1
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Helali Y, Delporte C. Updates of the current strategies of labeling for N-glycan analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1237:124068. [PMID: 38484674 DOI: 10.1016/j.jchromb.2024.124068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/20/2024] [Accepted: 02/24/2024] [Indexed: 04/13/2024]
Abstract
This mini review summarizes the current methods used for screening N-glycosylation of glycoproteins, with a specific focus on therapeutic proteins and on techniques involving the release of N-glycans. With the continuous development of biopharmaceuticals, particularly monoclonal antibodies (mAbs), which are N-glycosylated proteins, monitoring has gained importance in recent decades. Glycosylation of therapeutic glycoproteins is considered a critical quality attribute because it can impact the efficacy and safety of these therapeutic drugs. The protocols and instrumentation have evolved with the advancement of technologies. Nowadays, methods are becoming increasingly robust, rapid, and sensitive. For the release of N-glycans, the most commonly used method is enzymatic release using PNGase F. The latter is discussed in light of the advent of rapid release that is now possible. The strategy for separating N-glycans using either liquid chromatography (LC) with hydrophilic interaction liquid chromatography (HILIC) chemistry or capillary electrophoresis will be discussed. The selection of the labeling agent is a crucial step in sample preparation for the analysis of released N-glycans. This review also discusses labeling agents that are compatible with and dependent on the separation and detection techniques employed. The emergence of multiplex labeling agents is also summarized. The latter enables the analysis of multiple samples in a single run, but it requires MS analysis.
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Affiliation(s)
- Yosra Helali
- RD3-Pharmacognosis, Bioanalysis and Drug Discovery Unit & Analytical Platform of the Faculty of Pharmacy (APFP), Faculty of Pharmacy, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Cédric Delporte
- RD3-Pharmacognosis, Bioanalysis and Drug Discovery Unit & Analytical Platform of the Faculty of Pharmacy (APFP), Faculty of Pharmacy, Université libre de Bruxelles (ULB), Brussels, Belgium.
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2
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Li M, Feng Y, Ma M, Li L. 12-Plex Isobaric Multiplex Labeling Reagents for Carbonyl-Containing Compound (SUGAR) Tag-Enabled High-Throughput Quantitative Glycomics. Methods Mol Biol 2024; 2823:155-172. [PMID: 39052220 DOI: 10.1007/978-1-0716-3922-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Glycans, which are ubiquitously distributed on most proteins and cell surfaces, are a class of important biomolecules playing crucial roles in various biological processes such as molecular recognition and cellular communication. Modern mass spectrometry (MS) coupled with novel chemical probe labeling strategies has greatly advanced analysis of glycans. However, the requirement of high-throughput and robust quantitative analysis still calls for the development of more advanced tools. Recently, we devised isobaric multiplex reagents for carbonyl-containing compound (SUGAR) tags for 4-plex N-glycan analysis. To further improve the throughput, we utilized the mass-defect strategy and expanded the multiplexing capacity to 12 channels without changing the chemical structure of the SUGAR tag, achieving a threefold enhancement in throughput compared with the original design and managing to perform high-throughput N-glycan analysis in a single LC - MS/MS injection. Herein, we present detailed methods for the synthesis of 12-plex SUGAR isobaric tags, the procedure to release and label the N-glycans from proteins, and the analysis by high-resolution LC-MS/MS, as well as data processing to achieve multiplexed quantitative glycomics.
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Affiliation(s)
- Miyang Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yu Feng
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
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3
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Ma M, Li M, Zhu Y, Zhao Y, Wu F, Wang Z, Feng Y, Chiang HY, Patankar MS, Chang C, Li L. 6-Plex mdSUGAR Isobaric-Labeling Guide Fingerprint Embedding for Glycomics Analysis. Anal Chem 2023; 95:17637-17645. [PMID: 37982459 PMCID: PMC10794169 DOI: 10.1021/acs.analchem.3c03342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Glycans are vital biomolecules with diverse functions in biological processes. Mass spectrometry (MS) has become the most widely employed technology for glycomics studies. However, in the traditional data-dependent acquisition mode, only a subset of the abundant ions during MS1 scans are isolated and fragmented in subsequent MS2 events, which reduces reproducibility and prevents the measurement of low-abundance glycan species. Here, we reported a new method termed 6-plex mdSUGAR isobaric-labeling guide fingerprint embedding (MAGNI), to achieve multiplexed, quantitative, and targeted glycan analysis. The glycan peak signature was embedded by a triplicate-labeling strategy with a 6-plex mdSUGAR tag, and using ultrahigh-resolution mass spectrometers, the low-abundance glycans that carry the mass fingerprints can be recognized on the MS1 spectra through an in-house developed software tool, MAGNIFinder. These embedded unique fingerprints can guide the selection and fragmentation of targeted precursor ions and further provide rich information on glycan structures. Quantitative analysis of two standard glycoproteins demonstrated the accuracy and precision of MAGNI. Using this approach, we identified 304 N-glycans in two ovarian cancer cell lines. Among them, 65 unique N-glycans were found differentially expressed, which indicates a distinct glycosylation pattern for each cell line. Remarkably, 31 N-glycans can be quantified in only 1 × 103 cells, demonstrating the high sensitivity of our method. Taken together, our MAGNI method offers a useful tool for low-abundance N-glycan characterization and is capable of determining small quantitative differences in N-glycan profiling. Therefore, it will be beneficial to the field of glycobiology and will expand our understanding of glycosylation.
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Affiliation(s)
- Min Ma
- School of Pharmacy, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Miyang Li
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Yinlong Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yingyi Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Feixuan Wu
- School of Pharmacy, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Zicong Wang
- School of Pharmacy, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Yu Feng
- School of Pharmacy, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Hung-Yu Chiang
- Biophysics Program, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Manish S. Patankar
- Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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4
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Xu M, Yang A, Xia J, Jiang J, Liu CF, Ye Z, Ma J, Yang S. Protein glycosylation in urine as a biomarker of diseases. Transl Res 2023; 253:95-107. [PMID: 35952983 DOI: 10.1016/j.trsl.2022.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023]
Abstract
Human body fluids have become an indispensable resource for clinical research, diagnosis and prognosis. Urine is widely used to discover disease-specific glycoprotein biomarkers because of its recurrently non-invasive collection and disease-indicating properties. While urine is an unstable fluid in that its composition changes with ingested nutrients and further as it is excreted through micturition, urinary proteins are more stable and their abnormal glycosylation is associated with diseases. It is known that aberrant glycosylation can define tumor malignancy and indicate disease initiation and progression. However, a thorough and translational survey of urinary glycosylation in diseases has not been performed. In this article, we evaluate the clinical applications of urine, introduce methods for urine glycosylation analysis, and discuss urine glycoprotein biomarkers. We emphasize the importance of mining urinary glycoproteins and searching for disease-specific glycosylation in various diseases (including cancer, neurodegenerative diseases, diabetes, and viral infections). With advances in mass spectrometry-based glycomics/glycoproteomics/glycopeptidomics, characterization of disease-specific glycosylation will optimistically lead to the discovery of disease-related urinary biomarkers with better sensitivity and specificity in the near future.
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Affiliation(s)
- Mingming Xu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Arthur Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Jun Xia
- Clinical Laboratory Center, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Junhong Jiang
- Department of Pulmonary and Critical Care Medicine, Dushu Lake Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chun-Feng Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhenyu Ye
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, District of Columbia.
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China.
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5
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Li M, Feng Y, Ma M, Kapur A, Patankar M, Li L. High-Throughput Quantitative Glycomics Enabled by 12-plex Isobaric Multiplex Labeling Reagents for Carbonyl-Containing Compound (SUGAR) Tags. J Proteome Res 2023; 22:1557-1563. [PMID: 36700627 PMCID: PMC10164053 DOI: 10.1021/acs.jproteome.2c00773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Glycans, which are widely distributed on most proteins and cell surfaces, are a class of important biomolecules playing crucial roles in various biological processes such as immune response and cellular communication. Modern mass spectrometry (MS) coupled with novel chemical probes greatly facilitates routine analysis of glycans. However, the requirement of high-throughput analysis still calls for advanced tools to be developed. Recently, we devised isobaric multiplex reagents for carbonyl-containing compound (SUGAR) tags for 4-plex N-glycan analysis. To further improve the throughput, we utilized the subtle mass differences among different isotopologues and expanded the multiplexing capacity to 12 channels, a 3-fold throughput improvement for the original SUGAR tag design and achieved high-throughput N-glycan analysis in a single LC-MS/MS injection. We then applied 12-plex SUGAR tags to profile the N-glycans in four subtypes of human Immunoglobulin G (IgG) and to investigate the N-glycan changes in the endometrial cancer cells (ECC1) treated with Atovaquone, a quinone antimicrobial medication, and a dihydroorotate dehydrogenase (DHODH) inhibitor. Data are available via ProteomeXchange with the identifier PXD038501.
