1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Su J, Zhang X, Zhang Z, Wang H, Wu J, Shi G, Jin C, Dong M. Real-World Visual Experience Alters Baseline Brain Activity in the Resting State: A Longitudinal Study Using Expertise Model of Radiologists. Front Neurosci 2022; 16:904623. [PMID: 35712457 PMCID: PMC9195622 DOI: 10.3389/fnins.2022.904623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/25/2022] [Indexed: 12/20/2022] Open
Abstract
Visual experience modulates the intensity of evoked brain activity in response to training-related stimuli. Spontaneous fluctuations in the restful brain actively encode previous learning experience. However, few studies have considered how real-world visual experience alters the level of baseline brain activity in the resting state. This study aimed to investigate how short-term real-world visual experience modulates baseline neuronal activity in the resting state using the amplitude of low-frequency (<0.08 Hz) fluctuation (ALFF) and a visual expertise model of radiologists, who possess fine-level visual discrimination skill of homogeneous stimuli. In detail, a group of intern radiologists (n = 32) were recruited. The resting-state fMRI data and the behavioral data regarding their level of visual expertise in radiology and face recognition were collected before and after 1 month of training in the X-ray department in a local hospital. A machine learning analytical method, i.e., support vector machine, was used to identify subtle changes in the level of baseline brain activity. Our method led to a superb classification accuracy of 86.7% between conditions. The brain regions with highest discriminative power were the bilateral cingulate gyrus, the left superior frontal gyrus, the bilateral precentral gyrus, the bilateral superior parietal lobule, and the bilateral precuneus. To the best of our knowledge, this study is the first to investigate baseline neurodynamic alterations in response to real-world visual experience using longitudinal experimental design. These results suggest that real-world visual experience alters the resting-state brain representation in multidimensional neurobehavioral components, which are closely interrelated with high-order cognitive and low-order visual factors, i.e., attention control, working memory, memory, and visual processing. We propose that our findings are likely to help foster new insights into the neural mechanisms of visual expertise.
Collapse
Affiliation(s)
- Jiaxi Su
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Sciences and Technology, Xidian University, Xi’an, China
- Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Sciences and Technology, Xidian University, Xi’an, China
| | - Xiaoyan Zhang
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Sciences and Technology, Xidian University, Xi’an, China
- Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Sciences and Technology, Xidian University, Xi’an, China
| | - Ziyuan Zhang
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Sciences and Technology, Xidian University, Xi’an, China
- Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Sciences and Technology, Xidian University, Xi’an, China
| | - Hongmei Wang
- Department of Medical Imaging, First Affiliated Hospital of Medical College, Xi’an Jiaotong University, Xi’an, China
| | - Jia Wu
- School of Foreign Languages, Northwestern Polytechnical University, Xi’an, China
| | - Guangming Shi
- Key Laboratory of Intelligent Perception and Image Understanding of Ministry of Education, School of Artificial Intelligence, Xidian University, Xi’an, China
| | - Chenwang Jin
- Department of Medical Imaging, First Affiliated Hospital of Medical College, Xi’an Jiaotong University, Xi’an, China
| | - Minghao Dong
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Sciences and Technology, Xidian University, Xi’an, China
- Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Sciences and Technology, Xidian University, Xi’an, China
- Key Laboratory of Intelligent Perception and Image Understanding of Ministry of Education, School of Artificial Intelligence, Xidian University, Xi’an, China
| |
Collapse
|
3
|
Tikhonov A, Smoldovskaya O, Feyzkhanova G, Kushlinskii N, Rubina A. Glycan-specific antibodies as potential cancer biomarkers: a focus on microarray applications. Clin Chem Lab Med 2021; 58:1611-1622. [PMID: 32324152 DOI: 10.1515/cclm-2019-1161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 03/10/2020] [Indexed: 02/06/2023]
Abstract
Glycosylation is one of the most common posttranslational modifications of proteins and lipids. In the case of tumors, cell transformation accompanied by aberrant glycosylation results in the expression of tumor-associated glycans that promote tumor invasion. As part of the innate immunity, anti-glycan antibodies recognize tumor-associated glycans, and these antibodies can be present in the bloodstream in the early stages of cancer. Recently, anti-glycan antibody profiles have been of interest in various cancer studies. Novel advantages in the field of analytical techniques have simplified the analysis of anti-glycan antibodies and made it easier to have more comprehensive knowledge about their functions. One of the robust approaches for studying anti-glycan antibodies engages in microarray technology. The analysis of glycan microarrays can provide more expanded information to simultaneously specify or suggest the role of antibodies to a wide variety of glycans in the progression of different diseases, therefore making it possible to identify new biomarkers for diagnosing cancer and/or the state of the disease. Thus, in this review, we discuss antibodies to various glycans, their application for diagnosing cancer and one of the most promising tools for the investigation of these molecules, microarrays.
