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Computationally guided conversion of the specificity of E-selectin to mimic that of Siglec-8. Proc Natl Acad Sci U S A 2022; 119:e2117743119. [PMID: 36191232 PMCID: PMC9564326 DOI: 10.1073/pnas.2117743119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sulfated glycans have been found to be associated with various diseases and therefore have significant potential in molecular pathology as biomarkers. Although lectins are useful reagents for detecting glycans, there is a paucity of sulfate-recognizing lectins, and those that exist, such as from Maackia amurensis, display mixed specificities. Recombinant lectin engineering offers an emerging tool for creating novel glycan recognition by altering and/or enhancing endogenous specificities. The present study demonstrated the use of computational approaches in the engineering of a mutated form of E-selectin that displayed highly specific recognition of 6'-sulfo-sialyl Lewis X (6'-sulfo-sLex), with negligible binding to its endogenous nonsulfated ligand, sLex. This new specificity mimics that of the unrelated protein Siglec-8, for which 6'-sulfo-sLex is its preferred ligand. Molecular dynamics simulations and energy calculations predicted that two point mutations (E92A/E107A) would be required to stabilize binding to the sulfated oligosaccharide with E-selectin. In addition to eliminating putative repulsions between the negatively charged side chains and the sulfate moiety, the mutations also abolished favorable interactions with the endogenous ligand. Glycan microarray screening of the recombinantly expressed proteins confirmed the predicted specificity change but also identified the introduction of unexpected affinity for the unfucosylated form of 6'-sulfo-sLex (6'-sulfo-sLacNAc). Three key requirements were demonstrated in this case for engineering specificity for sulfated oligosaccharide: 1) removal of unfavorable interactions with the 6'-sulfate, 2) introduction of favorable interactions for the sulfate, and 3) removal of favorable interactions with the endogenous ligand.
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Tseng HC, Hsiao CT, Yamakawa N, Guérardel Y, Khoo KH. Discovery Sulfoglycomics and Identification of the Characteristic Fragment Ions for High-Sensitivity Precise Mapping of Adult Zebrafish Brain-Specific Glycotopes. Front Mol Biosci 2022; 8:771447. [PMID: 34988116 PMCID: PMC8721812 DOI: 10.3389/fmolb.2021.771447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
Mass spectrometry-based high-sensitivity mapping of terminal glycotopes relies on diagnostic MS2 and/or MS3 ions that can differentiate linkage and define the location of substituents including sulfates. Unambiguous identification of adult zebrafish glycotopes is particularly challenging due to the presence of extra β4-galactosylation on the basic building block of Galβ1-4GlcNAc that can be fucosylated and variably sialylated by N-acetyl, N-glycolyl, or deaminated neuraminic acids. Building on previous groundwork that have identified various organ-specific N- and O-glycans of adult zebrafish, we show here that all the major glycotopes of interest can be readily mapped by direct nano-LC-MS/MS analysis of permethylated glycans. Homing in on the brain-, intestine-, and ovary-derived samples, organ-specific glycomic reference maps based on overlaid extracted ion chromatograms of resolved glycan species, and composite charts of summed intensities of diagnostic MS2 ions representing the distribution and relative abundance of each of the glycotopes and sialic acid variants were established. Moreover, switching to negative mode analysis of sample fractions enriched in negatively charged glycans, we show, for the first time, that a full range of sulfated glycotopes is expressed in adult zebrafish. In particular, 3-O-sulfation of terminal Gal was commonly found, whereas terminal sulfated HexNAc as in GalNAcβ1-4GlcNAc (LacdiNAc), and 3-O-sulfated hexuronic acid as in HNK-1 epitope (SO3-3GlcAβ1-3Galβ1-4GlcNAc) were identified only in the brain and not in the intestine or ovaries analyzed in parallel. Other characteristic structural features of sulfated O- and N-glycans along with their diagnostic ions detected in this discovery mode sulfoglycomic work collectively expand our adult zebrafish glycome atlas, which can now allow for a more complete navigation and probing of the underlying sulfotransferases and glycosyltransferases, in search of the functional relevance of zebrafish-specific glycotopes. Of particular importance is the knowledge of glycomic features distinct from those of humans when using adult zebrafish as an alternative vertebrate model, rather than mouse, for brain-related glyco-neurobiology studies.