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6
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Patabandige MW, Pfeifer LD, Nguyen HT, Desaire H. Quantitative clinical glycomics strategies: A guide for selecting the best analysis approach. MASS SPECTROMETRY REVIEWS 2022; 41:901-921. [PMID: 33565652 PMCID: PMC8601598 DOI: 10.1002/mas.21688] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/13/2020] [Accepted: 01/24/2021] [Indexed: 05/05/2023]
Abstract
Glycans introduce complexity to the proteins to which they are attached. These modifications vary during the progression of many diseases; thus, they serve as potential biomarkers for disease diagnosis and prognosis. The immense structural diversity of glycans makes glycosylation analysis and quantitation difficult. Fortunately, recent advances in analytical techniques provide the opportunity to quantify even low-abundant glycopeptides and glycans derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Understanding the strengths and weaknesses of different quantitative glycomics analysis methods is important for selecting the best strategy to analyze glycosylation changes in any given set of clinical samples. To provide guidance towards selecting the proper approach, we discuss four widely used quantitative glycomics analysis platforms, including fluorescence-based analysis of released N-linked glycans and three different varieties of MS-based analysis: liquid chromatography (LC)-mass spectrometry (MS) analysis of glycopeptides, matrix-assisted laser desorption ionization-time of flight MS, and LC-ESI-MS analysis of released N-linked glycans. These methods' strengths and weaknesses are compared, particularly associated with the figures of merit that are important for clinical biomarker studies, including: the initial sample requirements, the methods' throughput, sample preparation time, the number of species identified, the methods' utility for isomer separation and structural characterization, method-related challenges associated with quantitation, repeatability, the expertise required, and the cost for each analysis. This review, therefore, provides unique guidance to researchers who endeavor to undertake a clinical glycomics analysis by offering insights on the available analysis technologies.
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Affiliation(s)
- Milani Wijeweera Patabandige
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - Leah D. Pfeifer
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - Hanna T. Nguyen
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - Heather Desaire
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
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7
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Gülmez C. Glucose Tolerance, Antiprotease Activity and Total Oxidant/Antioxidant Capacity Studies of β-Glucosidase Hybrid Nanoflower for Industrial Applications. Chem Biodivers 2022; 19:e202200170. [PMID: 35675565 DOI: 10.1002/cbdv.202200170] [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: 02/22/2022] [Accepted: 05/27/2022] [Indexed: 11/09/2022]
Abstract
β-Glycosidases, which catalyse the hydrolysis of glycoside bonds, have a wide spectrum of industrial applications. However, the reaction product glucose inhibits the activities of many β-glucosidases. Consequently, the reduced catalytic activities of the enzyme limit the industrial applications of the enzymes. For that reason, the studies dealing with maintaining the activities of the relevant enzymes at high glucose concentrations are a great interest among the researchers. In this context, herein, protein-inorganic hybrid nanoflowers were synthesized using β-glucosidase and copper ion by fast sonication method for 10 min. After characterization of synthesized nanoflowers, pH/temperature studies, glucose tolerance, anti-protease activity, recyclability and total antioxidant and total oxidative capacity levels were estimated. Accordingly, the optimum pHs of free β-glucosidase and hybrid nanoflower (β-GNF) were found to be 6 and 5, respectively, and the optimum temperature values for both hybrid nanoflowers and free enzyme were 40 °C. β-GNF exhibited better activity than free enzyme in low acidic and alkaline environment and at high temperature. The nanoflower retained nearly all (99 %) of its initial activity at all glucose concentrations (0.01, 0.05 and 0.1 mg/mL), especially at pH 5 and 6. Also, β-GNF maintained more than 90 % of initial activity at 0.01 and 0.05 mg/mL glucose at pH 4 and 7. It also displayed about 96 % high residual activity after proteinase K treatment for 3 h at 37 °C, while that of the free β-glucosidase was about 87 %. The reusability studies showed that β-GNF only lost ∼28 % of its initial activities at the end of five cycles. The hybrid nanoflowers at 5 mg/mL concentration exhibited the high total antioxidant capacity. In addition, low total oxidant capacity and oxidative stress index levels were recorded at the same concentration of the hybrid nanoflower. The findings of the present study revealed that β-GNFs may be evaluated as a candidate for various industrial applications due to its high glucose tolerance, anti-protease activity, reusability and resistance to low acidic/alkaline environment and high temperature.
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Affiliation(s)
- Canan Gülmez
- Department of Pharmacy Services, Tuzluca Vocational High School, Igdir University, 76000, Igdir, Türkiye
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8
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Mahmoud M, Abdollah MRA, Elsesy ME, Abou El Ella DA, Zada SK, Tolba MF. The natural isoflavone Biochanin-A synergizes 5-fluorouracil anticancer activity in vitro and in vivo in Ehrlich solid-phase carcinoma model. Phytother Res 2022; 36:1310-1325. [PMID: 35112408 DOI: 10.1002/ptr.7388] [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: 07/09/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022]
Abstract
Isoflavones are considered one of the most extensively studied plant-derived phytoestrogenic compounds. Of these, Biochanin A (Bio-A), a natural isoflavone abundant in cabbage, alfalfa, and red clover, has drawn a lot of attention. As reported in multiple studies, Bio-A possesses a promising anticancer activity against estrogen receptor-positive (ER+) breast cancer. The current study investigated the working hypothesis that Bio-A could synergistically enhance the potency of 5-fluorouracil (5-FU) in ER+ breast cancer. The hypothesis was tested both in vitro on hormone receptor-positive (MCF-7) and triple-negative breast cancer cells (MDA-MB231). Additionally, in vivo studies were performed in the Ehrlich solid-phase carcinoma mouse model. The in vitro cytotoxicity studies revealed that Bio-A synergistically increased the potency of 5-FU in both MCF-7 and MDA-MB231 cell lines. The synergistic effect of 5-FU/Bio-A combination was verified in vivo. The combination therapy (where 5-FU was used at one fourth its full dose) led to a significant 75% reduction in tumor volume after two treatment cycles. This was in addition to producing a significant 2.1-fold increase in tumor necrosis area% compared to mock-treated control. In conclusion, the current study presents the first preclinical evidence for the potential merit of 5-FU/Bio-A combination for the treatment of ER+ breast cancer. The synergistic antitumor effect of Bio-A/ 5-FU combination can be, at least partly, attributed to Bio-A-mediated suppression of ER-α/Akt axis and the augmentation of 5-FU-mediated proapoptotic effects. © 2022 John Wiley & Sons, Ltd.
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Affiliation(s)
- Mohamed Mahmoud
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Maha R A Abdollah
- Department of Pharmacology and Biochemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo, Egypt.,The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), El-Sherouk City, Cairo, Egypt
| | - Mohamed E Elsesy
- Pharmacology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt.,Department of Radiotherapy and Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dalal A Abou El Ella
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Suher K Zada
- Biology Department, School of Sciences and Engineering, the American University in Cairo (AUC), New Cairo, Egypt
| | - Mai F Tolba
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.,Center of Drug Discovery Research and Development, Ain Shams University, Cairo, Egypt.,School of Life and Medical Sciences, The University of Hertfordshire-hosted by Global Academic Foundation, New Administrative Capital, Egypt
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9
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Kim J, Yin D, Lee J, An HJ, Kim TY. Deuterium Oxide Labeling for Global Omics Relative Quantification (DOLGOReQ): Application to Glycomics. Anal Chem 2021; 93:14497-14505. [PMID: 34724788 DOI: 10.1021/acs.analchem.1c03157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new relative quantification strategy for glycomics, named deuterium oxide (D2O) labeling for global omics relative quantification (DOLGOReQ), has been developed based on the partial metabolic D2O labeling, which induces a subtle change in the isotopic distribution of glycan ions. The relative abundance of unlabeled to D-labeled glycans was extracted from the overlapped isotopic envelope obtained from a mixture containing equal amounts of unlabeled and D-labeled glycans. The glycan quantification accuracy of DOLGOReQ was examined with mixtures of unlabeled and D-labeled HeLa glycans combined in varying ratios according to the number of cells present in the samples. The relative quantification of the glycans mixed in an equimolar ratio revealed that 92.4 and 97.8% of the DOLGOReQ results were within a 1.5- and 2-fold range of the predicted mixing ratio, respectively. Furthermore, the dynamic quantification range of DOLGOReQ was investigated with unlabeled and D-labeled HeLa glycans mixed in different ratios from 20:1 to 1:20. A good correlation (Pearson's r > 0.90) between the expected and measured quantification ratios over 2 orders of magnitude was observed for 87% of the quantified glycans. DOLGOReQ was also applied in the measurement of quantitative HeLa cell glycan changes that occur under normoxic and hypoxic conditions. Given that metabolic D2O labeling can incorporate D into all types of glycans, DOLGOReQ has the potential as a universal quantification platform for large-scale comparative glycomic experiments.
