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López-Cortés R, Muinelo-Romay L, Fernández-Briera A, Gil Martín E. High-Throughput Mass Spectrometry Analysis of N-Glycans and Protein Markers after FUT8 Knockdown in the Syngeneic SW480/SW620 Colorectal Cancer Cell Model. J Proteome Res 2024; 23:1379-1398. [PMID: 38507902 PMCID: PMC11002942 DOI: 10.1021/acs.jproteome.3c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Disruption of the glycosylation machinery is a common feature in many types of cancer, and colorectal cancer (CRC) is no exception. Core fucosylation is mediated by the enzyme fucosyltransferase 8 (FucT-8), which catalyzes the addition of α1,6-l-fucose to the innermost GlcNAc residue of N-glycans. We and others have documented the involvement of FucT-8 and core-fucosylated proteins in CRC progression, in which we addressed core fucosylation in the syngeneic CRC model formed by SW480 and SW620 tumor cell lines from the perspective of alterations in their N-glycosylation profile and protein expression as an effect of the knockdown of the FUT8 gene that encodes FucT-8. Using label-free, semiquantitative mass spectrometry (MS) analysis, we found noticeable differences in N-glycosylation patterns in FUT8-knockdown cells, affecting core fucosylation and sialylation, the Hex/HexNAc ratio, and antennarity. Furthermore, stable isotopic labeling of amino acids in cell culture (SILAC)-based proteomic screening detected the alteration of species involved in protein folding, endoplasmic reticulum (ER) and Golgi post-translational stabilization, epithelial polarity, and cellular response to damage and therapy. This data is available via ProteomeXchange with identifier PXD050012. Overall, the results obtained merit further investigation to validate their feasibility as biomarkers of progression and malignization in CRC, as well as their potential usefulness in clinical practice.
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Affiliation(s)
- Rubén López-Cortés
- Doctoral
Program in Methods and Applications in Life Sciences, Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Laura Muinelo-Romay
- Liquid
Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago de Compostela
(IDIS), CIBERONC, Travesía da Choupana, 15706 Santiago de Compostela, A Coruña
(Galicia), Spain
| | - Almudena Fernández-Briera
- Molecular
Biomarkers, Biomedical Research Centre (CINBIO), Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Emilio Gil Martín
- Nutrition
and Food Science Group, Department of Biochemistry, Genetics and Immunology,
Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
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2
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Shimazaki H, Nakamura K, Ono A, Segawa O, Sawakami K, Koizuka M, Hirayama M, Hori K, Tajima H, Kuno A. Auto-Lectin Dotcoding by Two Octopuses: Rapid Analysis of Fluorescence-Labeled Glycoproteins by an 8-channel Fully-Automatic Bead Array Scanner with a Rolling-Circle Detector. Anal Chem 2023; 95:11868-11873. [PMID: 37535807 DOI: 10.1021/acs.analchem.3c01395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Protein glycosylation is a crucial factor that must be evaluated in biological pharmaceuticals. The glycoform profile of a protein can vary depending on the conditions of the cultivation, purification process, and the selection of a host cell. Lectin microarrays are reliable bioanalytical methods used in the early phases of bioprocesses for the detection of glycosylation. The concept of a fully automated glycan detection with a bead array has been previously reported; however, no simple system has been constructed on fluorescence-based detection using a microarray. Here, we present a fully automated detection system equipped with a novel fluorescence detector for a 13-lectin bead array with a single tip. The lattice-like arrangement of a set of fibers proximate to the tip of the light emitting diode and photomultiplier tube detector minimized the noise caused by the reflection of incident light on the plastic capillary tip and bead. A unique rolling-circle fiber unit with quadruple lattices stacked in two layers realizes the 8-parallel automeasurement with a drastic reduction in scanning time and machine size. The 8-glycan profiles obtained automatically within 25 min were identical with those obtained with the conventional lectin microarray after overnight incubation. The signals obtained were represented as lectin dotcodes. Therefore, autolectin dotcoding assisted by the twin 8 legs named as "detection and irradiation octopuses" may be a rapid glyco-evaluation system during the production and development of biopharmaceuticals.
