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Guo J, Teymur A, Tang C, Saxena R, Wu T. Advancing Point-of-Care Diagnosis: Digitalizing Combinatorial Biomarker Signals for Lupus Nephritis. BIOSENSORS 2024; 14:147. [PMID: 38534254 DOI: 10.3390/bios14030147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
To improve the efficiency and patient coverage of the current healthcare system, user-friendly novel homecare devices are urgently needed. In this work, we developed a smartphone-based analyzing and reporting system (SBARS) for biomarker detection in lupus nephritis (LN). This system offers a cost-effective alternative to traditional, expensive large equipment in signal detection and quantification. This innovative approach involves using a portable and affordable microscopic reader to capture biomarker signals. Through smartphone-based image processing techniques, the intensity of each biomarker signal is analyzed. This system exhibited comparable performance to a commercial Genepix scanner in the detection of two potential novel biomarkers of LN, VISG4 and TNFRSF1b. Importantly, this smartphone-based analyzing and reporting system allows for discriminating LN patients with active renal disease from healthy controls with the area-under-the-curve (AUC) value = 0.9 for TNFRSF1b and 1.0 for VSIG4, respectively, indicating high predictive accuracy.
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Affiliation(s)
- Jiechang Guo
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
- Department of Computer Science, University of Houston, Houston, TX 77024, USA
| | - Aygun Teymur
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
| | - Chenling Tang
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
| | - Ramesh Saxena
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tianfu Wu
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
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2
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Molnarova K, Chobotova M, Kozlik P. IgG glycopeptide enrichment using hydrophilic interaction chromatography-based solid-phase extraction on an aminopropyl column. Anal Bioanal Chem 2024; 416:1867-1881. [PMID: 38349535 PMCID: PMC10901958 DOI: 10.1007/s00216-024-05187-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 03/01/2024]
Abstract
The sample preparation step is pivotal in glycoproteomic analysis. An effective approach in glycoprotein sample preparation involves enriching glycopeptides by solid-phase extraction (SPE) using polar stationary phases in hydrophilic interaction liquid chromatography (HILIC) mode. The aim of this work is to show how different experimental conditions influence the enrichment efficiency of glycopeptides from human immunoglobulin G (IgG) on an aminopropyl-modified SPE column. Different compositions of the elution solvent (acetonitrile, methanol, and isopropanol), along with varying concentrations of elution solvent acidifiers (formic and acetic acid), and different concentrations of acetonitrile for the conditioning and washing solvents (65%, 75%, and 85% acetonitrile) were tested to observe their effects on the glycopeptide enrichment process. Isopropanol proved less effective in enriching glycopeptides, while acetonitrile was the most efficient, with methanol in between. Higher formic acid concentrations in the elution solvent weakened the ionic interactions, particularly with sialylated glycopeptides. Substituting formic acid with acetic acid led to earlier elution of more glycopeptides. The acetonitrile concentration in conditioning and washing solutions played a key role; at 65% acetonitrile, glycopeptides were not retained on the SPE column and were detected in the flow-through fraction. Ultimately, it was proven that the enrichment method was applicable to human plasma samples, resulting in a significant decrease in the abundances of non-glycosylated peptides. To the best of our knowledge, this study represents the first systematic investigation into the impact of the mobile phase on glycopeptide enrichment using an aminopropyl-modified SPE column in HILIC mode. This study demonstrates the substantial impact of even minor variations in experimental conditions, which have not yet been considered in the literature, on SPE-HILIC glycopeptide enrichment. Consequently, meticulous optimization of these conditions is imperative to enhance the specificity and selectivity of glycoproteomic analysis, ensuring accurate and reliable quantification.
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Affiliation(s)
- Katarina Molnarova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Michaela Chobotova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Petr Kozlik
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic.
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3
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Lubman DM. David M. Lubman-The University of Michigan-A retrospective in research. MASS SPECTROMETRY REVIEWS 2023; 42:643-651. [PMID: 34289523 PMCID: PMC8903096 DOI: 10.1002/mas.21718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
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4
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McDowell CT, Lu X, Mehta AS, Angel PM, Drake RR. Applications and continued evolution of glycan imaging mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:674-705. [PMID: 34392557 PMCID: PMC8946722 DOI: 10.1002/mas.21725] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/16/2021] [Accepted: 08/03/2021] [Indexed: 05/03/2023]
Abstract
Glycosylation is an important posttranslational modifier of proteins and lipid conjugates critical for the stability and function of these macromolecules. Particularly important are N-linked glycans attached to asparagine residues in proteins. N-glycans have well-defined roles in protein folding, cellular trafficking and signal transduction, and alterations to them are implicated in a variety of diseases. However, the non-template driven biosynthesis of these N-glycans leads to significant structural diversity, making it challenging to identify the most biologically and clinically relevant species using conventional analyses. Advances in mass spectrometry instrumentation and data acquisition, as well as in enzymatic and chemical sample preparation strategies, have positioned mass spectrometry approaches as powerful analytical tools for the characterization of glycosylation in health and disease. Imaging mass spectrometry expands upon these strategies by capturing the spatial component of a glycan's distribution in-situ, lending additional insight into the organization and function of these molecules. Herein we review the ongoing evolution of glycan imaging mass spectrometry beginning with widely adopted tissue imaging approaches and expanding to other matrices and sample types with potential research and clinical implications. Adaptations of these techniques, along with their applications to various states of disease, are discussed. Collectively, glycan imaging mass spectrometry analyses broaden our understanding of the biological and clinical relevance of N-glycosylation to human disease.
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Affiliation(s)
- Colin T. McDowell
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Xiaowei Lu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
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5
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Yin H, Zhu J. Methods for quantification of glycopeptides by liquid separation and mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:887-917. [PMID: 35099083 PMCID: PMC9339036 DOI: 10.1002/mas.21771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/14/2021] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
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Affiliation(s)
- Haidi Yin
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
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6
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Roopashri AN, Divyashree M, Savitha J. High-sensitivity profiling of glycoproteins from ovarian cancer sera using lectin-affinity and LC-ESI-Q-TOF-MS/MS. CURRENT RESEARCH IN BIOTECHNOLOGY 2023. [DOI: 10.1016/j.crbiot.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
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7
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Mechref Y, Peng W, Gautam S, Ahmadi P, Lin Y, Zhu J, Zhang J, Liu S, Singal AG, Parikh ND, Lubman DM. Mass spectrometry based biomarkers for early detection of HCC using a glycoproteomic approach. Adv Cancer Res 2022; 157:23-56. [PMID: 36725111 PMCID: PMC10014290 DOI: 10.1016/bs.acr.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is the fourth most common cause of cancer-related mortality worldwide and 80%-90% of HCC develops in patients that have underlying cirrhosis. Better methods of surveillance are needed to increase early detection of HCC and the proportion of patients that can be offered curative therapies. Recent work in novel mass spec-based methods for glycomic and glycopeptide analysis for discovery and confirmation of markers for early detection of HCC versus cirrhosis is reviewed in this chapter. Results from recent work in these fields by several groups and the progress made in developing markers of early HCC which can outperform the current serum-based markers are described and discussed. Also, recent developments in isoform analysis of glycans and glycopeptides and in various mass spec fragmentation methods will be described and discussed.
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Affiliation(s)
- Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States.
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Yu Lin
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Jie Zhang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Suyu Liu
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Amit G Singal
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Neehar D Parikh
- Division of Gastroenterology and Hepatology, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, United States.
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8
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Lin Y, Zhu J, Zhang J, Dai J, Liu S, Arroyo A, Rose M, Singal AG, Parikh ND, Lubman DM. Glycopeptides with Sialyl Lewis Antigen in Serum Haptoglobin as Candidate Biomarkers for Nonalcoholic Steatohepatitis Hepatocellular Carcinoma Using a Higher-Energy Collision-Induced Dissociation Parallel Reaction Monitoring-Mass Spectrometry Method. ACS OMEGA 2022; 7:22850-22860. [PMID: 35811936 PMCID: PMC9261276 DOI: 10.1021/acsomega.2c02600] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Nonalcoholic steatohepatitis (NASH) is the fastest growing cause of hepatocellular carcinoma (HCC) in the United States. Changes in N-glycosylation on specific glycosites of serum proteins have been investigated as potential markers for the early detection of NASH-related HCC. Herein, we report a glycopeptide with a Sialyl Lewis structure derived from serum haptoglobin (Hp) as a potential marker for NASH related HCCs among 95 patients with NASH, including 46 cirrhosis, 32 early-stage HCC, and 17 late-stage HCC. Hp immuno-isolated from patient serum was analyzed using LC-HCD-PRM-MS/MS followed by data analysis via Skyline software. Two glycopeptides involving site N184 and four glycopeptides involving site N241 were significantly changed in patients with HCC vs NASH cirrhosis (P < 0.05). The two-marker panel using N-glycopeptide N241_A4G4F2S4 showed the best performance for HCC detection when combined with α-fetoprotein (AFP), with an improved estimated area under the curve (AUC) = 0.898 (95% CI: 0.835, 0.951), compared to the AUC of 0.790(95% CI, 0.697 0.872) using AFP alone (P = 0.048). At 90% specificity, the combination of N241_A4G4F2S4 + AFP had an improved sensitivity of 63.3%, compared to the sensitivity of 52.3% using AFP alone. When using three markers, the panel of AFP + N241_A2G2F1S2 + N241_A4G4F2S4 yielded an estimated AUC of 0.928 (95% CI: 0.877, 0.970). Our findings indicated that N241_A4G4F2S4 may play an important role in distinguishing HCC from NASH cirrhosis.