Collapse
Affiliation(s)
- Aleksei Tikhonov
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Smoldovskaya
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Guzel Feyzkhanova
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay Kushlinskii
- Laboratory of Clinical Biochemistry, Federal State Budgetary Institution «N.N. Blokhin National Medical Research Center of Oncology» оf the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alla Rubina
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
4
|
Jeong S, Kim U, Oh M, Nam J, Park S, Choi Y, Lee D, Kim J, An H. Detection of Aberrant Glycosylation of Serum Haptoglobin for Gastric Cancer Diagnosis Using a Middle-Up-Down Glycoproteome Platform. J Pers Med 2021; 11:575. [PMID: 34207451 PMCID: PMC8235735 DOI: 10.3390/jpm11060575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022] Open
Abstract
Gastric cancer is a frequently occurring cancer and is the leading cause of cancer-related deaths. Recent studies have shown that aberrant glycosylation of serum haptoglobin is closely related to gastric cancer and has enormous potential for use in diagnosis. However, there is no platform with high reliability and high reproducibility to comprehensively analyze haptoglobin glycosylation covering microheterogeneity to macroheterogeneity for clinical applications. In this study, we developed a middle-up-down glycoproteome platform for fast and accurate monitoring of haptoglobin glycosylation. This platform utilizes an online purification of LC for sample desalting, and an in silico haptoglobin glycopeptide library constructed by combining peptides and N-glycans to readily identify glycopeptides. In addition, site-specific glycosylation with glycan heterogeneity can be obtained through only a single MS analysis. Haptoglobin glycosylation in clinical samples consisting of healthy controls (n = 47) and gastric cancer patients (n = 43) was extensively investigated using three groups of tryptic glycopeptides: GP1 (including Asn184), GP2 (including Asn207 and Asn211), and GP3 (including Asn241). A total of 23 individual glycopeptides were determined as potential biomarkers (p < 0.00001). In addition, to improve diagnostic efficacy, we derived representative group biomarkers with high AUC values (0.929 to 0.977) through logistic regression analysis for each GP group. It has been found that glycosylation of haptoglobin is highly associated with gastric cancer, especially the glycosite Asn241. Our assay not only allows to quickly and easily obtain information on glycosylation heterogeneity of a target glycoprotein but also makes it an efficient tool for biomarker discovery and clinical diagnosis.
Collapse
Affiliation(s)
- Seunghyup Jeong
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, Korea; (S.J.); (M.O.); (J.N.)
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
| | | | - Myungjin Oh
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, Korea; (S.J.); (M.O.); (J.N.)
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
| | - Jihyeon Nam
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, Korea; (S.J.); (M.O.); (J.N.)
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
| | - Sehoon Park
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Yoonjin Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Dongho Lee
- Department of Internal Medicine for Gastroenterology, Seoul National University Bundang Hospital, Seongnam 13620, Korea;
| | - Jaehan Kim
- Department of Food and Nutrition, Chungnam National University, Daejeon 34134, Korea;
| | - Hyunjoo An
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, Korea; (S.J.); (M.O.); (J.N.)
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
| |
Collapse
|
5
|
Chen S, Qin R, Mahal LK. Sweet systems: technologies for glycomic analysis and their integration into systems biology. Crit Rev Biochem Mol Biol 2021; 56:301-320. [PMID: 33820453 DOI: 10.1080/10409238.2021.1908953] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Found in virtually every organism, glycans are essential molecules that play important roles in almost every aspect of biology. The composition of glycome, the repertoire of glycans in an organism or a biological sample, is often found altered in many diseases, including cancer, infectious diseases, metabolic and developmental disorders. Understanding how glycosylation and glycomic changes enriches our knowledge of the mechanisms of disease progression and sheds light on the development of novel therapeutics. However, the inherent diversity of glycan structures imposes challenges on the experimental characterization of glycomes. Advances in high-throughput glycomic technologies enable glycomic analysis in a rapid and comprehensive manner. In this review, we discuss the analytical methods currently used in high-throughput glycomics, including mass spectrometry, liquid chromatography and lectin microarray. Concomitant with the technical advances is the integration of glycomics into systems biology in the recent years. Herein we elaborate on some representative works from this recent trend to underline the important role of glycomics in such integrated approaches to disease.