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Affiliation(s)
- Hiroko Shimazaki
- Molecular & Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Kazuhiro Nakamura
- Precision System Science, Kamihongou, Matsudo, Chiba 271-0064, Japan
| | - Ayaka Ono
- Molecular & Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Osamu Segawa
- Precision System Science, Kamihongou, Matsudo, Chiba 271-0064, Japan
| | - Kazumi Sawakami
- Precision System Science, Kamihongou, Matsudo, Chiba 271-0064, Japan
| | - Michinori Koizuka
- Precision System Science, Kamihongou, Matsudo, Chiba 271-0064, Japan
| | - Makoto Hirayama
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-7528, Japan
| | - Kanji Hori
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-7528, Japan
| | - Hideji Tajima
- Precision System Science, Kamihongou, Matsudo, Chiba 271-0064, Japan
| | - Atsushi Kuno
- Molecular & Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
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Liu X, Yang Z, Liu C, Xu B, Wang X, Li Y, Xia J, Li D, Zhang C, Sun H, Yang Q. Identification of a type II LacNAc specific binding lectin CMRBL from Cordyceps militaris. Int J Biol Macromol 2023; 230:123207. [PMID: 36632960 DOI: 10.1016/j.ijbiomac.2023.123207] [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: 03/28/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/10/2023]
Abstract
The Cordyceps militaris gene CCM_03832 encodes a ricin-B like lectin. The gene was cloned and expressed in Escherichia coli, and its protein product, named CMRBL (C. militaris ricin-B like lectin), was purified by galactose affinity chromatography. Of nine different sources of erythrocytes, CMRBL showed only specific hemagglutinating activity against rat and rabbit erythrocytes with titers of 22 and 28, respectively. Glycan array analyses by the Consortium for Functional Glycomics showed that CMRBL possesses very high specific binding activity of glycans terminated with type II LacNAc (non-reducing Galβ1-4GlcNAc). Compared with other well-known Gal-terminated binding lectins such as Erythrina cristagalli agglutinin, Ricinus communis agglutinin, and Jacalin, CMRBL showed better binding specificity to type II LacNAc compared the other lectins. CMRBL showed lowest binding activity to ZR-75-30 and MDA-MB-468 cell lines among five tested cell lines (H22, THP-1, MDA-MB-231, ZR-75-30, and MDA-MB-468 cells). Transfection of type II LacNAc main galactosyltransferase B4GALT3 to ZR-75-30 significantly improved CMRBL binding activity compared with control. CMRBL was also applied for testing the type II LacNAc modification of Etanercept successfully. Our data suggest that CMRBL would be a useful tool to recognize type II LacNAc, especially distinguish type II from other galactose-terminated glycans in glycan biology research.
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Affiliation(s)
- Xiaomei Liu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zelan Yang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chenglong Liu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Bo Xu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xueqing Wang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yang Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jing Xia
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Danni Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Can Zhang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hui Sun
- College of Life Sciences, Wuhan University, Wuhan 430072, China; Hubei Province key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430071, China; Wuhan Huayang Animal Pharmaceutical Co., Ltd, China.
| | - Qing Yang
- School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
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Recent advances and trends in sample preparation and chemical modification for glycan analysis. J Pharm Biomed Anal 2022; 207:114424. [PMID: 34653745 DOI: 10.1016/j.jpba.2021.114424] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/26/2022]
Abstract
Growing significance of glycosylation in protein functions has accelerated the development of methodologies for detection, identification, and characterization of protein glycosylation. In the past decade, glycobiology research has been advanced by innovative techniques with further progression in the post-genome era. Although significant technical progress has been made in terms of analytical throughput, comprehensiveness, and sensitivity, most methods for glycosylation analysis still require laborious and time-consuming sample preparation tasks. Additionally, sample preparation methods that are focused on specific glycan(s) require an in-depth understanding of various issues in glycobiology. In this review, modern sample preparation and chemical modification methods for the structural and quantitative glycan analyses together with the challenges and advantages of recent sample preparation methods are summarized. The techniques presented herein can facilitate the exploration of biomarkers, understanding of unknown glycan functions, and development of biopharmaceuticals.