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Affiliation(s)
- Yu Lin
- Department
of Surgery, University of Michigan Medical
Center, Ann Arbor, Michigan 48109, United States
| | - Jianhui Zhu
- Department
of Surgery, University of Michigan Medical
Center, Ann Arbor, Michigan 48109, United States
| | - Jie Zhang
- Department
of Surgery, University of Michigan Medical
Center, Ann Arbor, Michigan 48109, United States
| | - Jianliang Dai
- Department
of Biostatistics, University of Texas MD
Anderson Cancer Center, Houston, Texas 77030, United States
| | - Suyu Liu
- Department
of Biostatistics, University of Texas MD
Anderson Cancer Center, Houston, Texas 77030, United States
| | - Ana Arroyo
- Department
of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Marissa Rose
- Department
of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Amit G. Singal
- Department
of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Neehar D. Parikh
- Division
of Gastroenterology and Hepatology, University
of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - David M. Lubman
- Department
of Surgery, University of Michigan Medical
Center, Ann Arbor, Michigan 48109, United States
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9
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Lin Y, Zhang J, Arroyo A, Singal AG, Parikh ND, Lubman DM. A Fucosylated Glycopeptide as a Candidate Biomarker for Early Diagnosis of NASH Hepatocellular Carcinoma Using a Stepped HCD Method and PRM Evaluation. Front Oncol 2022; 12:818001. [PMID: 35372033 PMCID: PMC8970044 DOI: 10.3389/fonc.2022.818001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/21/2022] [Indexed: 12/19/2022] Open
Abstract
Aberrant specific N-glycosylation, especially the increase in fucosylation on specific peptide sites of serum proteins have been investigated as potential markers for diagnosis of nonalcoholic steatohepatitis (NASH)-related HCC. We have combined a workflow involving broad scale marker discovery in serum followed by targeted marker evaluation of these fucosylated glycopeptides. This workflow involved an LC-Stepped HCD-DDA-MS/MS method coupled with offline peptide fractionation for large-scale identification of N-glycopeptides directly from pooled serum samples (each n=10) as well as differential determination of N-glycosylation changes between disease states. We then evaluated the fucosylation level of the glycoprotein ceruloplasmin among 62 patient samples (35 cirrhosis, 27 early-stage NASH HCC) by LC-Stepped HCD-PRM-MS/MS to quantitatively analyze 18 targeted glycopeptides. Of these targets, we found the ratio of fucosylation of a tri-antennary glycopeptide from site N762, involving N762_ HexNAc(5)Hex(6)Fuc(2)NeuAc(3) (P=0.0486), increased significantly from cirrhosis to early HCC. This fucosylation ratio of a tri-antennary glycopeptide in CERU could be a potential biomarker for further validation in a larger sample set and could be a promising candidate for early detection of NASH HCC.
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Affiliation(s)
- Yu Lin
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Jie Zhang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Ana Arroyo
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Amit G. Singal
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Neehar D. Parikh
- Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - David M. Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, United States
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10
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Guo Y, Jia W, Yang J, Zhan X. Cancer glycomics offers potential biomarkers and therapeutic targets in the framework of 3P medicine. Front Endocrinol (Lausanne) 2022; 13:970489. [PMID: 36072925 PMCID: PMC9441633 DOI: 10.3389/fendo.2022.970489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
Glycosylation is one of the most important post-translational modifications (PTMs) in a protein, and is the most abundant and diverse biopolymer in nature. Glycans are involved in multiple biological processes of cancer initiation and progression, including cell-cell interactions, cell-extracellular matrix interactions, tumor invasion and metastasis, tumor angiogenesis, and immune regulation. As an important biomarker, tumor-associated glycosylation changes have been extensively studied. This article reviews recent advances in glycosylation-based biomarker research, which is useful for cancer diagnosis and prognostic assessment. Truncated O-glycans, sialylation, fucosylation, and complex branched structures have been found to be the most common structural patterns in malignant tumors. In recent years, immunochemical methods, lectin recognition-based methods, mass spectrometry (MS)-related methods, and fluorescence imaging-based in situ methods have greatly promoted the discovery and application potentials of glycomic and glycoprotein biomarkers in various cancers. In particular, MS-based proteomics has significantly facilitated the comprehensive research of extracellular glycoproteins, increasing our understanding of their critical roles in regulating cellular activities. Predictive, preventive and personalized medicine (PPPM; 3P medicine) is an effective approach of early prediction, prevention and personalized treatment for different patients, and it is known as the new direction of medical development in the 21st century and represents the ultimate goal and highest stage of medical development. Glycosylation has been revealed to have new diagnostic, prognostic, and even therapeutic potentials. The purpose of glycosylation analysis and utilization of biology is to make a fundamental change in health care and medical practice, so as to lead medical research and practice into a new era of 3P medicine.
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Affiliation(s)
- Yuna Guo
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Wenshuang Jia
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Jingru Yang
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- *Correspondence: Xianquan Zhan,
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11
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Wang M, Zhu J, Lubman DM, Gao C. Aberrant glycosylation and cancer biomarker discovery: a promising and thorny journey. Clin Chem Lab Med 2019; 57:407-416. [PMID: 30138110 DOI: 10.1515/cclm-2018-0379] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/15/2018] [Indexed: 12/12/2022]
Abstract
Glycosylation is among the most important post-translational modifications for proteins and is of intrinsic complex character compared with DNAs and naked proteins. Indeed, over 50%-70% of proteins in circulation are glycosylated, and the "sweet attachments" have versatile structural and functional implications. Both the configuration and composition of the attached glycans affect the biological activities of consensus proteins significantly. Glycosylation is generated by complex biosynthetic pathways comprising hundreds of glycosyltransferases, glycosidases, transcriptional factors, transporters and the protein backbone. In addition, lack of direct genetic templates and glyco-specific antibodies such as those commonly used in DNA amplification and protein capture makes research on glycans and glycoproteins even more difficult, thus resulting in sparse knowledge on the pathophysiological implications of glycosylation. Fortunately, cutting-edge technologies have afforded new opportunities and approaches for investigating cancer-related glycosylation. Thus, glycans as well as aberrantly glycosylated protein-based cancer biomarkers have been increasingly recognized. This mini-review highlights the most recent developments in glyco-biomarker studies in an effort to discover clinically relevant cancer biomarkers using advanced analytical methodologies such as mass spectrometry, high-performance liquid chromatographic/ultra-performance liquid chromatography, capillary electrophoresis, and lectin-based technologies. Recent clinical-centered glycobiological studies focused on determining the regulatory mechanisms and the relation with diagnostics, prognostics and even therapeutics are also summarized. These studies indicate that glycomics is a treasure waiting to be mined where the growth of cancer-related glycomics and glycoproteomics is the next great challenge after genomics and proteomics.
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Affiliation(s)
- Mengmeng Wang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, P.R. China
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David M Lubman
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chunfang Gao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, P.R. China, Phone: +86-21-81875131, Fax: +86-21-65562400
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12
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McQuillan AM, Byrd-Leotis L, Heimburg-Molinaro J, Cummings RD. Natural and Synthetic Sialylated Glycan Microarrays and Their Applications. Front Mol Biosci 2019; 6:88. [PMID: 31572731 PMCID: PMC6753469 DOI: 10.3389/fmolb.2019.00088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/28/2019] [Indexed: 12/28/2022] Open
Abstract
This focused chapter serves as a short survey of glycan microarrays that are available with sialylated glycans, including both defined and shotgun arrays, their generation, and their utility in studying differential binding interactions to sialylated compounds, highlighting N-glycolyl (Gc) modified sialylated compounds. A brief discussion of binding interactions by lectins, antibodies, and viruses, and their relevance that have been observed with sialylated glycan microarrays is presented, as well as a discussion of cross-comparisons of array platforms and efforts to centralize and standardize the glycan microarray data.
