correlation analysis, binding experiments with J99 wt, and J99ΔbabAΔsabA and inhibition experiments using synthetic glycoconjugates demonstrated that the differences in H. pylori-binding ability among these four groups were governed by BabA-dependent binding to fucosylated structures. LacdiNAc levels were lower in mucins that bound to J99 lacking BabA and SabA than in mucins that did not, suggesting that LacdiNAc did not significantly contribute to the binding. We identified 24 O-glycans from Leb-negative mucins that correlated well with H. pylori binding whereof 23 contained α1,2-linked fucosylation. The large and diverse gastric glycan library identified, including structures that correlated with H. pylori binding, could be used to select glycodeterminants to experimentally investigate further for their importance in host-pathogen interactions and as candidates to develop glycan-based therapies.
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de Haan N, Narimatsu Y, Koed Møller Aasted M, Larsen ISB, Marinova IN, Dabelsteen S, Vakhrushev SY, Wandall HH. In-Depth Profiling of O-Glycan Isomers in Human Cells Using C18 Nanoliquid Chromatography-Mass Spectrometry and Glycogenomics. Anal Chem 2022; 94:4343-4351. [PMID: 35245040 PMCID: PMC8928149 DOI: 10.1021/acs.analchem.1c05068] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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O-Glycosylation is an omnipresent modification
of the human proteome affecting many cellular functions, including
protein cleavage, protein folding, and cellular signaling, interactions,
and trafficking. The functions are governed by differentially regulated O-glycan types and terminal structures. It is therefore
essential to develop analytical methods that facilitate the annotation
of O-glycans in biological material. While various
successful strategies for the in-depth profiling of released O-glycans have been reported, these methods are often limitedly
accessible to the nonspecialist or challenged by the high abundance
of O-glycan structural isomers. Here, we developed
a high-throughput sample preparation approach for the nonreductive
release and characterization of O-glycans from human
cell material. Reducing-end labeling allowed efficient isomer separation
and detection using C18 nanoliquid chromatography coupled to Orbitrap
mass spectrometry. Using the method in combination with a library
of genetically glycoengineered cells displaying defined O-glycan types and structures, we were able to annotate individual O-glycan structural isomers from a complex mixture. Applying
the method in a model system of human keratinocytes, we found a wide
variety of O-glycan structures, including O-fucose, O-glucose, O-GlcNAc, and O-GalNAc glycosylation, with the latter
carrying both elongated core1 and core2 structures and varying numbers
of fucoses and sialic acids. The method, including the now well-characterized
standards, provides the opportunity to study glycomic changes in human
tissue and disease models using rather mainstream analytical equipment.
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Affiliation(s)
- Noortje de Haan
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | | | - Ida S B Larsen
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Irina N Marinova
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sally Dabelsteen
- Department of Odontology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
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6
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Hirano K, Furukawa K. Biosynthesis and Biological Significances of LacdiNAc Group on N- and O-Glycans in Human Cancer Cells. Biomolecules 2022; 12:biom12020195. [PMID: 35204696 PMCID: PMC8961560 DOI: 10.3390/biom12020195] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 01/27/2023] Open
Abstract
An increasing number of studies have shown that the disaccharide GalNAcβ1→4GlcNAc (LacdiNAc) group bound to N- and O-glycans in glycoproteins is expressed in a variety of mammalian cells. Biosynthesis of the LacdiNAc group was well studied, and two β4-N-acetylgalactosaminyltransferases, β4GalNAcT3 and β4GalNAcT4, have been shown to transfer N-acetylgalactosamine (GalNAc) to N-acetylglucosamine (GlcNAc) of N- and O-glycans in a β-1,4-linkage. The LacdiNAc group is often sialylated, sulfated, and/or fucosylated, and the LacdiNAc group, with or without these modifications, is recognized by receptors and lectins and is thus involved in the regulation of several biological phenomena, such as cell differentiation. The occurrences of the LacdiNAc group and the β4GalNAcTs appear to be tissue specific and are closely associated with the tumor progression or regression, indicating that they will be potent diagnostic markers of particular cancers, such as prostate cancer. It has been demonstrated that the expression of the LacdiNAc group on N-glycans of cell surface glycoproteins including β1-integrin is involved in the modulation of their protein functions, thus affecting cellular invasion and other malignant properties of cancer cells. The biological roles of the LacdiNAc group in cancer cells have not been fully understood. However, the re-expression of the LacdiNAc group on N-glycans, which is lost in breast cancer cells by transfection of the β4GalNAcT4 gene, brings about the partial restoration of normal properties and subsequent suppression of malignant phenotypes of the cells. Therefore, elucidation of the biological roles of the LacdiNAc group in glycoproteins will lead to the suppression of breast cancers.