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Affiliation(s)
- Jonghyun Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Dongtan Yin
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, South Korea.,Graduate School of Analytical & Science Technology, Chungnam National University, Daejeon 34134, South Korea
| | - Jua Lee
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, South Korea.,Graduate School of Analytical & Science Technology, Chungnam National University, Daejeon 34134, South Korea
| | - Hyun Joo An
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, South Korea.,Graduate School of Analytical & Science Technology, Chungnam National University, Daejeon 34134, South Korea
| | - Tae-Young Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
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10
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Yun J, Jo JY, Tuomivaara ST, Lim JM. Isotope labeling strategies of glycans for mass spectrometry-based quantitative glycomics. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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11
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Heininen J, Julku U, Myöhänen T, Kotiaho T, Kostiainen R. Multiplexed analysis of amino acids in mice brain microdialysis samples using isobaric labeling and liquid chromatography-high resolution tandem mass spectrometry. J Chromatogr A 2021; 1656:462537. [PMID: 34537659 DOI: 10.1016/j.chroma.2021.462537] [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: 05/27/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 11/29/2022]
Abstract
We developed a new multiplexed reversed phase liquid chromatography-high resolution tandem mass spectrometric (LC-MS/MS) method. The method is based on isobaric labeling with a tandem mass tag (TMT10-plex) and stable isotope-labeled internal standards, and was used to analyze amino acids in mouse brain microdialysis samples. The TMT10-plex labeling of amino acids allowed analysis of ten samples in one LC-MS/MS run, significantly increasing the sample throughput. The method provides good chromatographic performance (peak half-width between 0.04-0.12 min), allowing separation of all TMT-labeled amino acids with acceptable resolution and high sensitivity (limits of detection typically around 10 nM). The use of stable isotope-labeled internal standards, together with TMT10-plex labeling, ensured good repeatability (relative standard deviation ≤ 12.1 %) and linearity (correlation coefficient > 0.994), indicating good quantitative performance of the multiplexed method. The method was applied to study the effect of d-amphetamine microdialysis perfusion on amino acid concentrations in the mouse brain. All amino acids were reliably detected and quantified, indicating that the method is sensitive enough to detect low concentrations of amino acids in brain microdialysis samples.
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Affiliation(s)
- Juho Heininen
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland
| | - Ulrika Julku
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland
| | - Timo Myöhänen
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland
| | - Tapio Kotiaho
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland; Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box. 55, FIN-00014, Finland
| | - Risto Kostiainen
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland.
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12
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Heffner KM, Wang Q, Hizal DB, Can Ö, Betenbaugh MJ. Glycoengineering of Mammalian Expression Systems on a Cellular Level. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021. [PMID: 29532110 DOI: 10.1007/10_2017_57] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mammalian expression systems such as Chinese hamster ovary (CHO), mouse myeloma (NS0), and human embryonic kidney (HEK) cells serve a critical role in the biotechnology industry as the production host of choice for recombinant protein therapeutics. Most of the recombinant biologics are glycoproteins that contain complex oligosaccharide or glycan attachments representing a principal component of product quality. Both N-glycans and O-glycans are present in these mammalian cells, but the engineering of N-linked glycosylation is of critical interest in industry and many efforts have been directed to improve this pathway. This is because altering the N-glycan composition can change the product quality of recombinant biotherapeutics in mammalian hosts. In addition, sialylation and fucosylation represent components of the glycosylation pathway that affect circulatory half-life and antibody-dependent cellular cytotoxicity, respectively. In this chapter, we first offer an overview of the glycosylation, sialylation, and fucosylation networks in mammalian cells, specifically CHO cells, which are extensively used in antibody production. Next, genetic engineering technologies used in CHO cells to modulate glycosylation pathways are described. We provide examples of their use in CHO cell engineering approaches to highlight these technologies further. Specifically, we describe efforts to overexpress glycosyltransferases and sialyltransfereases, and efforts to decrease sialidase cleavage and fucosylation. Finally, this chapter covers new strategies and future directions of CHO cell glycoengineering, such as the application of glycoproteomics, glycomics, and the integration of 'omics' approaches to identify, quantify, and characterize the glycosylated proteins in CHO cells. Graphical Abstract.
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Affiliation(s)
- Kelley M Heffner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Qiong Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Deniz Baycin Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Özge Can
- Department of Medical Engineering, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
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13
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Xu M, Hu W, Liu Z, Xia J, Chen S, Wang PG, Yang S. Glycoproteomic bioanalysis of exosomes by LC-MS for early diagnosis of pancreatic cancer. Bioanalysis 2021; 13:861-864. [PMID: 34002632 DOI: 10.4155/bio-2021-0036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Mingming Xu
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Wenhua Hu
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Zhaoliang Liu
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Jun Xia
- Department of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, PR China
| | - Sufeng Chen
- Department of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, PR China
| | - Perry G Wang
- Center for Food Safety & Applied Nutrition, US Food & Drug Administration, College Park, MD 20740, USA
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
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14
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Bryan L, Clynes M, Meleady P. The emerging role of cellular post-translational modifications in modulating growth and productivity of recombinant Chinese hamster ovary cells. Biotechnol Adv 2021; 49:107757. [PMID: 33895332 DOI: 10.1016/j.biotechadv.2021.107757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023]
Abstract
Chinese hamster ovary (CHO) cells are one of the most commonly used host cell lines used for the production human therapeutic proteins. Much research over the past two decades has focussed on improving the growth, titre and cell specific productivity of CHO cells and in turn lowering the costs associated with production of recombinant proteins. CHO cell engineering has become of particular interest in recent years following the publication of the CHO cell genome and the availability of data relating to the proteome, transcriptome and metabolome of CHO cells. However, data relating to the cellular post-translational modification (PTMs) which can affect the functionality of CHO cellular proteins has only begun to be presented in recent years. PTMs are important to many cellular processes and can further alter proteins by increasing the complexity of proteins and their interactions. In this review, we describe the research presented from CHO cells to date related on three of the most important PTMs; glycosylation, phosphorylation and ubiquitination.
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Affiliation(s)
- Laura Bryan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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15
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Xu MM, Zhou MT, Li SW, Zhen XC, Yang S. Glycoproteins as diagnostic and prognostic biomarkers for neurodegenerative diseases: A glycoproteomic approach. J Neurosci Res 2021; 99:1308-1324. [PMID: 33634546 DOI: 10.1002/jnr.24805] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/21/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases (NDs) are incurable and can develop progressively debilitating disorders, including dementia and ataxias. Alzheimer's disease and Parkinson's disease are the most common NDs that mainly affect the elderly people. There is an urgent need to develop new diagnostic tools so that patients can be accurately stratified at an early stage. As a common post-translational modification, protein glycosylation plays a key role in physiological and pathological processes. The abnormal changes in glycosylation are associated with the altered biological pathways in NDs. The pathogenesis-related proteins, like amyloid-β and microtubule-associated protein tau, have altered glycosylation. Importantly, specific glycosylation changes in cerebrospinal fluid, blood and urine are valuable for revealing neurodegeneration in the early stages. This review describes the emerging biomarkers based on glycoproteomics in NDs, highlighting the potential applications of glycoprotein biomarkers in the early detection of diseases, monitoring of the disease progression, and measurement of the therapeutic responses. The mass spectrometry-based strategies for characterizing glycoprotein biomarkers are also introduced.
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Affiliation(s)
- Ming-Ming Xu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | | | - Shu-Wei Li
- Nanjing Apollomics Biotech, Inc., Nanjing, China
| | - Xue-Chu Zhen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
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16
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Delafield DG, Li L. Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation. Mol Cell Proteomics 2021; 20:100054. [PMID: 32576592 PMCID: PMC8724918 DOI: 10.1074/mcp.r120.002095] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 12/13/2022] Open
Abstract
Growing implications of glycosylation in physiological occurrences and human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by seminal methodologies and increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. Mass-spectrometry-based strategies for glycomic quantitation have grown to include metabolic incorporation of stable isotopes, deposition of mass difference and mass defect isotopic labels, and isobaric chemical labeling, providing researchers with ample tools for accurate and robust quantitation. Beyond this, workflows have been designed to harness instrument capability for label-free quantification, and numerous software packages have been developed to facilitate reliable spectrum scoring. In this review, we present and highlight the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification.
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Affiliation(s)
- Daniel G Delafield
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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17
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Patabandige MW, Go EP, Desaire H. Clinically Viable Assay for Monitoring Uromodulin Glycosylation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:436-443. [PMID: 33301684 PMCID: PMC8541689 DOI: 10.1021/jasms.0c00317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Uromodulin, also known as the Tamm-Horsfall protein or THP, is the most abundant protein excreted in human urine. It is associated with the progression of kidney diseases; therefore, changes in the glycosylation profile of this protein could serve as a potential biomarker for kidney health. The typical glycomics analysis approaches used to quantify uromodulin glycosylation involve time-consuming and tedious glycoprotein isolation and labeling steps, which limit their utility in clinical glycomics assays, where sample throughput is important. Herein, we introduce a radically simplified sample preparation workflow, with direct ESI-MS analysis, enabling the quantification of N-linked glycans that originate from uromodulin. The method omits any glycan labeling steps but includes steps to reduce the salt content of the samples, thereby minimizing ion suppression. The method is effective for quantifying subtle glycosylation differences of uromodulin samples derived from different biological states. As a proof of concept, glycosylation from samples that differ by pregnancy status were shown to be differentiable.