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Affiliation(s)
- Huan-Chuan Tseng
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Cheng-Te Hsiao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Nao Yamakawa
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41-UMS 2014-PLBS, Lille, France
| | - Yann Guérardel
- Université de Lille, CNRS, UMR 8576-UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France.,Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
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A mass spectrometry-based glycotope-centric cellular glycomics is the more fruitful way forward to see the forest for the trees. Biochem Soc Trans 2021; 49:55-69. [PMID: 33492355 DOI: 10.1042/bst20190861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 02/08/2023]
Abstract
The nature of protein glycosylation renders cellular glycomics a very challenging task in having to deal with all the disparate glycans carried on membrane glycoproteins. Rapid mapping by mass spectrometry analysis provides only a coarse sketch of the glycomic complexity based primarily on glycosyl compositions, whereby the missing high-resolution structural details require a combination of multi-mode separations and multi-stages of induced fragmentation to gain sufficiently discriminative precision, often at the expenses of throughput and sensitivity. Given the available technology and foreseeable advances in the near future, homing in on resolving the terminal fucosylated, sialylated and/or sulfated structural units, or glycotopes, maybe a more pragmatic and ultimately more rewarding approach to gain insights into myriad biological processes mediated by these terminal coding units carried on important glycoproteins, to be decoded by a host of endogenous glycan-binding proteins and antibodies. A broad overview of recent technical advances and limitations in cellular glycomics is first provided as a backdrop to the propounded glycotope-centric approach based on advanced nanoLC-MS2/MS3 analysis of permethylated glycans. To prioritize analytical focus on the more tangible glycotopes is akin to first identifying the eye-catching and characteristic-defining flowers and fruits of the glyco-forest, to see the forest for the trees. It has the best prospects of attaining the much-needed balance in sensitivity, structural precision and analytical throughput to match advances in other omics.
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Kuo CW, Guu SY, Khoo KH. Distinctive and Complementary MS 2 Fragmentation Characteristics for Identification of Sulfated Sialylated N-Glycopeptides by nanoLC-MS/MS Workflow. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1166-1178. [PMID: 29644550 DOI: 10.1007/s13361-018-1919-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 06/08/2023]
Abstract
High sensitivity identification of sulfated glycans carried on specific sites of glycoproteins is an important requisite for investigation of molecular recognition events involved in diverse biological processes. However, aiming for resolving site-specific glycosylation of sulfated glycopeptides by direct LC-MS2 sequencing is technically most challenging. Other than the usual limiting factors such as lower abundance and ionization efficiency compared to analysis of non-glycosylated peptides, confident identification of sulfated glycopeptides among the more abundant non-sulfated glycopeptides requires additional considerations in the selective enrichment and detection strategies. Metal oxide has been applied to enrich phosphopeptides and sialylated glycopeptides, but its use to capture sulfated glycopeptides has not been investigated. Likewise, various complementary MS2 fragmentation modes have yet to be tested against sialylated and non-sialylated sulfoglycopeptides due to limited appropriate sample availability. In this study, we have investigated the feasibility of sequencing tryptic sulfated N-glycopeptide and its MS2 fragmentation characteristics by first optimizing the enrichment methods to allow efficient LC-MS detection and MS2 analysis by a combination of CID, HCD, ETD, and EThcD on hybrid and tribrid Orbitrap instruments. Characteristic sulfated glyco-oxonium ions and direct loss of sulfite from precursors were detected as evidences of sulfate modification. It is anticipated that the technical advances demonstrated in this study would allow a feasible extension of our sulfoglycomic analysis to sulfoglycoproteomics. Graphical Abstract ᅟ.
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Affiliation(s)
- Chu-Wei Kuo
- Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan
| | - Shih-Yun Guu
- Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan.