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Affiliation(s)
- Alyssa M. McQuillan
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
| | - Lauren Byrd-Leotis
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, United States
| | - Jamie Heimburg-Molinaro
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
| | - Richard D. Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
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Abstract
Cancer has high incidence and it will continue to increase over the next decades. Detection and quantification of cancer-associated biomarkers is frequently carried out for diagnosis, prognosis and treatment monitoring at various disease stages. It is well-known that glycosylation profiles change significantly during oncogenesis. Aberrant glycans produced during tumorigenesis are, therefore, valuable molecules for detection and characterization of cancer, and for therapeutic design and monitoring. Although glycoproteomics has benefited from the development of analytical tools such as high performance liquid chromatography, two-dimensional gel and capillary electrophoresis and mass spectrometry, these approaches are not well suited for rapid point-of-care (POC) testing easily performed by medical staff. Lectins are biomolecules found in nature with specific affinities toward particular glycan structures and bind them thus forming a relatively strong complex. Because of this characteristic, lectins have been used in analytical techniques for the selective capture or separation of certain glycans in complex samples, namely, in lectin affinity chromatography, or to characterize glycosylation profiles in diverse clinical situations, using lectin microarrays. Lectin-based biosensors have been developed for the detection of specific aberrant and cancer-associated glycostructures to aid diagnosis, prognosis and treatment assessment of these patients. The attractive features of biosensors, such as portability and simple use make them highly suitable for POC testing. Recent developments in lectin biosensors, as well as their potential and pitfalls in cancer glycan biomarker detection, are presented in this chapter.
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Affiliation(s)
- M Luísa S Silva
- Centre of Chemical Research, Autonomous University of Hidalgo State, Pachuca, Hidalgo, México.
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14
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Xiao H, Sun F, Suttapitugsakul S, Wu R. Global and site-specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:356-379. [PMID: 30605224 PMCID: PMC6610820 DOI: 10.1002/mas.21586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/27/2018] [Indexed: 05/16/2023]
Abstract
Protein glycosylation is ubiquitous in biological systems and plays essential roles in many cellular events. Global and site-specific analysis of glycoproteins in complex biological samples can advance our understanding of glycoprotein functions and cellular activities. However, it is extraordinarily challenging because of the low abundance of many glycoproteins and the heterogeneity of glycan structures. The emergence of mass spectrometry (MS)-based proteomics has provided us an excellent opportunity to comprehensively study proteins and their modifications, including glycosylation. In this review, we first summarize major methods for glycopeptide/glycoprotein enrichment, followed by the chemical and enzymatic methods to generate a mass tag for glycosylation site identification. We next discuss the systematic and quantitative analysis of glycoprotein dynamics. Reversible protein glycosylation is dynamic, and systematic study of glycoprotein dynamics helps us gain insight into glycoprotein functions. The last part of this review focuses on the applications of MS-based proteomics to study glycoproteins in different biological systems, including yeasts, plants, mice, human cells, and clinical samples. Intact glycopeptide analysis is also included in this section. Because of the importance of glycoproteins in complex biological systems, the field of glycoproteomics will continue to grow in the next decade. Innovative and effective MS-based methods will exponentially advance glycoscience, and enable us to identify glycoproteins as effective biomarkers for disease detection and drug targets for disease treatment. © 2019 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2019.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
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15
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Zhu J, Warner E, Parikh ND, Lubman DM. Glycoproteomic markers of hepatocellular carcinoma-mass spectrometry based approaches. MASS SPECTROMETRY REVIEWS 2019; 38:265-290. [PMID: 30472795 PMCID: PMC6535140 DOI: 10.1002/mas.21583] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/19/2018] [Indexed: 05/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is the third most-common cause of cancer-related death worldwide. Most cases of HCC develop in patients that already have liver cirrhosis and have been recommended for surveillance for an early onset of HCC. Cirrhosis is the final common pathway for several etiologies of liver disease, including hepatitis B and C, alcohol, and increasingly non-alcoholic fatty liver disease. Only 20-30% of patients with HCC are eligible for curative therapy due primarily to inadequate early-detection strategies. Reliable, accurate biomarkers for HCC early detection provide the highest likelihood of curative therapy and survival; however, current early-detection methods that use abdominal ultrasound and serum alpha fetoprotein are inadequate due to poor adherence and limited sensitivity and specificity. There is an urgent need for convenient and highly accurate validated biomarkers for HCC early detection. The theme of this review is the development of new methods to discover glycoprotein-based markers for detection of HCC with mass spectrometry approaches. We outline the non-mass spectrometry based methods that have been used to discover HCC markers including immunoassays, capillary electrophoresis, 2-D gel electrophoresis, and lectin-FLISA assays. We describe the development and results of mass spectrometry-based assays for glycan screening based on either MALDI-MS or ESI analysis. These analyses might be based on the glycan content of serum or on glycan screening for target molecules from serum. We describe some of the specific markers that have been developed as a result, including for proteins such as Haptoglobin, Hemopexin, Kininogen, and others. We discuss the potential role for other technologies, including PGC chromatography and ion mobility, to separate isoforms of glycan markers. Analyses of glycopeptides based on new technologies and innovative softwares are described and also their potential role in discovery of markers of HCC. These technologies include new fragmentation methods such as EThcD and stepped HCD, which can identify large numbers of glycopeptide structures from serum. The key role of lectin extraction in various assays for intact glycopeptides or their truncated versions is also described, where various core-fucosylated and hyperfucosylated glycopeptides have been identified as potential markers of HCC. Finally, we describe the role of LC-MRMs or lectin-FLISA MRMs as a means to validate these glycoprotein markers from patient samples. These technological advancements in mass spectrometry have the potential to lead to novel biomarkers to improve the early detection of HCC.
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Affiliation(s)
- Jianhui Zhu
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
| | - Elisa Warner
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
| | - Neehar D. Parikh
- Department of Internal Medicine, The University of Michigan, Ann Arbor 48109, Michigan
| | - David M. Lubman
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
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16
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Tu HC, Lee YP, Liu XY, Chang CF, Lin PC. Direct Screening of Glycan Patterns from Human Sera: A Selective Glycoprotein Microarray Strategy. ACS APPLIED BIO MATERIALS 2019; 2:1286-1297. [DOI: 10.1021/acsabm.9b00001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hsiu-Chung Tu
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yen-Pin Lee
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Xuan-Yu Liu
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chuan-Fa Chang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Chiao Lin
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
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17
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Dahabiyeh LA, Tooth D, Barrett DA. Profiling of 54 plasma glycoproteins by label-free targeted LC-MS/MS. Anal Biochem 2019; 567:72-81. [DOI: 10.1016/j.ab.2018.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 01/02/2023]
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18
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Brambilla D, Chiari M, Gori A, Cretich M. Towards precision medicine: the role and potential of protein and peptide microarrays. Analyst 2019; 144:5353-5367. [DOI: 10.1039/c9an01142k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Techniques to comprehensively analyze protein signatures are pivotal to unravel disease mechanisms, develop novel biomarkers and targeted therapies. In this frame, protein and peptide microarrays can play a major role in fuelling precision medicine.
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Affiliation(s)
- Dario Brambilla
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
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19
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Oliveira FMSD, Mereiter S, Lönn P, Siart B, Shen Q, Heldin J, Raykova D, Karlsson NG, Polom K, Roviello F, Reis CA, Kamali-Moghaddam M. Detection of post-translational modifications using solid-phase proximity ligation assay. N Biotechnol 2017; 45:51-59. [PMID: 29101055 DOI: 10.1016/j.nbt.2017.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/21/2023]
Abstract
Post-translational modifications (PTMs) regulate protein activities to help orchestrate and fine-tune cellular processes. Dysregulation of PTMs is often related with disorders and malignancies, and may serve as a precise biomarker of disease. Developing sensitive tools to measure and monitor low-abundant PTMs in tissue lysates or serum will be instrumental for opening up new PTM-based diagnostic avenues. Here, we investigate the use of solid-phase proximity ligation assay (SP-PLA) for detection of different PTMs. The assay depends on the recognition of the target protein molecule and its modification by three affinity binders. Using antibodies and lectins, we applied the method for detection of glycosylated CD44 and E-Cadherin, and phosphorylated p53 and EGFR. The assay was found to have superior dynamic range and limit of detection compared to standard ELISAs. In summary, we have established the use of SP-PLA as an appropriate method for sensitive detection of PTMs in lysates and sera, which may provide a basis for future PTM-based diagnostic and prognostic biomarkers.