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Affiliation(s)
- Kiyoko Hirano
- Glycoinformatics Project, The Noguchi Institute, Itabashi, Tokyo 173-0003, Japan
- Correspondence: ; Tel.: +81-3-3961-3255
| | - Kiyoshi Furukawa
- Department of Endocrinology and Diabetes, Medical Center, Saitama Medical University, Kawagoe 350-8550, Japan;
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7
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Mateoiu C, Vitiazeva V, Kristjansdottir B, Weijdegård B, Örnros J, Gallini R, Kamali-Moghaddam M, Sundfeldt K, Karlsson NG. Analysis of blood group antigens on MUC5AC in mucinous ovarian cancer tissues using in situ proximity ligation assay. Glycobiology 2021; 31:1464-1471. [PMID: 34459484 PMCID: PMC8684467 DOI: 10.1093/glycob/cwab090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/10/2023] Open
Abstract
MUC5AC has been indicated to be a marker for mucinous ovarian cancer (OC). We investigated the use of in situ proximity ligation assay (PLA) for blood group ABH expressing MUC5AC to differentiate between serous and mucinous OC, to validate preceding observations that also MUC5AC ABH expression is increased in mucinous OC. We developed PLA for anti-A, B, and H/anti-MUC5AC and a PLA using a combined lectin Ulex europaeus agglutinin I (UEA I)/anti-MUC5AC assay. The PLAs were verified with mass spectrometry, where mucinous OC secretor positive patients’ cysts fluids containing ABH O-linked oligosaccharides also showed positive OC tissue PLA staining. A nonsecretor mucinous OC cyst fluid was negative for ABH and displayed negative PLA staining of the matched tissue. Using the UEA I/MUC5AC PLA, we screened a tissue micro array of 410 ovarian tissue samples from patients with various stages of mucinous or serous OC, 32 samples with metastasis to the ovaries and 34 controls. The PLA allowed differentiating mucinous tumors with a sensitivity of 84% and a specificity of 97% both against serous cancer but also compared to tissues from controls. This sensitivity is close to the expected incidence of secretor individuals in a population. The recorded sensitivity was also found to be higher compared to mucinous type cancer with metastasis to the ovaries, where only 32% were positive. We conclude that UEA 1/MUC5AC PLA allows glycospecific differentiation between serous and mucinous OC in patients with positive secretor status and will not identify secretor negative individuals with mucinous OC.
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Affiliation(s)
- Constantina Mateoiu
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden.,Department of Gynecology, Region Västra Götaland, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Varvara Vitiazeva
- Department of Medical Biochemistry, Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Björg Kristjansdottir
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden.,Department of Gynecology, Region Västra Götaland, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Birgitta Weijdegård
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Jessica Örnros
- Department of Medical Biochemistry, Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Radiosa Gallini
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, 751 08, Uppsala, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, 751 08, Uppsala, Sweden
| | - Karin Sundfeldt
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden.,Department of Gynecology, Region Västra Götaland, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry, Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, 405 30, Gothenburg, Sweden.,Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
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8
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Bertokova A, Bertok T, Jane E, Hires M, Ďubjaková P, Novotná O, Belan V, Fillo J, Tkac J. Detection of N,N-diacetyllactosamine (LacdiNAc) containing free prostate-specific antigen for early stage prostate cancer diagnostics and for identification of castration-resistant prostate cancer patients. Bioorg Med Chem 2021; 39:116156. [PMID: 33894508 DOI: 10.1016/j.bmc.2021.116156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
Prostate cancer (PCa) is one of the most common cancer types among men and also acommon cause of death globally. With an increasing incidence, there is aneed for low-cost, reliable biomarkers present in samples, which could be provided non-invasively (without a need to perform prostate biopsy). Glycosylation changes of free-PSA (fPSA) are considered cancer-specific, while the level of different PSA forms can increase under other than cancerous conditions. In the present study, we investigated the role ofN,N-diacetyllactosamine (LacdiNAc) epitope of fPSA (i.e. glycoprofile of fPSA or gPSA) in combination with total-PSA (tPSA), prostate volume, and tPSA density (tPSA level divided by prostate volume i.e. PSAd) as biomarkers for monitoring of PCa development and progression in 105 men. Furthermore, we applied an genetic (evolutionary) algorithm to identify any suspicious individuals in abenign cohort having benign prostatic hyperplasia (BPH). We identified 3 suspicious men originally diagnosed with BPH using gPSA analysis. In thefollow-up we found out that two men should not be considered as BPH patients since multiparametric magnetic resonance imaging (mpMRI) identified one man with clinically significant PCa via Prostate Imaging - Reporting and Data System (PI RADS v2 = 4) and the second man was with High-gradeprostatic intraepithelial neoplasia (HG PIN), commonly described as apre-cancerous stage. Moreover, in the study we described for the first time that changed LacdiNAc on PSA can be applied to identify prostatitis patients and most importantly this is the first study suggesting that changed glycosylation on PSA can be applied to identify castration-resistant prostate cancer (CRPCa) patients.