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Affiliation(s)
- Milani Wijeweera Patabandige
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - Eden P. Go
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - Heather Desaire
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
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18
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Ferreira JA, Relvas-Santos M, Peixoto A, M N Silva A, Lara Santos L. Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:25-43. [PMID: 34118464 PMCID: PMC8498922 DOI: 10.1016/j.gpb.2021.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/25/2021] [Accepted: 03/01/2021] [Indexed: 12/24/2022]
Abstract
Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing (NGS), supported by robust bioinformatics. The quest for genomics-based cancer medicine set the foundations for improved patient stratification, while unveiling a wide array of neoantigens for immunotherapy. Upfront pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target effects. However, the low mutational burden presented by many lesions challenges the generalization of these solutions, requiring the diversification of neoantigen sources. Oncoproteogenomics utilizing customized databases for protein annotation by mass spectrometry (MS) is a powerful tool toward this end. Expanding the concept toward exploring proteoforms originated from post-translational modifications (PTMs) will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer specificity. Walking through the path of systems biology, we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted therapeutics. Moreover, we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics platforms. We envisage that such rationale may flag a rather neglected research field, generating novel paradigms for precision oncology and immunotherapy.
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Affiliation(s)
- José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal.
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal
| | - André M N Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal
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19
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Jeong S, Lim J. Isotope Labeling of
N
‐linked Glycans by Transglycosylation of
Endo‐M
and Isotopic Glucose for Quantitative Glycomics. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Su‐Hee Jeong
- Department of Chemistry Changwon National University Gyeongnam 51140 South Korea
| | - Jae‐Min Lim
- Department of Chemistry Changwon National University Gyeongnam 51140 South Korea
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20
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Glycomics studies using sialic acid derivatization and mass spectrometry. Nat Rev Chem 2020; 4:229-242. [PMID: 37127981 DOI: 10.1038/s41570-020-0174-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2020] [Indexed: 12/13/2022]
Abstract
Proteins can undergo glycosylation during and/or after translation to afford glycoconjugates, which are often secreted by a cell or populate cell surfaces. Changes in the glycan portion can have a strong influence on a glycoconjugate and are associated with a multitude of human pathologies. Of particular interest are sialylated glycoconjugates, which exist as constitutional isomers that differ in their linkages (α2,3, α2,6, α2,8 or α2,9) between sialic acids and their neighbouring monosaccharides. In general, mass spectrometry enables the rapid and sensitive characterization of glycosylation, but there are challenges specific to identifying and (relatively) quantifying sialic acid isomers. These challenges can be addressed using linkage-specific methodologies for sialic acid derivatization, after which mass spectrometry can enable product identification. This Review is concerned with the new and important derivatization approaches reported in the past decade, which have been implemented in various mass-spectrometry-glycomics workflows and have found clinical glycomics applications. The convenience and wide applicability of the approaches make them attractive for studies of sialylation in different types of glycoconjugate.
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21
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A streamlined workflow for twoplexing of N-linked glycan analysis using light ( 12C 6) and heavy ( 13C 6) isotopologues of 3-aminobenzenesulfonic acid. Anal Chim Acta 2020; 1099:155-164. [PMID: 31986272 DOI: 10.1016/j.aca.2019.11.055] [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: 10/03/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 11/20/2022]
Abstract
Comparative glycosylation analysis of biopharmaceuticals requires the development of methods that deliver the necessary throughput, support structural elucidation and relative quantitation of glycans released from therapeutics. The current study presents the development and applicability assessment of a twoplex approach using light and heavy isotopolouges of 3-aminobenzenesulfonic acid (3-ASA) under wet labeling conditions followed by UHPLC-MS analysis in data dependent acquisition mode. Excellent labelling efficiency, >90%, was achieved for both the light and heavy variants of the reagent. Glycan distributions of two human IgG lots labeled by light and heavy isotopolouges were identical, demonstrating no labeling bias introduced by either of the isotopologues. Peak area distributions of glycan profiles of two human IgG lots were compared to 2-aminobenzamide (2-AB) and RapiFluor-MS protocols. The comparison led to identical results in peak area distribution across the three dyes, but differences in chromatographic selectivity attributed to the different tags. MS1 based relative quantitation was further validated by releasing glycans from the same lot of human IgG, with glycan pools obtained labeled with light and heavy isotopologues separately, followed by mixing and clean-up of the same amount of light and heavy labeled glycan pools. MS analyses of each glycan resulted in a ratio of light and heavy XIC in the range of 0.97 ≤ x ≤ 1.05, demonstrating the method is amenable for the relative quantitation of glycans. Excellent correlation between the relative quantitation data of N-glycans from two human IgG N-glycan pools using the twoplex approach and ratios from peak area distribution calculated from the fluorescent chromatogram was observed (r = 0.986), further corroborating the reliability of the method and its potential applicability in the biopharmaceutical industry. Highly informative HCD-MS2 spectra dominated mostly by Y- and Z-type single and double glycosidic fragment ions facilitate structural interpretation of the oligosaccharides.
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22
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Zhu H, Aloor A, Ma C, Kondengaden SM, Wang PG. Mass Spectrometric Analysis of Protein Glycosylation. ACS SYMPOSIUM SERIES 2020. [DOI: 10.1021/bk-2020-1346.ch010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- He Zhu
- These authors contributed equally
| | | | | | | | - Peng George Wang
- Current Address: Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P. R. China
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23
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Feng Y, Li M, Lin Y, Chen B, Li L. Multiplex Quantitative Glycomics Enabled by Periodate Oxidation and Triplex Mass Defect Isobaric Multiplex Reagents for Carbonyl-Containing Compound Tags. Anal Chem 2019; 91:11932-11937. [PMID: 31407884 DOI: 10.1021/acs.analchem.9b02736] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glycosylation is one of the most important post-translational modifications (PTMs) with essential physiological functions, including protein folding, cell signaling, and immune response. Thus, various qualitative and quantitative glycomics analysis strategies have been developed. Recently, the isobaric multiplex reagents for carbonyl-containing compound (SUGAR) tag was developed for quantitative glycomics with multiplexing capacity and increased reporter ion yield. To further improve quantification efficiency and enable quantifying low-abundance species, the mass defect based triplex SUGAR (mdSUGAR) tag has been designed. In addition, we also introduce additional reaction sites for mdSUGAR at the terminal sialic acid by periodate oxidation of the polyhydroxy chain to extend the mass difference and lower the requirement for resolving power. As a result, mdSUGAR tags show complete labeling efficiency, improved fragmentation pattern, and accurate quantification. Moreover, the quantitative performance of the mdSUGAR tags in a complex system has been systematically evaluated and demonstrated reliable results.
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Affiliation(s)
| | | | - Yuanyuan Lin
- School of Pharmacy , Xi'an Jiaotong University , Xi'an , 710061 , People's Republic of China
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24
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Li Q, Xie Y, Wong M, Lebrilla CB. Characterization of Cell Glycocalyx with Mass Spectrometry Methods. Cells 2019; 8:E882. [PMID: 31412618 PMCID: PMC6721671 DOI: 10.3390/cells8080882] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023] Open
Abstract
The cell membrane plays an important role in protecting the cell from its extracellular environment. As such, extensive work has been devoted to studying its structure and function. Crucial intercellular processes, such as signal transduction and immune protection, are mediated by cell surface glycosylation, which is comprised of large biomolecules, including glycoproteins and glycosphingolipids. Because perturbations in glycosylation could result in dysfunction of cells and are related to diseases, the analysis of surface glycosylation is critical for understanding pathogenic mechanisms and can further lead to biomarker discovery. Different mass spectrometry-based techniques have been developed for glycan analysis, ranging from highly specific, targeted approaches to more comprehensive profiling studies. In this review, we summarized the work conducted for extensive analysis of cell membrane glycosylation, particularly those employing liquid chromatography with mass spectrometry (LC-MS) in combination with various sample preparation techniques.
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Affiliation(s)
- Qiongyu Li
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Yixuan Xie
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Maurice Wong
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA 95616, USA.
- Department of Biochemistry, University of California, Davis, CA 95616, USA.