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Affiliation(s)
| | - Stefan Mereiter
- i3S - Instituto de Investigação e Inovação em Saúde and IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Portugal
| | - Peter Lönn
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Benjamin Siart
- Department of Anthropology, University of Vienna, Austria; Department of Behavioral Biology, University of Vienna, Austria
| | - Qiujin Shen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Heldin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Pharmaceutical Biosciences, Uppsala University, Sweden
| | - Doroteya Raykova
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Pharmaceutical Biosciences, Uppsala University, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology at Institute of Biomedicine, Gothenburg University, Sweden
| | - Karol Polom
- Department of Surgical Oncology, Medical University of Gdansk, Poland; General Surgery and Surgical Oncology Department, Università deli Studi di Siena, Italy
| | - Franco Roviello
- General Surgery and Surgical Oncology Department, Università deli Studi di Siena, Italy
| | - Celso A Reis
- i3S - Instituto de Investigação e Inovação em Saúde and IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Portugal; Faculty of Medicine of the University of Porto, Portugal
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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20
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Shimoda A, Tahara Y, Sawada SI, Sasaki Y, Akiyoshi K. Glycan profiling analysis using evanescent-field fluorescence-assisted lectin array: Importance of sugar recognition for cellular uptake of exosomes from mesenchymal stem cells. Biochem Biophys Res Commun 2017; 491:701-707. [PMID: 28751214 DOI: 10.1016/j.bbrc.2017.07.126] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/22/2017] [Indexed: 12/29/2022]
Abstract
Studies involving the functional analysis of exosomal contents including proteins, DNA, and RNA have been reported. Most membrane proteins and lipids are glycosylated, which controls their physical properties and functions, but little is known about glycans on exosomes owing to the difficulty of analysing them. To shed light on these issues, we collected exosomes from mesenchymal stem cells (MSCs) derived from human adipose tissue for glycan profiling using evanescent-field fluorescence-assisted lectin array as well as analysis of their uptake in vivo. Initial analyses showed that the mean diameter of the collected exosomes was 178 nm and they presented with typical exosomal and MSC markers. Regarding the glycan profiling, exosomes interacted more strongly than the membrane of the original MSCs did with a range of lectins, especially sialic acid-binding lectins. The findings also showed that cellular exosome uptake involved recognition by HeLa cell-surface-bound sialic acid-binding immunoglobulin (Ig)-like lectins (siglecs). Confirming this siglec-related uptake, in vivo experiments involving subcutaneous injection of the fluorescently labelled exosomes into mice showed their transport into lymph nodes and internalization by antigen-presenting cells, particularly those expressing CD11b. Closer analysis revealed the colocalization of the exosomes with siglecs, indicating their involvement in the uptake. These findings provide us with an improved understanding of the importance of exosomal transport and targeting in relation to glycans on exosomal surfaces, potentially enabling us to standardize exosomes when using them for therapeutic purposes.
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Affiliation(s)
- Asako Shimoda
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan; Japan Science and Technology Agency (JST), The Exploratory Research for Advanced Technology (ERATO), Bio-nanotransporter Project, Katsura Int'tech Center, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
| | - Yoshiro Tahara
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan; Japan Science and Technology Agency (JST), The Exploratory Research for Advanced Technology (ERATO), Bio-nanotransporter Project, Katsura Int'tech Center, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
| | - Shin-Ichi Sawada
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan; Japan Science and Technology Agency (JST), The Exploratory Research for Advanced Technology (ERATO), Bio-nanotransporter Project, Katsura Int'tech Center, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan; Japan Science and Technology Agency (JST), The Exploratory Research for Advanced Technology (ERATO), Bio-nanotransporter Project, Katsura Int'tech Center, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan.
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21
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Largy E, Cantais F, Van Vyncht G, Beck A, Delobel A. Orthogonal liquid chromatography-mass spectrometry methods for the comprehensive characterization of therapeutic glycoproteins, from released glycans to intact protein level. J Chromatogr A 2017; 1498:128-146. [PMID: 28372839 DOI: 10.1016/j.chroma.2017.02.072] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/04/2017] [Accepted: 02/28/2017] [Indexed: 01/16/2023]
Abstract
Proteins are increasingly used as therapeutics. Their characterization is challenging due to their size and inherent heterogeneity notably caused by post-translational modifications, among which glycosylation is probably the most prominent. The glycosylation profile of therapeutic proteins must therefore be thoroughly analyzed. Here, we illustrate how the use of a combination of various cutting-edge LC or LC/MS(/MS) methods, and operating at different levels of analysis allows the comprehensive characterization of both the N- and O-glycosylations of therapeutic proteins without the need for other approaches (capillary electrophoresis, MALDI-TOF). This workflow does not call for the use of highly specialized/custom hardware and software nor an extensive knowledge of glycan analysis. Most notably, we present the point of view of a contract research organization, with the constraints associated to the work in a regulated environment (GxP). Two salient points of this work are i) the use of mixed-mode chromatography as a fast and straightforward mean of profiling N-glycans sialylation as well as an orthogonal method to separate N-glycans co-eluting in the HILIC mode; and ii) the use of widepore HILIC/MS to analyze challenging N/O-glycosylation profiles at both the peptide and subunit levels. A particular attention was given to the sample preparations in terms of duration, specificity, versatility, and robustness, as well as the ease of data processing.
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Affiliation(s)
- Eric Largy
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Fabrice Cantais
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Géry Van Vyncht
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Alain Beck
- Centre d'Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164, Saint-Julien-en-Genevois, France
| | - Arnaud Delobel
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium.
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22
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Carvalho S, Reis CA, Pinho SS. Cadherins Glycans in Cancer: Sweet Players in a Bitter Process. Trends Cancer 2016; 2:519-531. [PMID: 28741480 DOI: 10.1016/j.trecan.2016.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/01/2016] [Accepted: 08/13/2016] [Indexed: 01/23/2023]
Abstract
Cadherins are key components in tissue morphogenesis and architecture, contributing to the establishment of cohesive cell adhesion. Reduced cellular adhesiveness as a result of cadherin dysfunction is a defining feature of cancer. During tumor development and progression, major changes in the glycan repertoire of cancer cells take place, affecting the stability, trafficking, and cell-adhesion properties of cadherins. Importantly, the different glycoforms of cadherins are promising biomarkers, with potential clinical application to improve the management of patients, and constitute targets for the development of new therapies. This review discusses the most recent insights on the impact of glycan structure on the regulation of cadherin function in cancer, and provides a perspective on how cadherin glycans constitute tumor biomarkers and potential therapeutic targets.
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Affiliation(s)
- Sandra Carvalho
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-465 Porto, Portugal
| | - Celso A Reis
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-465 Porto, Portugal; Institute of Biomedical Sciences of Abel Salazar (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira, 4050-313 Porto, Portugal; Medical Faculty, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Salomé S Pinho
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-465 Porto, Portugal; Medical Faculty, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
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23
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Mereiter S, Balmaña M, Gomes J, Magalhães A, Reis CA. Glycomic Approaches for the Discovery of Targets in Gastrointestinal Cancer. Front Oncol 2016; 6:55. [PMID: 27014630 PMCID: PMC4783390 DOI: 10.3389/fonc.2016.00055] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/24/2016] [Indexed: 12/22/2022] Open
Abstract
Gastrointestinal (GI) cancer is the most common group of malignancies and many of its types are among the most deadly. Various glycoconjugates have been used in clinical practice as serum biomarker for several GI tumors, however, with limited diagnose application. Despite the good accessibility by endoscopy of many GI organs, the lack of reliable serum biomarkers often leads to late diagnosis of malignancy and consequently low 5-year survival rates. Recent advances in analytical techniques have provided novel glycoproteomic and glycomic data and generated functional information and putative biomarker targets in oncology. Glycosylation alterations have been demonstrated in a series of glycoconjugates (glycoproteins, proteoglycans, and glycosphingolipids) that are involved in cancer cell adhesion, signaling, invasion, and metastasis formation. In this review, we present an overview on the major glycosylation alterations in GI cancer and the current serological biomarkers used in the clinical oncology setting. We further describe recent glycomic studies in GI cancer, namely gastric, colorectal, and pancreatic cancer. Moreover, we discuss the role of glycosylation as a modulator of the function of several key players in cancer cell biology. Finally, we address several state-of-the-art techniques currently applied in this field, such as glycomic and glycoproteomic analyses, the application of glycoengineered cell line models, microarray and proximity ligation assay, and imaging mass spectrometry, and provide an outlook to future perspectives and clinical applications.