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Yu H, Shu J, Li Z. Lectin microarrays for glycoproteomics: an overview of their use and potential. Expert Rev Proteomics 2020; 17:27-39. [PMID: 31971038 DOI: 10.1080/14789450.2020.1720512] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Glycoproteomics is an important subdiscipline of proteomics, focusing on the role of protein glycosylation in various biological processes. Protein glycosylation is the enzymatic addition of sugars or oligosaccharides to proteins. Altered glycosylation often occurs in the early stages of disease development, for example, certain tumor-associated glycans have been shown to be expressed in precursor lesions of different types of cancer, making them powerful early diagnostic markers. Lectin microarrays have become a powerful tool for both the study of glycosylation and the diagnosis of various diseases including cancer.Areas covered: This review will discuss the most useful features of lectin microarrays, such as their technological advances, their capability for parallel/high-throughput analysis for the important glycopatterns of glycoprotein, and an overview of their use for glycosylation analysis of various complex protein samples, as well as their diagnostic potential in various diseases.Expert opinion: Lectin microarrays have proved to be useful in studying multiple lectin-glycan interactions in a single experiment and, with the advances made in the field, hold a promise of enabling glycopatterns of diseases in a fast and efficient manner. Lectin microarrays will become increasingly powerful early diagnostic tool for a variety of conditions.
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Affiliation(s)
- Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
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Saldova R, Kilcoyne M, Stöckmann H, Millán Martín S, Lewis AM, Tuite CME, Gerlach JQ, Le Berre M, Borys MC, Li ZJ, Abu-Absi NR, Leister K, Joshi L, Rudd PM. Advances in analytical methodologies to guide bioprocess engineering for bio-therapeutics. Methods 2016; 116:63-83. [PMID: 27832969 DOI: 10.1016/j.ymeth.2016.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 12/15/2022] Open
Abstract
This study was performed to monitor the glycoform distribution of a recombinant antibody fusion protein expressed in CHO cells over the course of fed-batch bioreactor runs using high-throughput methods to accurately determine the glycosylation status of the cell culture and its product. Three different bioreactors running similar conditions were analysed at the same five time-points using the advanced methods described here. N-glycans from cell and secreted glycoproteins from CHO cells were analysed by HILIC-UPLC and MS, and the total glycosylation (both N- and O-linked glycans) secreted from the CHO cells were analysed by lectin microarrays. Cell glycoproteins contained mostly high mannose type N-linked glycans with some complex glycans; sialic acid was α-(2,3)-linked, galactose β-(1,4)-linked, with core fucose. Glycans attached to secreted glycoproteins were mostly complex with sialic acid α-(2,3)-linked, galactose β-(1,4)-linked, with mostly core fucose. There were no significant differences noted among the bioreactors in either the cell pellets or supernatants using the HILIC-UPLC method and only minor differences at the early time-points of days 1 and 3 by the lectin microarray method. In comparing different time-points, significant decreases in sialylation and branching with time were observed for glycans attached to both cell and secreted glycoproteins. Additionally, there was a significant decrease over time in high mannose type N-glycans from the cell glycoproteins. A combination of the complementary methods HILIC-UPLC and lectin microarrays could provide a powerful and rapid HTP profiling tool capable of yielding qualitative and quantitative data for a defined biopharmaceutical process, which would allow valuable near 'real-time' monitoring of the biopharmaceutical product.