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25
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26
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Le Mauff F, Bamford NC, Alnabelseya N, Zhang Y, Baker P, Robinson H, Codée JDC, Howell PL, Sheppard DC. Molecular mechanism of Aspergillus fumigatus biofilm disruption by fungal and bacterial glycoside hydrolases. J Biol Chem 2019; 294:10760-10772. [PMID: 31167793 DOI: 10.1074/jbc.ra119.008511] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 05/31/2019] [Indexed: 12/30/2022] Open
Abstract
During infection, the fungal pathogen Aspergillus fumigatus forms biofilms that enhance its resistance to antimicrobials and host defenses. An integral component of the biofilm matrix is galactosaminogalactan (GAG), a cationic polymer of α-1,4-linked galactose and partially deacetylated N-acetylgalactosamine (GalNAc). Recent studies have shown that recombinant hydrolase domains from Sph3, an A. fumigatus glycoside hydrolase involved in GAG synthesis, and PelA, a multifunctional protein from Pseudomonas aeruginosa involved in Pel polysaccharide biosynthesis, can degrade GAG, disrupt A. fumigatus biofilms, and attenuate fungal virulence in a mouse model of invasive aspergillosis. The molecular mechanisms by which these enzymes disrupt biofilms have not been defined. We hypothesized that the hydrolase domains of Sph3 and PelA (Sph3h and PelAh, respectively) share structural and functional similarities given their ability to degrade GAG and disrupt A. fumigatus biofilms. MALDI-TOF enzymatic fingerprinting and NMR experiments revealed that both proteins are retaining endo-α-1,4-N-acetylgalactosaminidases with a minimal substrate size of seven residues. The crystal structure of PelAh was solved to 1.54 Å and structure alignment to Sph3h revealed that the enzymes share similar catalytic site residues. However, differences in the substrate-binding clefts result in distinct enzyme-substrate interactions. PelAh hydrolyzed partially deacetylated substrates better than Sph3h, a finding that agrees well with PelAh's highly electronegative binding cleft versus the neutral surface present in Sph3h Our insight into PelAh's structure and function necessitate the creation of a new glycoside hydrolase family, GH166, whose structural and mechanistic features, along with those of GH135 (Sph3), are reported here.
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Affiliation(s)
- François Le Mauff
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, H3A 2B4 Quebec, Canada,; Infectious Disease and Immunity in Global Health, Research Institute of McGill University Health Center, Montreal, H4A 3J1 Quebec, Canada,; McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, H3A 1Y2 Quebec, Canada
| | - Natalie C Bamford
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, M5G 1X8 Ontario, Canada,; Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, M5S 1A8 Ontario, Canada
| | - Noor Alnabelseya
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, M5G 1X8 Ontario, Canada,; Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, M5S 1A8 Ontario, Canada
| | - Yongzhen Zhang
- Leiden Institute of Chemistry, Leiden University, 2300RA Leiden, The Netherlands, and
| | - Perrin Baker
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, M5G 1X8 Ontario, Canada
| | - Howard Robinson
- Photon Science Division, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, 2300RA Leiden, The Netherlands, and
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, M5G 1X8 Ontario, Canada,; Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, M5S 1A8 Ontario, Canada,.
| | - Donald C Sheppard
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, H3A 2B4 Quebec, Canada,; Infectious Disease and Immunity in Global Health, Research Institute of McGill University Health Center, Montreal, H4A 3J1 Quebec, Canada,; McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, H3A 1Y2 Quebec, Canada,.
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27
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Feng Y, Chen B, Yu Q, Zhong X, Frost DC, Ikonomidou C, Li L. Isobaric Multiplex Labeling Reagents for Carbonyl-Containing Compound (SUGAR) Tags: A Probe for Quantitative Glycomic Analysis. Anal Chem 2019; 91:3141-3146. [PMID: 30649853 DOI: 10.1021/acs.analchem.8b05757] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glycans are highly complex entities with multiple building units and different degrees of branched polymerization. Intensive research efforts have been directed to mass spectrometry (MS)-based qualitative and quantitative glycomic analysis due to the important functions of glycans. Among various strategies, isobaric labeling has become popular because of its higher multiplexing capacity. Over the past few years, several isobaric chemical tags have been developed for quantitative glycomics. However, caveats also exist for these tags, such as relatively low reporter ion yield for aminoxyTMT-labeled complex glycans. To overcome the limitations of existing isobaric chemical tags, we designed a class of novel isobaric multiplex reagents for carbonyl-containing compound (SUGAR) tags that can be used to label glycans for quantitative glycomic analysis. The quantitative performance including labeling efficiency, quantification accuracy, and dynamic range of these SUGAR tags has been evaluated, showing promising results. Finally, the 4-plex SUGAR tags have been utilized to investigate N-glycan changes of B-cell acute lymphoblastic leukemia (ALL) pediatric patients before and after chemotherapy.
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28
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Yang G, Hu Y, Sun S, Ouyang C, Yang W, Wang Q, Betenbaugh M, Zhang H. Comprehensive Glycoproteomic Analysis of Chinese Hamster Ovary Cells. Anal Chem 2018; 90:14294-14302. [PMID: 30457839 PMCID: PMC6440468 DOI: 10.1021/acs.analchem.8b03520] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Chinese hamster ovary (CHO) cell line is a major expression system for the production of therapeutic proteins, the majority of which are glycoproteins, such as antibodies and erythropoietin (EPO). The characterization glycosylation profile of therapeutic proteins produced from engineered CHO cells and therapeutic functions, as well as side effects, are critical to understand the important roles of glycosylation. In this study, a large scale glycoproteomic workflow was established and applied to CHO-K1 cells expressing EPO. The workflow includes enrichment of intact glycopeptides from CHO-K1 cell lysate and medium using hydrophilic enrichment, fractionation of the obtained intact glycopeptides (IGPs) by basic reversed phase liquid chromatography (bRPLC), analyzing the glycopeptides using LC-MS/MS, and annotating the results by GPQuest 2.0. A total of 10 338 N-linked glycosite-containing IGPs were identified, representing 1162 unique glycosites in 530 glycoproteins, including 71 unique atypical N-linked IGPs on 18 atypical N-glycosylation sequons with an overrepresentation of the N-X-C motifs. Moreover, we compared the glycoproteins from CHO cell lysate with those from medium using the in-depth N-linked glycoproteome data. The obtained large scale glycoproteomic data from intact N-linked glycopeptides in this study is complementary to the genomic, proteomic, and N-linked glycomic data previously reported for CHO cells. Our method has the potential to monitor the production of recombinant therapeutic glycoproteins.
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Affiliation(s)
- Ganglong Yang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Shisheng Sun
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Chuanzi Ouyang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Qiong Wang
- Department of Chemical and Molecular Engineering, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Michael Betenbaugh
- Department of Chemical and Molecular Engineering, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
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29
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Huang T, Armbruster MR, Coulton JB, Edwards JL. Chemical Tagging in Mass Spectrometry for Systems Biology. Anal Chem 2018; 91:109-125. [DOI: 10.1021/acs.analchem.8b04951] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tianjiao Huang
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - Michael R. Armbruster
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - John B. Coulton
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - James L. Edwards
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
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30
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Smith J, Mittermayr S, Váradi C, Bones J. Quantitative glycomics using liquid phase separations coupled to mass spectrometry. Analyst 2018; 142:700-720. [PMID: 28170017 DOI: 10.1039/c6an02715f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Post-translational modification of proteins by the attachment of glycans is governed by a variety of highly specific enzymes and is associated with fundamental impacts on the parent protein's physical, chemical and biological properties. The inherent connection between cellular physiology and specific glycosylation patterns has been shown to offer potential for diagnostic and prognostic monitoring of altered glycosylation in the disease state. Conversely, glycoprotein based biopharmaceuticals have emerged as dominant therapeutic strategies in the treatment of intricate diseases. Glycosylation present on these biopharmaceuticals represents a major critical quality attribute with impacts on both pharmacokinetics and pharmacodynamics. The structural variety of glycans, based upon their non-template driven assembly, poses a significant analytical challenge for both qualitative and quantitative analysis. Labile monosaccharide constituents, isomeric species and often low sample availability from biological sources necessitates meticulous sample handling, ultra-high-resolution analytical separation and sensitive detection techniques, respectively. In this article a critical review of analytical quantitation approaches using liquid phase separations coupled to mass spectrometry for released glycans of biopharmaceutical and biomedical significance is presented. Considerations associated with sample derivatisation strategies, ionisation, relative quantitation through isotopic as well as isobaric labelling, metabolic/enzymatic incorporation and targeted analysis are all thoroughly discussed.
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Affiliation(s)
- Josh Smith
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland. and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590, Ireland
| | - Stefan Mittermayr
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland.
| | - Csaba Váradi
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland.
| | - Jonathan Bones
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland. and School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1 W8, Ireland
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31
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Dong X, Huang Y, Cho BG, Zhong J, Gautam S, Peng W, Williamson SD, Banazadeh A, Torres-Ulloa KY, Mechref Y. Advances in mass spectrometry-based glycomics. Electrophoresis 2018; 39:3063-3081. [PMID: 30199110 DOI: 10.1002/elps.201800273] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/22/2022]
Abstract
The diversification of the chemical properties and biological functions of proteins is attained through posttranslational modifications, such as glycosylation. Glycans, which are covalently attached to proteins, play a vital role in cell activities. The microheterogeneity and complexity of glycan structures associated with proteins make comprehensive glycomic analysis challenging. However, recent advancements in mass spectrometry (MS), separation techniques, and sample preparation methods have primarily facilitated structural elucidation and quantitation of glycans. This review focuses on describing recent advances in MS-based techniques used for glycomic analysis (2012-2018), including ionization, tandem MS, and separation techniques coupled with MS. Progress in glycomics workflow involving glycan release, purification, derivatization, and separation will also be highlighted here. Additionally, the recent development of quantitative glycomics through comparative and multiplex approaches will also be described.