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Affiliation(s)
- Stefan Mereiter
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Institute of Biomedical Sciences of Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Meritxell Balmaña
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona , Girona , Spain
| | - Joana Gomes
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Ana Magalhães
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Celso A Reis
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Institute of Biomedical Sciences of Abel Salazar (ICBAS), University of Porto, Porto, Portugal; Medical Faculty, University of Porto, Porto, Portugal
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24
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010. MASS SPECTROMETRY REVIEWS 2015; 34:268-422. [PMID: 24863367 PMCID: PMC7168572 DOI: 10.1002/mas.21411] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 05/07/2023]
Abstract
This review is the sixth update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis.
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Affiliation(s)
- David J. Harvey
- Department of BiochemistryOxford Glycobiology InstituteUniversity of OxfordOxfordOX1 3QUUK
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25
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Betzen C, Alhamdani MSS, Lueong S, Schröder C, Stang A, Hoheisel JD. Clinical proteomics: promises, challenges and limitations of affinity arrays. Proteomics Clin Appl 2015; 9:342-7. [PMID: 25594918 PMCID: PMC5024047 DOI: 10.1002/prca.201400156] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/16/2014] [Accepted: 01/13/2015] [Indexed: 12/14/2022]
Abstract
After the establishment of DNA/RNA sequencing as a means of clinical diagnosis, the analysis of the proteome is next in line. As a matter of fact, proteome‐based diagnostics is bound to be even more informative, since proteins are directly involved in the actual cellular processes that are responsible for disease. However, the structural variation and the biochemical differences between proteins, the much wider range in concentration and their spatial distribution as well as the fact that protein activity frequently relies on interaction increase the methodological complexity enormously, particularly if an accuracy and robustness is required that is sufficient for clinical utility. Here, we discuss the contribution that protein microarray formats could play towards proteome‐based diagnostics.
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Affiliation(s)
- Christian Betzen
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany; Department of Pediatric Medicine I, University Children's Hospital Heidelberg, Heidelberg, Germany
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26
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Hirao Y, Matsuzaki H, Iwaki J, Kuno A, Kaji H, Ohkura T, Togayachi A, Abe M, Nomura M, Noguchi M, Ikehara Y, Narimatsu H. Glycoproteomics Approach for Identifying Glycobiomarker Candidate Molecules for Tissue Type Classification of Non-small Cell Lung Carcinoma. J Proteome Res 2014; 13:4705-16. [DOI: 10.1021/pr5006668] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yoshitoshi Hirao
- Research
Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Hideki Matsuzaki
- Research
Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Jun Iwaki
- Research
Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Atsushi Kuno
- Research
Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Hiroyuki Kaji
- Research
Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Takashi Ohkura
- Research
Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Akira Togayachi
- Research
Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Minako Abe
- Research
Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Masaharu Nomura
- Department
of Surgery I, Tokyo Medical University, 6-7-1 Nishi-shinjuku, Shinjuku, Tokyo 160-0023, Japan
| | - Masayuki Noguchi
- Department
of Pathology, Institute of Basic Medical Science, Graduated School
of Comprehensive Human Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuzuru Ikehara
- Research
Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Hisashi Narimatsu
- Research
Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1
Umezono, Tsukuba, Ibaraki 305-8568, Japan
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27
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Chen W, Smeekens JM, Wu R. A universal chemical enrichment method for mapping the yeast N-glycoproteome by mass spectrometry (MS). Mol Cell Proteomics 2014; 13:1563-72. [PMID: 24692641 DOI: 10.1074/mcp.m113.036251] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycosylation is one of the most common and important protein modifications in biological systems. Many glycoproteins naturally occur at low abundances, which makes comprehensive analysis extremely difficult. Additionally, glycans are highly heterogeneous, which further complicates analysis in complex samples. Lectin enrichment has been commonly used, but each lectin is inherently specific to one or several carbohydrates, and thus no single or collection of lectin(s) can bind to all glycans. Here we have employed a boronic acid-based chemical method to universally enrich glycopeptides. The reaction between boronic acids and sugars has been extensively investigated, and it is well known that the interaction between boronic acid and diols is one of the strongest reversible covalent bond interactions in an aqueous environment. This strong covalent interaction provides a great opportunity to catch glycopeptides and glycoproteins by boronic acid, whereas the reversible property allows their release without side effects. More importantly, the boronic acid-diol recognition is universal, which provides great capability and potential for comprehensively mapping glycosylation sites in complex biological samples. By combining boronic acid enrichment with PNGase F treatment in heavy-oxygen water and MS, we have identified 816 N-glycosylation sites in 332 yeast proteins, among which 675 sites were well-localized with greater than 99% confidence. The results demonstrated that the boronic acid-based chemical method can effectively enrich glycopeptides for comprehensive analysis of protein glycosylation. A general trend seen within the large data set was that there were fewer glycosylation sites toward the C termini of proteins. Of the 332 glycoproteins identified in yeast, 194 were membrane proteins. Many proteins get glycosylated in the high-mannose N-glycan biosynthetic and GPI anchor biosynthetic pathways. Compared with lectin enrichment, the current method is more cost-efficient, generic, and effective. This method can be extensively applied to different complex samples for the comprehensive analysis of protein glycosylation.
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Affiliation(s)
- Weixuan Chen
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Johanna M Smeekens
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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28
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Amaya M, Baer A, Voss K, Campbell C, Mueller C, Bailey C, Kehn-Hall K, Petricoin E, Narayanan A. Proteomic strategies for the discovery of novel diagnostic and therapeutic targets for infectious diseases. Pathog Dis 2014; 71:177-89. [PMID: 24488789 PMCID: PMC7108530 DOI: 10.1111/2049-632x.12150] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/18/2014] [Accepted: 01/23/2014] [Indexed: 12/14/2022] Open
Abstract
Viruses have developed numerous and elegant strategies to manipulate the host cell machinery to establish a productive infectious cycle. The interaction of viral proteins with host proteins plays an important role in infection and pathogenesis, often bypassing traditional host defenses such as the interferon response and apoptosis. Host–viral protein interactions can be studied using a variety of proteomic approaches ranging from genetic and biochemical to large‐scale high‐throughput technologies. Protein interactions between host and viral proteins are greatly influenced by host signal transduction pathways. In this review, we will focus on comparing proteomic information obtained through differing technologies and how their integration can be used to determine the functional aspect of the host response to infection. We will briefly review and evaluate techniques employed to elucidate viral–host interactions with a primary focus on Protein Microarrays (PMA) and Mass Spectrometry (MS) as potential tools in the discovery of novel therapeutic targets. As many potential molecular markers and targets are proteins, proteomic profiling is expected to yield both clearer and more direct answers to functional and pharmacologic questions.
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Affiliation(s)
- Moushimi Amaya
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, USA
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29
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Wu J, Zhu J, Yin H, Buckanovich RJ, Lubman DM. Analysis of glycan variation on glycoproteins from serum by the reverse lectin-based ELISA assay. J Proteome Res 2014; 13:2197-204. [PMID: 24575722 PMCID: PMC3993964 DOI: 10.1021/pr401061c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Altered
glycosylation in glycoproteins is associated with carcinogenesis,
and certain glycan structures and glycoproteins are well-known markers
for tumor progression. To identify potential diagnostic candidate
markers, we have developed a novel method for analysis of glycosylation
changes of glycoproteins from crude serum samples using lectin-based
glycoprotein capture followed by detection with biotin/HRP-conjugated
antibodies. The amount of lectin coated on the microplate well was
optimized to achieve low background and improved S/N compared with
current lectin ELISA methods. In the presence of competing sugars
of lectin AAL or with sialic acid removed from the glycoproteins,
we confirmed that this method specifically detects glycosylation changes
of proteins rather than protein abundance variation. Using our reverse
lectin-based ELISA assay, increased fucosylated haptoglobin was observed
in sera of patients with ovarian cancer, while the protein level of
haptoglobin remained the same between cancers and noncases. The combination
of fucosylated haptoglobin and CA125 (AUC = 0.88) showed improved
performance for distinguishing stage-III ovarian cancer from noncases
compared with CA125 alone (AUC = 0.86). In differentiating early-stage
ovarian cancer from noncases, fucosylated haptoglobin showed comparable
performance to CA125. The combination of CA125 and fucosylated haptoglobin
resulted in an AUC of 0.855, which outperforms CA125 to distinguish
early-stage cancer from noncases. Our study provides an alternative
method to quantify glycosylation changes of proteins from serum samples,
which will be essential for biomarker discovery and validation studies.