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Affiliation(s)
- Aniko Bertokova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovakia; Glycanostics, Ltd., Dubravska cesta 9, Bratislava 845 38, Slovakia
| | - Tomas Bertok
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovakia; Glycanostics, Ltd., Dubravska cesta 9, Bratislava 845 38, Slovakia
| | - Eduard Jane
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovakia
| | - Michal Hires
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovakia
| | - Petra Ďubjaková
- University Hospital Bratislava, Mickiewiczova 13, 811 07 Bratislava, Slovakia
| | - Oľga Novotná
- University Hospital Bratislava, Mickiewiczova 13, 811 07 Bratislava, Slovakia
| | | | - Juraj Fillo
- University Hospital Bratislava, Mickiewiczova 13, 811 07 Bratislava, Slovakia
| | - Jan Tkac
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovakia; Glycanostics, Ltd., Dubravska cesta 9, Bratislava 845 38, Slovakia.
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9
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Čaval T, de Haan N, Konstantinidi A, Vakhrushev SY. Quantitative characterization of O-GalNAc glycosylation. Curr Opin Struct Biol 2021; 68:135-141. [PMID: 33508547 DOI: 10.1016/j.sbi.2020.12.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/26/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022]
Abstract
O-GalNAc type glycosylation is an abundant and complex protein modification. Recent developments in mass spectrometry resulted in significant success in quantitative analysis of O-GalNAc glycosylation. The analysis of released O-GalNAc type glycans expanded our horizons of understanding the glycome of various biological models. The site-specific analysis of glycosylation micro-heterogeneity of purified proteins opened perspectives for the improved design of glycoprotein therapeutics. Advanced gene editing and chemical technologies applied to O-glycoproteomics enabled to identify O-GalNAc glycosylation at unprecedented depth. Progress in the analysis of intact glycoproteins under native and reduced conditions enabled the monitoring of glycosylation proteoform variants. Despite of the astonishing results in quantitative O-GalNAc glycoproteomics, site-specific mapping of the full O-GalNAc structural repertoire in complex samples is yet a long way off. Here, we summarize the most common quantitative strategies in O-GalNAc glycoproteomics, review recent progress and discuss benefits and limitations of the various approaches in the field.
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Affiliation(s)
- Tomislav Čaval
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Noortje de Haan
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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10
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Pralow A, Cajic S, Alagesan K, Kolarich D, Rapp E. State-of-the-Art Glycomics Technologies in Glycobiotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 175:379-411. [PMID: 33112988 DOI: 10.1007/10_2020_143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycosylation affects the properties of biologics; thus regulatory bodies classified it as critical quality attribute and force biopharma industry to capture and control it throughout all phases, from R&D till end of product lifetime. The shift from originators to biosimilars further increases importance and extent of glycoanalysis, which thus increases the need for technology platforms enabling reliable high-throughput and in-depth glycan analysis. In this chapter, we will first summarize on established glycoanalytical methods based on liquid chromatography focusing on hydrophilic interaction chromatography, capillary electrophoresis focusing on multiplexed capillary gel electrophoresis, and mass spectrometry focusing on matrix-assisted laser desorption; we will then highlight two emerging technologies based on porous graphitized carbon liquid chromatography and on ion-mobility mass spectrometry as both are highly promising tools to deliver an additional level of information for in-depth glycan analysis; additionally we elaborate on the advantages and challenges of different glycoanalytical technologies and their complementarity; finally, we briefly review applications thereof to biopharmaceutical products. This chapter provides an overview of current state-of-the-art analytical approaches for glycan characterization of biopharmaceuticals that can be employed to capture glycoprotein heterogeneity in a biopharmaceutical context.