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Affiliation(s)
- Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Byeong Gwan Cho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Seth D Williamson
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Katya Y Torres-Ulloa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
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32
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 PMCID: PMC7757723 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California, Davis, Davis, California 95616, United States
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33
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Chen B, Feng Y, Frost DC, Zhong X, Buchberger AR, Johnson J, Xu M, Kim M, Puccetti D, Diamond C, Ikonomidou C, Li L. Quantitative Glycomic Analysis by Mass-Defect-Based Dimethyl Pyrimidinyl Ornithine (DiPyrO) Tags and High-Resolution Mass Spectrometry. Anal Chem 2018; 90:7817-7823. [PMID: 29779369 DOI: 10.1021/acs.analchem.8b00548] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We recently developed a novel amine-reactive mass-defect-based chemical tag, dimethyl pyrimidinyl ornithine (DiPyrO), for quantitative proteomic analysis at the MS1 level. In this work, we further extend the application of the DiPyrO tag, which provides amine group reactivity, optical detection capability, and improved electrospray sensitivity, to quantify N-linked glycans enzymatically released from glycoproteins in the glycosylamine form. Duplex DiPyrO tags that differ in mass by 45.3 mDa were used to label the glycosylamine moieties of freshly released N-glycosylamines from glycoprotein standards and human serum proteins. We demonstrate that both MALDI-LTQ-Orbitrap and nano-HILIC LC/MS/MS Fusion Lumos Orbitrap platforms are capable of resolving the singly or multiply charged N-glycans labeled with mass-defect DiPyrO tags. Dynamic range of quantification, based on MS1 peak intensities, was evaluated across 2 orders of magnitude. With optimized N-glycan release conditions, glycosylamine labeling conditions, and MS acquisition parameters, the N-glycan profiles and abundances in human serum proteins of cancer patients before and after chemotherapy were compared. Moreover, this study also opens a door for using well-developed amine-reactive tags for relative quantification of glycans, which could be widely applied.
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34
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Yang S, Chatterjee S, Cipollo J. The Glycoproteomics-MS for Studying Glycosylation in Cardiac Hypertrophy and Heart Failure. Proteomics Clin Appl 2018; 12:e1700075. [PMID: 29424483 DOI: 10.1002/prca.201700075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 11/10/2017] [Indexed: 12/13/2022]
Abstract
With recent advancements of analytical techniques and mass spectrometric instrumentations, proteomics has been widely exploited to study the regulation of protein expression associated with disease states. Many proteins may undergo abnormal change in response to the stimulants, leading to regulation of posttranslationally modified proteins. In this review, the physiological and pathological roles of protein glycosylation in cardiac hypertrophy is discussed, and how the signal pathways regulate heart function and leading to heart failure. The analytical methods for analysis of protein glycosylation, including glycans, glycosite, occupancy, and heterogeneity is emphasized. The rationale on glycoproteins as disease biomarkers is also discussed. The authors also propose potential research in this field and challenges in the diagnosis and treatment of this disease.
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Affiliation(s)
- Shuang Yang
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Subroto Chatterjee
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Cipollo
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
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35
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Otsuka Y, Sato T. Comparative Quantification Method for Glycosylated Products Elongated on β-Xylosides Using a Stable Isotope-Labeled Saccharide Primer. Anal Chem 2018. [PMID: 29533603 DOI: 10.1021/acs.analchem.7b05438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structures and amounts of glycosaminoglycan (GAG) produced by cells have attracted much interest because GAG biosynthesis activity can change in cellular processes such as disease and differentiation. β-Xylosides, also called saccharide primers, have been used as artificial acceptors not only to generate GAG oligosaccharides in cells and tissues but also to investigate their biosynthetic pathways. Various analytical methods have been applied to confirm the structure and amounts of GAG oligosaccharides elongated using saccharide primers, yet sample preparation processes such as solid-phase extraction in analysis can cause experimental error and disrupt accurate comparative quantification of glycosylated products. In this study, we developed a new quantification method using a deuterium-labeled saccharide primer. The "heavy" and "light" primers were chemically synthesized, and priming abilities were confirmed by liquid chromatography-tandem mass spectrometry. Relative peak areas of light/heavy products showed good linearity and were well correlated with the theoretical amounts of glycosylated products. Then, as a validation study, we carried out a biosynthesis inhibition assay using known GAG biosynthesis inhibitors. According to the relative quantification using saccharide primers, differences in the mode-of-action among the four GAG biosynthesis inhibitors were dependent on the GAG biosynthetic pathway. Our results indicate that the method will likely forge a new path for comparative glycosaminoglycomics using cultured cells and tissues.
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Affiliation(s)
- Yuya Otsuka
- Central Research Laboratories , Seikagaku Corporation , Higashiyamato , Tokyo 207-0021 , Japan.,Department of Biosciences and Informatics , Keio University , Hiyoshi, Yokohama , Kanagawa 223-8522 , Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics , Keio University , Hiyoshi, Yokohama , Kanagawa 223-8522 , Japan
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36
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Advances in sample preparation strategies for MS-based qualitative and quantitative N-glycomics. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2017.11.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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37
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Mookherjee A, Guttman M. Bridging the structural gap of glycoproteomics with ion mobility spectrometry. Curr Opin Chem Biol 2018; 42:86-92. [DOI: 10.1016/j.cbpa.2017.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/17/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022]
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38
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Barrientos RC, Zhang Q. Isobaric Labeling of Intact Gangliosides toward Multiplexed LC-MS/MS-Based Quantitative Analysis. Anal Chem 2018; 90:2578-2586. [PMID: 29384363 DOI: 10.1021/acs.analchem.7b04044] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gangliosides are sialic acid-containing glycosphingolipids recognized to play essential role in biological processes. Both the glycan and lipid structures influence their biological function and thus necessitate their determination as intact molecular species. To our knowledge, no multiplexed method for intact gangliosides currently exists. In this paper, we aimed to demonstrate an approach for isobaric labeling of intact gangliosides. Specifically, we carried out the rapid, chemoselective oxidation of sialic acid side chain in common ganglioside core structures using NaIO4 followed by ligation with a carbonyl-reactive isobaric tandem mass tag (TMT) reagent and subsequent RPLC-MS/MS analysis. Attachment of the isobaric label was observed to improve the ionization efficiency of complex gangliosides using electrospray ionization. Fragmentation of the resulting [M + 2H]2+ ions of TMT-labeled gangliosides provided information-rich spectra containing fragments from the glycan, lipid, and TMT reporter ions. This facile approach enabled simultaneous quantification of up to six samples as well as identification of glycan and lipid compositions in a single injection. As a proof-of-concept, using porcine brain total ganglioside extracts pooled at known ratios, we obtained overall sample-to-sample precision of <12% RSD and mean error of <10%. This showcased the great promise and feasibility of this strategy for high-throughput analysis of intact gangliosides in biological extracts.
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Affiliation(s)
- Rodell C Barrientos
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro , Greensboro, North Carolina 27412, United States.,UNCG Center for Translational Biomedical Research, NC Research Campus , Kannapolis, North Carolina 28081, United States
| | - Qibin Zhang
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro , Greensboro, North Carolina 27412, United States.,UNCG Center for Translational Biomedical Research, NC Research Campus , Kannapolis, North Carolina 28081, United States
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39
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Chen B, Zhong X, Feng Y, Snovida S, Xu M, Rogers J, Li L. Targeted MultiNotch MS 3 Approach for Relative Quantification of N-Glycans Using Multiplexed Carbonyl-Reactive Isobaric Tags. Anal Chem 2017; 90:1129-1135. [PMID: 29182308 DOI: 10.1021/acs.analchem.7b03289] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The recently developed and commercially available carbonyl-reactive tandem mass tags (aminoxyTMT) enable multiplexed quantification of glycans through comparison of reporter ion intensities. However, challenges still exist for collision activated dissociation (CAD) MS/MS based quantification of aminoxyTMT due to the relatively low reporter ion yield especially for glycans with labile structures. To circumvent this limitation, we utilized the unique structural features of N-glycan molecules, the common core sugar sequence (HexNAc)2(Man)3, and common m/z of Yn ions generated from different types of precursors by MS/MS and designed a Y1 ion triggered, targeted MultiNotch MS3 relative quantification approach based on aminoxyTMT labeling. This approach was implemented on a nanoHILIC-Tribrid quadrupole-ion trap-Orbitrap platform, which enables prescreening of aminoxyTMT labeled N-glycan precursor ions by Y1 ion fragment ion mass in a higher-energy collisional dissociation (HCD) MS/MS scan and coisolation and cofragmentation of multiple Yn fragment ions that carry the isobaric tags from the inclusion list in the MS/MS/MS scan. Through systematical optimization and evaluation using N-glycans released from several glycoprotein standards and human serum proteins, we demonstrated that the Y1 ion triggered, targeted MultiNotch MS3 approach offers improved accuracy, precision, and sensitivity for relative quantification compared to traditional data-dependent MS2 and Y1 ion MS3 quantification methods.