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Affiliation(s)
- Jing Wu
- University of Michigan , Department of Surgery, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109, United States
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30
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Chen W, Smeekens JM, Wu R. Comprehensive Analysis of Protein N-Glycosylation Sites by Combining Chemical Deglycosylation with LC–MS. J Proteome Res 2014; 13:1466-73. [DOI: 10.1021/pr401000c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Weixuan Chen
- School
of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Johanna M. Smeekens
- School
of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School
of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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31
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Kobayashi Y, Masuda K, Banno K, Kobayashi N, Umene K, Nogami Y, Tsuji K, Ueki A, Nomura H, Sato K, Tominaga E, Shimizu T, Saya H, Aoki D. Glycan profiling of gestational choriocarcinoma using a lectin microarray. Oncol Rep 2014; 31:1121-6. [PMID: 24424471 DOI: 10.3892/or.2014.2979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/09/2013] [Indexed: 11/05/2022] Open
Abstract
Glycosylation is an important post-translational modification, in which attachment of glycans to proteins has effects on biological functions and carcinogenesis. Analysis of human chorionic gonadotropin, a glycoprotein hormone produced by placental trophoblasts and trophoblastic tumors, has contributed to the diagnosis and treatment of trophoblastic disease, resulting in reduced incidence and mortality. However, alterations of the glycan structure itself in choriocarcinoma have not been characterized. We established a new choriocarcinoma cell line, induced choriocarcinoma cell-1 (iC3-1), which mimics the clinical pathohistology in vivo, to examine the tumorigenesis and pathogenesis of choriocarcinoma. In this study, the alterations of glycan structures in the development of choriocarcinoma were examined by performance of comprehensive glycan profiling in clinical samples and in iC3-1 cells using a conventional microarray and the recently introduced lectin microarray. Microarray comparison showed significant upregulation of several characteristic glycogenes in the iC3-1 cells as compared to the parental HTR8/SVneo cells. The lectin array showed increased α-2-6-sialic acid, Galβ1-4GlcNAc, GlcNAcβ1-3GalNAc, and decreased α-1-6 core fucose, high mannose, GalNacβ1-4Gal, GALNAc (Tn antigen) and Galβ1-3Gal in choriocarcinoma tissue compared to normal villi. This is the first report of a lectin array analysis in choriocarcinoma and provides useful information for understanding of the disease.
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Affiliation(s)
- Yusuke Kobayashi
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Kenta Masuda
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Kouji Banno
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Nana Kobayashi
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, Tokyo, Japan
| | - Kiyoko Umene
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Yuya Nogami
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Kosuke Tsuji
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Arisa Ueki
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Hiroyuki Nomura
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Kenji Sato
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Eiichiro Tominaga
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Takatsune Shimizu
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, Tokyo, Japan
| | - Hideyuki Saya
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, Tokyo, Japan
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
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32
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El-Hawiet A, Kitova EN, Klassen JS. Quantifying Protein Interactions with Isomeric Carbohydrate Ligands Using a Catch and Release Electrospray Ionization-Mass Spectrometry Assay. Anal Chem 2013; 85:7637-44. [DOI: 10.1021/ac401627t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amr El-Hawiet
- Alberta Glycomics Centre and Department
of Chemistry, University of Alberta, Edmonton,
Alberta, Canada T6G 2G2
| | - Elena N. Kitova
- Alberta Glycomics Centre and Department
of Chemistry, University of Alberta, Edmonton,
Alberta, Canada T6G 2G2
| | - John S. Klassen
- Alberta Glycomics Centre and Department
of Chemistry, University of Alberta, Edmonton,
Alberta, Canada T6G 2G2
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33
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Costa AR, Rodrigues ME, Henriques M, Oliveira R, Azeredo J. Glycosylation: impact, control and improvement during therapeutic protein production. Crit Rev Biotechnol 2013; 34:281-99. [PMID: 23919242 DOI: 10.3109/07388551.2013.793649] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of the biopharmaceutical industry represented a major revolution for modern medicine, through the development of recombinant therapeutic proteins that brought new hope for many patients with previously untreatable diseases. There is a ever-growing demand for these therapeutics that forces a constant technological evolution to increase product yields while simultaneously reducing costs. However, the process changes made for this purpose may also affect the quality of the product, a factor that was initially overlooked but which is now a major focus of concern. Of the many properties determining product quality, glycosylation is regarded as one of the most important, influencing, for example, the biological activity, serum half-life and immunogenicity of the protein. Consequently, monitoring and control of glycosylation is now critical in biopharmaceutical manufacturing and a requirement of regulatory agencies. A rapid evolution is being observed in this context, concerning the influence of glycosylation in the efficacy of different therapeutic proteins, the impact on glycosylation of a diversity of parameters/processes involved in therapeutic protein production, the analytical methodologies employed for glycosylation monitoring and control, as well as strategies that are being explored to use this property to improve therapeutic protein efficacy (glycoengineering). This work reviews the main findings on these subjects, providing an up-to-date source of information to support further studies.
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Affiliation(s)
- Ana Rita Costa
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar , Braga , Portugal
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34
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Kuzmanov U, Kosanam H, Diamandis EP. The sweet and sour of serological glycoprotein tumor biomarker quantification. BMC Med 2013; 11:31. [PMID: 23390961 PMCID: PMC3751898 DOI: 10.1186/1741-7015-11-31] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 02/07/2013] [Indexed: 12/25/2022] Open
Abstract
Aberrant and dysregulated protein glycosylation is a well-established event in the process of oncogenesis and cancer progression. Years of study on the glycobiology of cancer have been focused on the development of clinically viable diagnostic applications of this knowledge. However, for a number of reasons, there has been only sparse and varied success. The causes of this range from technical to biological issues that arise when studying protein glycosylation and attempting to apply it to practical applications. This review focuses on the pitfalls, advances, and future directions to be taken in the development of clinically applicable quantitative assays using glycan moieties from serum-based proteins as analytes. Topics covered include the development and progress of applications of lectins, mass spectrometry, and other technologies towards this purpose. Slowly but surely, novel applications of established and development of new technologies will eventually provide us with the tools to reach the ultimate goal of quantification of the full scope of heterogeneity associated with the glycosylation of biomarker candidate glycoproteins in a clinically applicable fashion.
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Affiliation(s)
- Uros Kuzmanov
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, 6th floor, 60 Murray Street, Box 32, Toronto, ON M5T 3L9, Canada
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35
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Hayes CA, Doohan R, Kirkley D, Leister K, Harhen B, Savage AV, Karlsson NG. Cross validation of liquid chromatography-mass spectrometry and lectin array for monitoring glycosylation in fed-batch glycoprotein production. Mol Biotechnol 2012; 51:272-82. [PMID: 22048797 DOI: 10.1007/s12033-011-9465-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycosylation analysis of recombinant glycoproteins is of importance for the biopharmaceutical industry and the production of glycoprotein pharmaceuticals. A commercially available lectin array technology was evaluated for its ability to present a reproducible fingerprint of a recombinant CTLY4-IgG fusion glycoprotein expressed in large scale CHO-cell fermentation. The glycosylation prediction from the array was compared to traditional negative mode capillary LC-MS of released oligosaccharides. It was shown that both methods provide data that allow samples to be distinguished by their glycosylation pattern. This included information about sialylation, the presence of reducing terminal galactose β1-, terminal N-acetylglucosamine β1-, and antennary distribution. With both methods it was found that a general trend of increased sialylation was associated with an increase of the antenna and reduced amount of terminal galactose β1-, while N-acetylglucosamine β1- was less affected. LC-MS, but not the lectin array, provided valuable information about the sialic acid isoforms present, including N-acetylneuraminic acid, N-glycolylneuraminic acid and their O-acetylated versions. Detected small amounts of high-mannose structures by LC-MS correlated with the detection of the same epitope by the lectin array.
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36
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Modern Carbohydrate Microarray Biochip Technologies. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2012. [DOI: 10.1016/s1872-2040(11)60584-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Etxebarria J, Calvo J, Martin-Lomas M, Reichardt NC. Lectin-array blotting: profiling protein glycosylation in complex mixtures. ACS Chem Biol 2012; 7:1729-37. [PMID: 22871985 DOI: 10.1021/cb300262x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By combining electrophoretic protein separation with lectin-array-based glycan profiling into a single experiment, we have developed a high-throughput method for the rapid analysis of protein glycosylation in biofluids. Fluorescently tagged proteins are separated by SDS-PAGE and transferred by diffusion to a microscope slide covered with multiple copies of 20 different lectins, where they are trapped by specific carbohydrate protein interactions while retaining their relative locations on the gel. A fluorescence scan of the slide then provides an affinity profile with each of the 20 lectins containing a wealth of structural information regarding the present glycans. The affinity of the employed lectins toward N-glycans was verified on a glycan array of 76 structures. While current lectin-based methods for glycan analysis provide only a picture of the bulk glycosylation in complex protein mixtures or are focused on a few specific known biomarkers, our array-based glycoproteomics method can be used as a biomarker discovery tool for the qualitative exploration of protein glycosylation in an unbiased fashion.