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Affiliation(s)
- Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Samanta Cajic
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
- ARC Centre of Excellence in Nanoscale Biophotonics, Griffith University, Gold Coast, QLD, Australia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
- glyXera GmbH, Magdeburg, Germany.
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11
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LacdiNAcylation of N-glycans in MDA-MB-231 human breast cancer cells results in changes in morphological appearance and adhesive properties of the cells. Histochem Cell Biol 2019; 153:17-26. [PMID: 31606752 DOI: 10.1007/s00418-019-01822-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/24/2022]
Abstract
We demonstrated previously that the expression of the disaccharide, GalNAcβ1 → 4GlcNAc (LacdiNAc), on N-glycans of cell surface glycoproteins in MDA-MB-231 human breast cancer cells suppresses their malignant properties such as tumor formation in nude mice. Here, we report changes in the morphological appearance and adhesive properties of two kinds of clonal cells of MDA-MB-231 cells overexpressing β4-N-acetyl-galactosaminyltransferase 4. The clonal cells exhibited a cobble stone-like shape as compared to a spindle-like shape of the mock-transfected cells and the original MDA-MB-231 cells. This was associated with an increased expression of cell surface E-cadherin, a marker of epithelial cells, and a decreased expression of N-cadherin, vimentin, α-smooth muscle actin and ZEB1, markers of mesenchymal cells. In addition, the clonal cells showed a lower migratory activity compared to the mock-transfected cells by wound-healing assay. These results suggest that mesenchymal-epithelial transition may be occurring in these clonal cells. Furthermore, increased adhesion to extracellular matrix proteins such as fibronectin, collagen type I, collagen type IV, and laminin was observed. The clonal cells spread and enlarged, whereas the mock-transfected cells demonstrated poor spreading on laminin-coated plates in the absence of fetal calf serum, indicating that expression of LacdiNAc on cell surface glycoproteins results in changes in cell adhesive and spreading properties particularly to laminin.
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Alocci D, Ghraichy M, Barletta E, Gastaldello A, Mariethoz J, Lisacek F. Understanding the glycome: an interactive view of glycosylation from glycocompositions to glycoepitopes. Glycobiology 2018. [PMID: 29518231 DOI: 10.1093/glycob/cwy019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nowadays, due to the advance of experimental techniques in glycomics, large collections of glycan profiles are regularly published. The rapid growth of available glycan data accentuates the lack of innovative tools for visualizing and exploring large amount of information. Scientists resort to using general-purpose spreadsheet applications to create ad hoc data visualization. Thus, results end up being encoded in publication images and text, while valuable curated data is stored in files as supplementary information. To tackle this problem, we have built an interactive pipeline composed with three tools: Glynsight, EpitopeXtractor and Glydin'. Glycan profile data can be imported in Glynsight, which generates a custom interactive glycan profile. Several profiles can be compared and glycan composition is integrated with structural data stored in databases. Glycan structures of interest can then be sent to EpitopeXtractor to perform a glycoepitope extraction. EpitopeXtractor results can be superimposed on the Glydin' glycoepitope network. The network visualization allows fast detection of clusters of glycoepitopes and discovery of potential new targets. Each of these tools is standalone or can be used in conjunction with the others, depending on the data and the specific interest of the user. All the tools composing this pipeline are part of the Glycomics@ExPASy initiative and are available at https://www.expasy.org/glycomics.
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Affiliation(s)
- Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Computer Science Department CUI, University of Geneva, 7 Route de Drize, 1227 Geneva, Switzerland
| | - Marie Ghraichy
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Elena Barletta
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Computer Science Department CUI, University of Geneva, 7 Route de Drize, 1227 Geneva, Switzerland
| | - Alessandra Gastaldello
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Computer Science Department CUI, University of Geneva, 7 Route de Drize, 1227 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Computer Science Department CUI, University of Geneva, 7 Route de Drize, 1227 Geneva, Switzerland
| | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Computer Science Department CUI, University of Geneva, 7 Route de Drize, 1227 Geneva, Switzerland.,Section of Biology, University of Geneva, Geneva, Switzerland
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Isomeric Separation and Characterisation of Glycoconjugates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1104:77-99. [DOI: 10.1007/978-981-13-2158-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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