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Rot A, Massberg S, Khandoga AG, von Andrian UH. Chemokines and Hematopoietic Cell Trafficking. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Lee M, Kiefel H, LaJevic MD, Macauley MS, Kawashima H, O'Hara E, Pan J, Paulson JC, Butcher EC. Transcriptional programs of lymphoid tissue capillary and high endothelium reveal control mechanisms for lymphocyte homing. Nat Immunol 2014; 15:982-95. [PMID: 25173345 PMCID: PMC4222088 DOI: 10.1038/ni.2983] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/31/2014] [Indexed: 12/13/2022]
Abstract
Lymphocytes are recruited from blood by high-endothelial venules (HEVs). We performed transcriptomic analyses and identified molecular signatures that distinguish HEVs from capillary endothelium and that define tissue-specific HEV specialization. Capillaries expressed gene programs for vascular development. HEV-expressed genes showed enrichment for genes encoding molecules involved in immunological defense and lymphocyte migration. We identify capillary and HEV markers and candidate mechanisms for regulated recruitment of lymphocytes, including a lymph node HEV-selective transmembrane mucin; transcriptional control of functionally specialized carbohydrate ligands for lymphocyte L-selectin; HEV expression of molecules for transendothelial migration; and metabolic programs for lipid mediators of lymphocyte motility and chemotaxis. We also elucidate a carbohydrate-recognition pathway that targets B cells to intestinal lymphoid tissues, defining CD22 as a lectin-homing receptor for mucosal HEVs.
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Affiliation(s)
- Mike Lee
- Laboratory of Immunology and Vascular Biology, Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Helena Kiefel
- Laboratory of Immunology and Vascular Biology, Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Melissa D LaJevic
- Laboratory of Immunology and Vascular Biology, Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew S Macauley
- Departments of Cell and Molecular Biology, Immunology and Microbial Science, and Chemical Physiology, The Scripps Research Institute, La Jolla, California USA
| | | | - Edward O'Hara
- Palo Alto Veterans Institute for Research, Palo Alto, California, USA
| | - Junliang Pan
- Palo Alto Veterans Institute for Research, Palo Alto, California, USA
| | - James C Paulson
- Departments of Cell and Molecular Biology, Immunology and Microbial Science, and Chemical Physiology, The Scripps Research Institute, La Jolla, California USA
| | - Eugene C Butcher
- 1] Laboratory of Immunology and Vascular Biology, Department of Pathology, Stanford University School of Medicine, Stanford, California, USA. [2] Palo Alto Veterans Institute for Research, Palo Alto, California, USA. [3] The Center for Molecular Biology and Medicine, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
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High expression of sLex associated with poor survival in Argentinian colorectal cancer patients. Int J Biol Markers 2014; 29:e30-9. [PMID: 24425323 DOI: 10.5301/jbm.5000060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2013] [Indexed: 12/16/2022]
Abstract
AIM Colorectal cancer (CRC) is one of the most prevalent malignancies in Argentina with 11,043 new cases and 6,596 deaths estimated to have occurred in 2008. The present study was developed to clarify the differential expression of MUC1, MUC2, sLex, and sLea in colorectal cancer patients and their relationship with survival and clinical and histological features. METHODS Ninety primary tumor samples and 43 metastatic lymph nodes from CRC patients were studied; follow-up was documented. Twenty-six adenoma and 68 histological normal mucosa specimens were analyzed. An immunohistochemical approach was applied and statistical analysis was performed. RESULTS In tumor samples, MUC1, sLea, and sLex were highly expressed (94%, 67%, and 91%, respectively); also, we found a significantly increased expression of the 3 antigens in primary tumors and metastatic lymph nodes compared with normal mucosa and adenomas. MUC2 was expressed in 52% of both normal mucosa and CRC samples; this reactivity significantly decreased in metastatic lymph nodes (p<0.05). A multiple comparison analysis showed that MUC1 and sLex discriminated among 3 groups: normal, adenoma, and CRC tissues. The increase of sLex expression showed an association with recurrence, and survival analysis showed that a high sLex staining was significantly associated with a poor survival. By multivariate analysis MUC1 inmunoreactivity correlated positively and significantly with tumor size, while MUC2 expression showed the opposite correlation. CONCLUSIONS The correlation of sLex overexpression in primary tumors and metastatic lymph nodes, the discrimination among the normal, adenoma, and CRC groups based on sLex expression, as well as its association with recurrence and survival, all suggest a prognostic role of sLex in Argentinian CRC patients.
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Nordén R, Nyström K, Aurelius J, Brisslert M, Olofsson S. Virus-induced appearance of the selectin ligand sLeX in herpes simplex virus type 1-infected T-cells: Involvement of host and viral factors. Glycobiology 2012; 23:310-21. [DOI: 10.1093/glycob/cws160] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Glycomics: An Overview of the Complex Glycocode. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 749:1-13. [DOI: 10.1007/978-1-4614-3381-1_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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