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Affiliation(s)
| | | | | | - Sergei Snovida
- Thermo Fisher Scientific , Rockford, Illinois 61101, United States
| | | | - John Rogers
- Thermo Fisher Scientific , Rockford, Illinois 61101, United States
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40
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Höti N, Yang S, Aiyetan P, Kumar B, Hu Y, Clark D, Eroglu AU, Shah P, Johnson T, Chowdery WH, Zhang H, Rodriguez R. Overexpression of Exportin-5 Overrides the Inhibitory Effect of miRNAs Regulation Control and Stabilize Proteins via Posttranslation Modifications in Prostate Cancer. Neoplasia 2017; 19:817-829. [PMID: 28881308 PMCID: PMC5587889 DOI: 10.1016/j.neo.2017.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 01/21/2023] Open
Abstract
Although XPO5 has been characterized to have tumor-suppressor features in the miRNA biogenesis pathway, the impact of altered expression of XPO5 in cancers is unexplored. Here we report a novel "oncogenic" role of XPO5 in advanced prostate cancer. Using prostate cancer models, we found that excess levels of XPO5 override the inhibitory effect of the canoncial miRNA-mRNA regulation, resulting in a global increase in proteins expression. Importantly, we found that decreased expression of XPO5 could promote an increase in proteasome degradation, whereas overexpression of XPO5 leads to altered protein posttranslational modification via hyperglycosylation, resulting in cellular protein stability. We evaluated the therapeutic advantage of targeting XPO5 in prostate cancer and found that knocking down XPO5 in prostate cancer cells suppressed cellular proliferation and tumor development without significantly impacting normal fibroblast cells survival. To our knowledge, this is the first report describing the oncogenic role of XPO5 in overriding the miRNAs regulation control. Furthermore, we believe that these findings will provide an explanation as to why, in some cancers that express higher abundance of mature miRNAs, fail to suppress their potential protein targets.
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Affiliation(s)
- Naseruddin Höti
- Brady Urological Institute, Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD; Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD.
| | - Shuang Yang
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Paul Aiyetan
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Binod Kumar
- Brady Urological Institute, Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Yingwei Hu
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - David Clark
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Arife Unal Eroglu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Punit Shah
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Tamara Johnson
- Brady Urological Institute, Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Wasim H Chowdery
- Department of Urology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Hui Zhang
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Ronald Rodriguez
- Department of Urology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
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41
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Yang S, Clark D, Liu Y, Li S, Zhang H. High-throughput analysis of N-glycans using AutoTip via glycoprotein immobilization. Sci Rep 2017; 7:10216. [PMID: 28860471 PMCID: PMC5578957 DOI: 10.1038/s41598-017-10487-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/11/2017] [Indexed: 12/15/2022] Open
Abstract
Analysis of a large number of samples requires an efficient, rapid and reproducible method. Automation is an ideal approach for high-throughput sample preparation. Multi-plexing sample preparation via a 96-well plate format becomes popular in recent years; however, those methods lack specificity and require several cleanup steps via chromatography purification. To overcome these drawbacks, a chemoenzymatic method has been developed utilizing protein conjugation on solid-phase. Previously, sample preparation was successfully performed in a snap-cap spin-column (SCSC) format. However, sample preparation using SCSC is time-consuming and lacks reproducibility. In this work, we integrated the chemoenzymatic technique in a pipette tip (AutoTip) that was operated by an automated liquid handler. We established a multi-step protocol involving protein immobilization, sialic acid modification, and N-glycan release. We first optimized our automated protocol using bovine fetuin as a standard glycoprotein, and then assessed the reproducibility of the AutoTip using isobaric tags for relative N-linked glycan quantification. We then applied this methodology to profile N-glycans from 58 prostate cancer patient urine samples, revealing increased sialyation on urinary N-glycans derived from prostate cancer patients. Our results indicated AutoTip has applications for high-throughput sample preparation for studying the N-linked glycans.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA.
| | - David Clark
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Yang Liu
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
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42
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Yang L, Peng Y, Jiao J, Tao T, Yao J, Zhang Y, Lu H. Metallic Element Chelated Tag Labeling (MeCTL) for Quantitation of N-Glycans in MALDI-MS. Anal Chem 2017. [PMID: 28636329 DOI: 10.1021/acs.analchem.7b01051] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
N-glycosylation plays an important role in chief biological and pathological processes. Quantifying the N-glycan is important since glycan alterations are related to many diseases. In this study, we developed a novel N-glycan quantitation approach using metallic element chelated tag labeling (MeCTL) through reductive amination. The MeCTL strategy is of high labeling efficiency and accurate in quantitation with high reproducibility (CV < 17.03%) and good linearity (R2 > 0.99) within 2 orders of magnitude of dynamic range. Additionally, it provides significant cross-ring fragmentation to distinguish N-glycan isomers. Furthermore, multiplex quantitation by chelation with several different rare earth elements can be achieved. At last, this strategy has been successfully used for evaluation of N-glycan changes in human serum associated with CRC, indicating its potential in clinical applications including disease N-glycome profiling and relative quantitation.
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Affiliation(s)
- Lijun Yang
- Shanghai Cancer Center and Department of Chemistry, Fudan University , Shanghai, 200032, P. R. China.,Institutes of Biomedical Sciences and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University , Shanghai 200032, P. R. China
| | - Ye Peng
- Institutes of Biomedical Sciences and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University , Shanghai 200032, P. R. China
| | - Jing Jiao
- Shanghai Cancer Center and Department of Chemistry, Fudan University , Shanghai, 200032, P. R. China
| | - Tao Tao
- Institutes of Biomedical Sciences and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University , Shanghai 200032, P. R. China
| | - Jun Yao
- Institutes of Biomedical Sciences and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University , Shanghai 200032, P. R. China
| | - Ying Zhang
- Shanghai Cancer Center and Department of Chemistry, Fudan University , Shanghai, 200032, P. R. China.,Institutes of Biomedical Sciences and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University , Shanghai 200032, P. R. China
| | - Haojie Lu
- Shanghai Cancer Center and Department of Chemistry, Fudan University , Shanghai, 200032, P. R. China.,Institutes of Biomedical Sciences and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University , Shanghai 200032, P. R. China
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43
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Shajahan A, Heiss C, Ishihara M, Azadi P. Glycomic and glycoproteomic analysis of glycoproteins-a tutorial. Anal Bioanal Chem 2017; 409:4483-4505. [PMID: 28585084 PMCID: PMC5498624 DOI: 10.1007/s00216-017-0406-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 01/18/2023]
Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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44
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Yang S, Hu Y, Sokoll L, Zhang H. Simultaneous quantification of N- and O-glycans using a solid-phase method. Nat Protoc 2017; 12:1229-1244. [PMID: 28518173 PMCID: PMC5877797 DOI: 10.1038/nprot.2017.034] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glycosylation has a pivotal role in a diverse range of biological activities, modulating the structure and function of proteins. Glycogens coupled to the nitrogen atom (N-linked) of asparagine side chains or to the oxygen atom (O-linked) of serine and threonine side chains represent the two major protein glycosylation forms. N-glycans can be released by glycosidases, whereas O-glycans are often cleaved by chemical reaction. However, it is challenging to combine these enzymatic and chemical reactions in order to analyze both N- and O-glycans. We recently developed a glycoprotei n immobilization for glycan extraction (GIG) method that allows for the simultaneous analysis of N- and O-glycans on a solid support. GIG enables quantitative analysis of N-glycans and O-glycans from a single specimen and can be applied to a high-throughput automated platform. Here we provide a step-by-step GIG protocol that includes procedures for (i) protein immobilization on an aldehyde-active solid support by reductive amination; (ii) stabilization of fragile sialic acids by carbodiimide coupling; (iii) release of N-glycans by PNGase F digestion; (iv) release of O-glycans by β-elimination using ammonia in the presence of 1-phenyl-3-methyl-5-pyrazolone (PMP) to prevent alditol peeling from O-glycans; (v) mass spectrometry (MS) analysis; and (vi) data analysis for identification of glycans using in-house developed software (GIG Tool; free to download via http://www.biomarkercenter.org/gigtool). The GIG tool extracts precursor masses, oxonium ions and glycan fragments from tandem (liquid chromatography (LC)-MS/MS) mass spectra for glycan identification, and reporter ions from quaternary amine containing isobaric tag for glycan (QUANTITY) isobaric tags are used for quantification of the relative abundance of N-glycans. The GIG protocol takes ∼3 d.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lori Sokoll
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Chen Z, Zhong X, Tie C, Chen B, Zhang X, Li L. Development of a hydrophilic interaction liquid chromatography coupled with matrix-assisted laser desorption/ionization-mass spectrometric imaging platform for N-glycan relative quantitation using stable-isotope labeled hydrazide reagents. Anal Bioanal Chem 2017; 409:4437-4447. [PMID: 28540462 DOI: 10.1007/s00216-017-0387-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 12/21/2022]
Abstract
In this work, the capability of newly developed hydrophilic interaction liquid chromatography (HILIC) coupled with matrix-assisted laser desorption/ionization-mass spectrometric imaging (MALDI-MSI) platform for quantitative analysis of N-glycans has been demonstrated. As a proof-of-principle experiment, heavy and light stable-isotope labeled hydrazide reagents labeled maltodextrin ladder were used to demonstrate the feasibility of the HILIC-MALDI-MSI platform for reliable quantitative analysis of N-glycans. MALDI-MSI analysis by an Orbitrap mass spectrometer enabled high-resolution and high-sensitivity detection of N-glycans eluted from HILIC column, allowing the re-construction of LC chromatograms as well as accurate mass measurements for structural inference. MALDI-MSI analysis of the collected LC traces showed that the chromatographic resolution was preserved. The N-glycans released from human serum was used to demonstrate the utility of this novel platform in quantitative analysis of N-glycans from a complex sample. Benefiting from the minimized ion suppression provided by HILIC separation, comparison between MALDI-MS and the newly developed platform HILIC-MALDI-MSI revealed that HILIC-MALDI-MSI provided higher N-glycan coverage as well as better quantitation accuracy in the quantitative analysis of N-glycans released from human serum. Graphical abstract Reconstructed chromatograms based on HILIC-MALDI-MSI results of heavy and light labeled maltodextrin enabling quantitative glycan analysis.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Xuefei Zhong
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Cai Tie
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Bingming Chen
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Xinxiang Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA.