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Affiliation(s)
- Juan Etxebarria
- Biofunctional Nanomaterials
Unit and ‡Mass Spectrometry Platform, CIC biomaGUNE, and §CIBER-BBN, Paseo Miramon
182, 20009 San Sebastian, Spain
| | - Javier Calvo
- Biofunctional Nanomaterials
Unit and ‡Mass Spectrometry Platform, CIC biomaGUNE, and §CIBER-BBN, Paseo Miramon
182, 20009 San Sebastian, Spain
| | - Manuel Martin-Lomas
- Biofunctional Nanomaterials
Unit and ‡Mass Spectrometry Platform, CIC biomaGUNE, and §CIBER-BBN, Paseo Miramon
182, 20009 San Sebastian, Spain
| | - Niels-Christian Reichardt
- Biofunctional Nanomaterials
Unit and ‡Mass Spectrometry Platform, CIC biomaGUNE, and §CIBER-BBN, Paseo Miramon
182, 20009 San Sebastian, Spain
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38
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Shoemaker LD, Achrol AS, Sethu P, Steinberg GK, Chang SD. Clinical neuroproteomics and biomarkers: from basic research to clinical decision making. Neurosurgery 2012; 70:518-25. [PMID: 21866062 DOI: 10.1227/neu.0b013e3182333a26] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Clinical neuroproteomics aims to advance our understanding of disease and injury affecting the central and peripheral nervous systems through the study of protein expression and the discovery of protein biomarkers to facilitate diagnosis and treatment. The general premise of the biomarker field is that in vivo factors present in either tissue or circulating biofluids, reflect pathological changes, and can be identified and analyzed. This approach offers an opportunity to illuminate changes occurring at both the population and patient levels toward the realization of personalized medicine. This review is intended to provide research-driven clinicians with an overview of protein biomarkers of disease and injury for clinical use and to highlight methodology and potential pitfalls. We examine the neuroproteomic biomarker field and discuss the hallmarks and the challenges of clinically relevant biomarker discovery relating to central nervous system pathology. We discuss the issues in the maturation of potential biomarkers from discovery to Food and Drug Administration approval and review several platforms for protein biomarker discovery, including protein microarray and mass spectrometry-based proteomics. We describe the application of microfluidic technologies to the evolution of a robust clinical test. Finally, we highlight several biomarkers currently in use for cancer, ischemia, and injury in the central nervous system. Future efforts using these technologies will result in the maturation of existing and the identification of de novo biomarkers that could guide clinical decision making and advance diagnostic and therapeutic options for the treatment of neurological disease and injury.
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Affiliation(s)
- Lorelei D Shoemaker
- Department of Neurosurgery, Stanford Institute for Neuro-Innovation and Translational Neurosciences, Stanford University, Stanford, California 94305, USA
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39
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Wu J, Xie X, Liu Y, He J, Benitez R, Buckanovich RJ, Lubman DM. Identification and confirmation of differentially expressed fucosylated glycoproteins in the serum of ovarian cancer patients using a lectin array and LC-MS/MS. J Proteome Res 2012; 11:4541-52. [PMID: 22827608 DOI: 10.1021/pr300330z] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In order to discover potential glycoprotein biomarkers in ovarian cancer, we applied a lectin array and Exactag labeling based quantitative glycoproteomics approach. A lectin array strategy was used to detect overall lectin-specific glycosylation changes in serum proteins from patients with ovarian cancer and those with benign conditions. Lectins, which showed significant differential response for fucosylation, were used to extract glycoproteins that had been labeled using isobaric chemical tags. The glycoproteins were then identified and quantified by LC-MS/MS, and five glycoproteins were found to be differentially expressed in the serum of ovarian cancer patients compared to benign diseases. The differentially expressed glycoproteins were further confirmed by lectin-ELISA and ELISA assay. Corticosteroid-binding globulin (CBG), serum amyloid p component (SAP), complement factor B (CFAB), and histidine-rich glycoprotein (HRG) were identified as potential markers for differentiating ovarian cancer from benign diseases or healthy controls. A combination of CBG and HRG (AUC = 0.825) showed comparable performance to CA125 (AUC = 0.829) in differentiating early stage ovarian cancer from healthy controls. The combination of CBG, SAP, and CA125 showed improved performance for distinguishing stage III ovarian cancer from benign diseases compared to CA125 alone. The ability of CBG, SAP, HRG, and CFAB to differentiate the serum of ovarian cancer patients from that of controls was tested using an independent set of samples. Our findings suggest that glycoprotein modifications may be a means to identify novel diagnostic markers for detection of ovarian cancer.
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Affiliation(s)
- Jing Wu
- Department of Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
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40
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Kaneshiro K, Watanabe M, Terasawa K, Uchimura H, Fukuyama Y, Iwamoto S, Sato TA, Shimizu K, Tsujimoto G, Tanaka K. Rapid quantitative profiling of N-glycan by the glycan-labeling method using 3-aminoquinoline/α-cyano-4-hydroxycinnamic acid. Anal Chem 2012; 84:7146-51. [PMID: 22830976 DOI: 10.1021/ac301484f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein glycosylation is a crucial phenomenon for understanding protein functions, since its patterns and degree are associated with many biological processes, such as intercellular signaling and immune response. We previously reported a novel glycan-labeling method using a 3-ainoquinoline/α-cyano-4-hydroxycinnamic acid (3-AQ/CHCA) liquid matrix for highly sensitive detection by matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry (MS). In the present study, we examined the practicality of this method for qualitative and quantitative glycan profile analysis. We first investigated the reproducibility of the data for 16 N-glycans prepared from human epidermal growth factor receptor type 2 (HER2). All of the data obtained in intra-assays and interassays were highly correlated with statistical significance (R(2) > 0.9, p < 0.05). In addition, the HER2 glycosylation pattern differed significantly between different breast cancer cell lines SK-BR-3 and BT474 in a comparative analysis of profile data. Finally, the quantitative capability of this method was examined by using PA-labeled monosialylated N-glycan as an internal standard (IS). Using IS for AQ-labeled neutral and sialylated standard glycans, the ion peak intensity was highly linear (R(2) > 0.9) from 0.5 to 5000 fmol. Furthermore, using IS for HER2 N-glycans, all of the N-glycans were highly linear with their dilution factors (R(2) > 0.9). These results suggest that our developed AQ labeling method enabled rapid qualitative and quantitative analyses of glycans. This glycan analysis method should contribute to the field of biomarker discovery and biomedicine in applications such as quality control of biotechnology-based drugs.
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Affiliation(s)
- Kaoru Kaneshiro
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan.
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41
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Safina G. Application of surface plasmon resonance for the detection of carbohydrates, glycoconjugates, and measurement of the carbohydrate-specific interactions: A comparison with conventional analytical techniques. A critical review. Anal Chim Acta 2012; 712:9-29. [DOI: 10.1016/j.aca.2011.11.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 10/07/2011] [Accepted: 11/04/2011] [Indexed: 12/16/2022]
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42
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Boschetti E, Chung MCM, Righetti PG. "The quest for biomarkers": are we on the right technical track? Proteomics Clin Appl 2011; 6:22-41. [PMID: 22213582 DOI: 10.1002/prca.201100039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 10/01/2011] [Accepted: 11/15/2011] [Indexed: 12/19/2022]
Abstract
The discovery phase of biomarkers of diagnostic or therapeutic interest started a decade ago with the very rapid development of proteomic investigations. In spite of the development of innovative technologies and multiple approaches, the "harvest" is still modest. Various reasons justified the encountered difficulties and most of them have been circumvented by specific sample treatments or dedicated analytical approaches. Nevertheless, the situation of very modest biomarker discovery level did not change much. This review intends to specifically analyze the main approaches used for biomarker discovery phase and evaluate related advantages and disadvantages. Thus, preliminary sample treatments such as fractionation, depletion and reduction of dynamic concentration range will critically be discussed and then the main differential expression investigation methods analyzed. Combinations of technologies are also discussed along with possible proposals to federate associations of complementary technologies for better chances of success.