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Affiliation(s)
- Radka Saldova
- NIBRT GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland.
| | - Michelle Kilcoyne
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland; Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
| | - Henning Stöckmann
- NIBRT GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland.
| | - Silvia Millán Martín
- NIBRT GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland.
| | - Amanda M Lewis
- Bristol-Myers Squibb, BMS, Biologics Development, 38 Jackson Road, Devens, MA 01434, USA.
| | - Catherine M E Tuite
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.
| | - Jared Q Gerlach
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland; Regenerative Medicine Institute, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.
| | - Marie Le Berre
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.
| | - Michael C Borys
- Bristol-Myers Squibb, BMS, Biologics Development, 38 Jackson Road, Devens, MA 01434, USA.
| | - Zheng Jian Li
- Bristol-Myers Squibb, BMS, Biologics Development, 38 Jackson Road, Devens, MA 01434, USA.
| | - Nicholas R Abu-Absi
- Bristol-Myers Squibb, BMS, Biologics Development, 38 Jackson Road, Devens, MA 01434, USA.
| | - Kirk Leister
- Bristol-Myers Squibb, BMS, Biologics Development, 38 Jackson Road, Devens, MA 01434, USA.
| | - Lokesh Joshi
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.
| | - Pauline M Rudd
- NIBRT GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland.
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Cook MC, Kaldas SJ, Muradia G, Rosu-Myles M, Kunkel JP. Comparison of orthogonal chromatographic and lectin-affinity microarray methods for glycan profiling of a therapeutic monoclonal antibody. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 997:162-78. [DOI: 10.1016/j.jchromb.2015.05.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
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8
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Chen W, Smeekens JM, Wu R. A universal chemical enrichment method for mapping the yeast N-glycoproteome by mass spectrometry (MS). Mol Cell Proteomics 2014; 13:1563-72. [PMID: 24692641 DOI: 10.1074/mcp.m113.036251] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycosylation is one of the most common and important protein modifications in biological systems. Many glycoproteins naturally occur at low abundances, which makes comprehensive analysis extremely difficult. Additionally, glycans are highly heterogeneous, which further complicates analysis in complex samples. Lectin enrichment has been commonly used, but each lectin is inherently specific to one or several carbohydrates, and thus no single or collection of lectin(s) can bind to all glycans. Here we have employed a boronic acid-based chemical method to universally enrich glycopeptides. The reaction between boronic acids and sugars has been extensively investigated, and it is well known that the interaction between boronic acid and diols is one of the strongest reversible covalent bond interactions in an aqueous environment. This strong covalent interaction provides a great opportunity to catch glycopeptides and glycoproteins by boronic acid, whereas the reversible property allows their release without side effects. More importantly, the boronic acid-diol recognition is universal, which provides great capability and potential for comprehensively mapping glycosylation sites in complex biological samples. By combining boronic acid enrichment with PNGase F treatment in heavy-oxygen water and MS, we have identified 816 N-glycosylation sites in 332 yeast proteins, among which 675 sites were well-localized with greater than 99% confidence. The results demonstrated that the boronic acid-based chemical method can effectively enrich glycopeptides for comprehensive analysis of protein glycosylation. A general trend seen within the large data set was that there were fewer glycosylation sites toward the C termini of proteins. Of the 332 glycoproteins identified in yeast, 194 were membrane proteins. Many proteins get glycosylated in the high-mannose N-glycan biosynthetic and GPI anchor biosynthetic pathways. Compared with lectin enrichment, the current method is more cost-efficient, generic, and effective. This method can be extensively applied to different complex samples for the comprehensive analysis of protein glycosylation.
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Affiliation(s)
- Weixuan Chen
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Johanna M Smeekens
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Hanneman AJ, Strand J, Huang CT. Profiling and Characterization of Sialylated N-glycans by 2D-HPLC (HIAX/PGC) with Online Orbitrap MS/MS and Offline MSn. J Pharm Sci 2014; 103:400-8. [DOI: 10.1002/jps.23792] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/14/2013] [Accepted: 10/30/2013] [Indexed: 01/14/2023]
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