- School of Life Sciences, Tianjin University, No.92 Weijin Road, Nankai District, Tianjin, 300072, China.
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Yang S, Zhang L, Thomas S, Hu Y, Li S, Cipollo J, Zhang H. Modification of Sialic Acids on Solid Phase: Accurate Characterization of Protein Sialylation. Anal Chem 2017; 89:6330-6335. [PMID: 28505427 DOI: 10.1021/acs.analchem.7b01048] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sialic acids play many important roles in several physiological and pathological processes, including cancers, infection, and blood diseases. Sialic acids are fragile and prone to fragmentation under electrospray ionization and matrix-assisted laser desorption/ionization. It is crucial to modify sialic acids for qualitative and quantitative identification of their change in abundance in complex biological samples. Permethylation is a method of choice for sialic acid stabilization, but the harsh conditions during permethylation may lead to the decomposition of O-acetyl groups. Esterification or amidation in solution effectively protects sialic acids, yet it is not trivial to purify glycans from their reagents. Quantitative analysis of glycans can be achieved by labeling their reducing end using fluorescent tags. Loss of sialic acids during labeling is a major concern. In this study, we demonstrated the utility of sialic acids modification for the analysis of sialyl oligosaccharides and glycopeptides. Without modification, sialic acids are partially or completely lost during sample preparation, leading to the presence of false glycans or glycopeptides in the sample. The stabilized sialic acids not only result in accurate identification of sialylated glycans but also improve the characterization of intact glycopeptides. The modification of sialic acids on the solid support facilitates analysis of glycans and their intact glycoproteins.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins University , Baltimore, Maryland 21231, United States.,Laboratory for Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , Silver Spring, Maryland 20993, United States
| | - Lei Zhang
- Department of Pathology, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Stefani Thomas
- Department of Pathology, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park , Rockville, Maryland 20850, United States
| | - John Cipollo
- Laboratory for Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , Silver Spring, Maryland 20993, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University , Baltimore, Maryland 21231, United States
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Chung CY, Wang Q, Yang S, Yin B, Zhang H, Betenbaugh M. Integrated Genome and Protein Editing Swaps α-2,6 Sialylation for α-2,3 Sialic Acid on Recombinant Antibodies from CHO. Biotechnol J 2017; 12. [PMID: 27943633 DOI: 10.1002/biot.201600502] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/12/2016] [Accepted: 12/08/2016] [Indexed: 12/24/2022]
Abstract
Immunoglobin G with α-2,6 sialylation has been reported to have an impact on antibody-dependent cellular cytotoxicity and anti-inflammatory efficacy. However, production of antibodies with α-2,6 sialylation from Chinese hamster ovary cells is challenging due to the inaccessibility of sialyltransferases for the heavy chain N-glycan site and the presence of exclusively α-2,3 sialyltransferases. In this study, combining mutations on the Fc regions to allow sialyltransferase accessibility with overexpression of α-2,6 sialyltransferase produced IgG with significant levels of both α-2,6 and α-2,3 sialylation. Therefore, ST3GAL4 and ST3GAL6 genes were disrupted by CRISPR/Cas9 to minimize the α-2,3 sialylation. Sialidase treatment and SNA lectin blot indicated greatly increased α-2,6 sialylation level relative to α-2,3 sialylation for the α-2,3 sialyltransferase knockouts when combined with α-2,6 sialyltransferase overexpression. Indeed, α-2,3 linked sialic acids were not detected on IgG produced from the α-2,3 sialyltransferase knockout-α-2,6 sialyltransferase overexpression pools. Finally, glycoprofiling of IgG with four amino acid substitutions expressed from an α-2,3 sialyltransferase knockout-α-2,6 sialyltransferase stable clone resulted in more than 77% sialylated glycans and more than 62% biantennary disialylated glycans as indicated by both MALDI-TOF and LC-ESI-MS. Engineered antibodies from these modified Chinese hamster ovary cell lines will provide biotechnologists with IgGs containing N-glycans with different structural variations for examining the role of glycosylation on protein performance.
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Affiliation(s)
- Cheng-Yu Chung
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Qiong Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Shuang Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Bojiao Yin
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
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Yang S, Höti N, Yang W, Liu Y, Chen L, Li S, Zhang H. Simultaneous analyses of N-linked and O-linked glycans of ovarian cancer cells using solid-phase chemoenzymatic method. Clin Proteomics 2017; 14:3. [PMID: 28100988 PMCID: PMC5237303 DOI: 10.1186/s12014-017-9137-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/29/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Glycans play critical roles in a number of biological activities. Two common types of glycans, N-linked and O-linked, have been extensively analyzed in the last decades. N-glycans are typically released from glycoproteins by enzymes, while O-glycans are released from glycoproteins by chemical methods. It is important to identify and quantify both N- and O-linked glycans of glycoproteins to determine the changes of glycans. METHODS The effort has been dedicated to study glycans from ovarian cancer cells treated with O-linked glycosylation inhibitor qualitatively and quantitatively. We used a solid-phase chemoenzymatic approach to systematically identify and quantify N-glycans and O-glycans in the ovarian cancer cells. It consists of three steps: (1) immobilization of proteins from cells and derivatization of glycans to protect sialic acids; (2) release of N-glycans by PNGase F and quantification of N-glycans by isobaric tags; (3) release and quantification of O-glycans by β-elimination in the presence of 1-phenyl-3-methyl-5-pyrazolone (PMP). RESULTS We used ovarian cancer cell lines to study effect of O-linked glycosylation inhibitor on protein glycosylation. Results suggested that the inhibition of O-linked glycosylation reduced the levels of O-glycans. Interestingly, it appeared to increase N-glycan level in a lower dose of the O-linked glycosylation inhibitor. The sequential release and analyses of N-linked and O-linked glycans using chemoenzymatic approach are a platform for studying N-glycans and O-glycans in complex biological samples. CONCLUSION The solid-phase chemoenzymatic method was used to analyze both N-linked and O-linked glycans sequentially released from the ovarian cancer cells. The biological studies on O-linked glycosylation inhibition indicate the effects of O-glycosylation inhibition to glycan changes in both O-linked and N-linked glycan expression.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Naseruddin Höti
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Yang Liu
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD 20850 USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
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Abstract
Glycosylation is one of the most common and essential protein modifications. Glycans conjugated to biomolecules modulate the function of such molecules through both direct recognition of glycan structures and indirect mechanisms that involve the control of protein turnover rates, stability, and conformation. The biological attributes of glycans in numerous biological processes and implications in a number of diseases highlight the necessity for comprehensive characterization of protein glycosylation. This chapter reviews cutting-edge methods and tools developed to facilitate quantitative glycomics. This chapter highlights the different methods employed for the release and purification of glycans from biological samples. The most effective labeling methods developed for sensitive quantitative glycomics are also described and discussed. The chromatographic approaches that have been used effectively in glycomics are also highlighted.
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Affiliation(s)
- L Veillon
- Texas Tech University, Lubbock, TX, United States
| | - S Zhou
- Texas Tech University, Lubbock, TX, United States
| | - Y Mechref
- Texas Tech University, Lubbock, TX, United States.
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Affiliation(s)
- Stefan Gaunitz
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Gabe Nagy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicola L. B. Pohl
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Regional Center for Applied Molecular Oncology, Masaryk Memorial Oncological Institute, 656 53 Brno, Czech Republic
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