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Affiliation(s)
- Egisto Boschetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, Italy.
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43
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Lundborg M, Fontana C, Widmalm G. Automatic structure determination of regular polysaccharides based solely on NMR spectroscopy. Biomacromolecules 2011; 12:3851-5. [PMID: 21955217 PMCID: PMC3215282 DOI: 10.1021/bm201169y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 09/20/2011] [Indexed: 01/22/2023]
Abstract
The structural analysis of polysaccharides requires that the sugar components and their absolute configurations are determined. We here show that this can be performed based on NMR spectroscopy by utilizing butanolysis with (+)- and (-)-2-butanol that gives the corresponding 2-butyl glycosides with characteristic (1)H and (13)C NMR chemical shifts. The subsequent computer-assisted structural determination by CASPER can then be based solely on NMR data in a fully automatic way as shown and implemented herein. The method is additionally advantageous in that reference data only have to be prepared once and from a user's point of view only the unknown sample has to be derivatized for use in CASPER.
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Affiliation(s)
- Magnus Lundborg
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Carolina Fontana
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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Zhou F, Sikorski TW, Ficarro SB, Webber JT, Marto JA. Online nanoflow reversed phase-strong anion exchange-reversed phase liquid chromatography-tandem mass spectrometry platform for efficient and in-depth proteome sequence analysis of complex organisms. Anal Chem 2011; 83:6996-7005. [PMID: 21851055 PMCID: PMC3196608 DOI: 10.1021/ac200639v] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The dynamic range of protein expression in complex organisms coupled with the stochastic nature of discovery-driven tandem mass spectrometry (MS/MS) analysis continues to impede comprehensive sequence analysis and often provides only limited information for low-abundance proteins. High-performance fractionation of proteins or peptides prior to mass spectrometry analysis can mitigate these effects, though achieving an optimal combination of automation, reproducibility, separation peak capacity, and sample yield remains a significant challenge. Here we demonstrate an automated nanoflow 3-D liquid chromatography (LC)-MS/MS platform based on high-pH reversed phase (RP), strong anion exchange (SAX), and low-pH reversed phase (RP) separation stages for analysis of complex proteomes. We observed that RP-SAX-RP outperformed RP-RP for analysis of tryptic peptides derived from Escherichia coli and enabled identification of proteins present at a level of 50 copies per cell in Saccharomyces cerevisiae, corresponding to an estimated detection limit of 500 amol, from 40 μg of total lysate on a low-resolution 3-D ion trap mass spectrometer. A similar study performed on a LTQ-Orbitrap yielded over 4000 unique proteins from 5 μg of total yeast lysate analyzed in a single, 101 fraction RP-SAX-RP LC-MS/MS acquisition, providing an estimated detection limit of 65 amol for proteins expressed at 50 copies per cell.
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Affiliation(s)
- Feng Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115-6084
| | - Timothy W. Sikorski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115-6084
| | - Scott B. Ficarro
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115-6084
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115-6084
| | - James T. Webber
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115-6084
| | - Jarrod A. Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115-6084
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115-6084
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45
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Hirabayashi J, Kuno A, Tateno H. Lectin-based structural glycomics: a practical approach to complex glycans. Electrophoresis 2011; 32:1118-28. [PMID: 21544837 DOI: 10.1002/elps.201000650] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Glycans exist in nature in various forms of glycoconjugates, i.e., glycoproteins, glycolipids, and glycosaminoglycans, either in soluble or membrane-bound forms. One of their prominent properties distinguished from nucleic acids and proteins is "heterogeneity" largely attributed to their inherent features of biosynthesis. In general, various methods based on the physicochemical principles have been taken for their separation and structural determination although all of them require prior liberation of glycans and appropriate labeling. On the other hand, a series of carbohydrate-binding proteins, or "lectins," have extensively been used in a more direct manner for cell typing, histochemical staining, and glycoprotein fractionation. Although most procedures conventionally used are useful, unfortunately they lack "throughput" comparable to a performance required for current omics studies. Recently, a novel technique called lectin microarray has attracted increasing attention from not only glycoscientists but also researchers in other fields, because it is straightforward and also informative. The method is innovating in that it enables direct approach to glycoconjugates such as glycoproteins and even cells without liberation of glycans from the core substrate, and therefore can be effectively applied for the sake of differential profiling in various fields. Concept, strategy, and technical advancement of lectin microarray are described. Also, as an introduction to glycomics, the authors explain the motivation to challenge this theme.
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Affiliation(s)
- Jun Hirabayashi
- Lectin Application and Analysis Team, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.
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Safina G, Duran IB, Alasel M, Danielsson B. Surface plasmon resonance for real-time study of lectin-carbohydrate interactions for the differentiation and identification of glycoproteins. Talanta 2011; 84:1284-90. [PMID: 21641439 DOI: 10.1016/j.talanta.2011.01.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 01/09/2011] [Accepted: 01/14/2011] [Indexed: 11/25/2022]
Abstract
A study of specific interactions between lectins and glycoproteins has been carried out using surface plasmon resonance (SPR) in a flow-injection mode. Lectins were covalently immobilised on the surfaces of the microfluidic sensor chip via amine coupling and serum glycoproteins were injected into the flow channels. Specific lectin-glycoprotein interactions caused the shift of refractive index proportional to the mass concentration accumulated on the channel surface. Lectins showed different affinity to the tested glycoproteins and each glycoprotein displayed its own lectin-binding pattern. It is possible to distinguish and identify even glycoproteins with similar sugar structures by simple and quick screening. The working conditions of the assay were optimised. The lectin-based SPR made it possible to carry out the label-free detection of glycoproteins within a broad concentration range with a good linearity. Regeneration conditions for the surface of the sensor chip were found and optimised. Combination of 10mM HCl and 10mM glycine-HCl (pH 2.5) removes the bound glycoproteins from the lectin surface without damaging it. The kinetic and affinity parameters of lectin-glycoprotein binding were evaluated. The proposed method was tested on human glycosylated serum. Combination of the lectin panel with SPR is suitable both for specific screening and for sensitive assay of serum glycoproteins.
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Affiliation(s)
- Gulnara Safina
- Department of Pure and Applied Biochemistry, Lund University, Box 124, 221 00 Lund, Sweden.
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47
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Sánchez-Pomales G, Zangmeister RA. Recent Advances in Electrochemical Glycobiosensing. INTERNATIONAL JOURNAL OF ELECTROCHEMISTRY 2011. [DOI: 10.4061/2011/825790] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Biosensors based on electrochemical transduction mechanisms have recently made advances into the field of glycan analysis. These glyco-biosensors offer simple, rapid, sensitive, and economical approaches to the measurement need for rapid glycan analysis for biomarker detection, cancer and disease diagnostics, and bioprocess monitoring of therapeutic glycoproteins. Although the prevalent methods of glycan analysis (high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy) provide detailed identification and structural analysis of glycan species, there are significantly few low-cost, rapid glycan assays available for diagnostic and screening applications. Here we review instances in which glyco-biosensors have been used for glycan analysis using a variety of electrochemical transduction mechanisms (e.g., amperometric, potentiometric, impedimetric, and voltammetric), selective binding agents (e.g., lectins and antibodies), and redox species (e.g., enzyme substrates, inorganic, and nanomaterial).
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Affiliation(s)
- Germarie Sánchez-Pomales
- Bioprocess Measurements Group, Biochemical Science Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Rebecca A. Zangmeister
- Bioprocess Measurements Group, Biochemical Science Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
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Merbl Y, Kirschner MW. Protein microarrays for genome-wide posttranslational modification analysis. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 3:347-56. [PMID: 20865779 DOI: 10.1002/wsbm.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein microarray technology has emerged as a powerful tool for comparing binding interactions, expression level, substrate specificities, and posttranslational modifications (PTMs) of different proteins in a parallel and high-throughput manner. The ability to immobilize proteins to a solid surface and register the specific address of each protein has bridged major limitations for investigating the proteome in biological samples, namely, the wide dynamic range of protein concentrations and the perturbation of the physical and chemical properties of proteins by their modification. Recent advances introduced the use of functional mammalian cell extracts to assay PTMs under different cellular conditions. This assay offers a new approach for performing large-scale complex biochemical analysis of protein modifications. Here, we review studies of PTM profiling using protein microarrays and discuss the limitations and potential applications of the system. We believe that the information generated from such proteomic studies may be of significant value in our elucidation of the molecular mechanisms that govern human physiology.
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Affiliation(s)
- Yifat Merbl
- Systems Biology Department, Harvard Medical School, Boston, MA, USA
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