Collapse
Affiliation(s)
- Shuhui Chen
- Department of Chemistry, New York University, New York City, NY, USA
| | - Rui Qin
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Lara K Mahal
- Department of Chemistry, New York University, New York City, NY, USA.,Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
6
|
Kori M, Aydin B, Gulfidan G, Beklen H, Kelesoglu N, Caliskan Iscan A, Turanli B, Erzik C, Karademir B, Arga KY. The Repertoire of Glycan Alterations and Glycoproteins in Human Cancers. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:139-168. [PMID: 33404348 DOI: 10.1089/omi.2020.0210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer as the leading cause of death worldwide has many issues that still need to be addressed. Since the alterations on the glycan compositions or/and structures (i.e., glycosylation, sialylation, and fucosylation) are common features of tumorigenesis, glycomics becomes an emerging field examining the structure and function of glycans. In the past, cancer studies heavily relied on genomics and transcriptomics with relatively little exploration of the glycan alterations and glycoprotein biomarkers among individuals and populations. Since glycosylation of proteins increases their structural complexity by several orders of magnitude, glycome studies resulted in highly dynamic biomarkers that can be evaluated for cancer diagnosis, prognosis, and therapy. Glycome not only integrates our genetic background with past and present environmental factors but also offers a promise of more efficient patient stratification compared with genetic variations. Therefore, studying glycans holds great potential for better diagnostic markers as well as developing more efficient treatment strategies in human cancers. While recent developments in glycomics and associated technologies now offer new possibilities to achieve a high-throughput profiling of glycan diversity, we aim to give an overview of the current status of glycan research and the potential applications of the glycans in the scope of the personalized medicine strategies for cancer.
Collapse
Affiliation(s)
- Medi Kori
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Busra Aydin
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Gizem Gulfidan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Hande Beklen
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Nurdan Kelesoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Ayşegul Caliskan Iscan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey.,Department of Pharmacy, Istinye University, Istanbul, Turkey
| | - Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Can Erzik
- Department of Medical Biology and School of Medicine, Marmara University, Istanbul, Turkey
| | - Betul Karademir
- Department of Biochemistry, School of Medicine, Marmara University, Istanbul, Turkey.,Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| |
Collapse
|
7
|
Yue H, Han Y, Yin B, Cheng C, Liu L. Comparison of the antipathogenic effect toward Staphylococcus aureus of N-linked and free oligosaccharides derived from human, bovine, and goat milk. J Food Sci 2020; 85:2329-2339. [PMID: 32662089 DOI: 10.1111/1750-3841.15150] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 12/19/2022]
Abstract
N-linked oligosaccharides (N-glycans) derived from milk were recently found to be antipathogenic. This study compares the antimicrobial activity of N-linked glycans and free oligosaccharides from human, bovine, and goat milk against Staphylococcus aureus. Milk N-glycans showed a bactericidal/bacteriostatic effect on the pathogen when compared to free milk oligosaccharides, evidenced by the clear zone from the halo assay, with the order of human milk >goat milk >bovine milk. None of the free milk oligosaccharide samples were bactericidal/bacteriostatic, despite its positive results in growth curve and minimum inhibitory concentration (MIC) assays which are believed to be related to hyperosmosis. Both N-glycans and free milk oligosaccharides can reduce the adhesion of Staphylococcus aureus to Caco-2 cells, however, N-glycans worked significantly more effective than free milk oligosaccharides. Structural analysis of all free oligosaccharide and N-glycan samples showed the obvious interspecies differences, and the structure/function relationship of the respected N-glycans is of interest for future study. The significant bactericidal/bacteriostatic activity possessed by human, bovine, and goat milk N-linked glycans holds great potential as a novel substitute for antibiotics.
Collapse
Affiliation(s)
- Haiyun Yue
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yuanyuan Han
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Binru Yin
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Cheng Cheng
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| |
Collapse
|
8
|
Kim KH, Kim JY, Yoo JS. Mass spectrometry analysis of glycoprotein biomarkers in human blood of hepatocellular carcinoma. Expert Rev Proteomics 2019; 16:553-568. [DOI: 10.1080/14789450.2019.1626235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kwang Hoe Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Han Y, Xiao K, Tian Z. Comparative Glycomics Study of Cell-Surface N-Glycomes of HepG2 versus LO2 Cell Lines. J Proteome Res 2019; 18:372-379. [PMID: 30343578 DOI: 10.1021/acs.jproteome.8b00655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cell-surface N-glycans play important roles in both inter- and intracellular processes, including cell adhesion and development, cell recognition, as well as cancer development and metastasis; detailed structural characterization of these N-glycans is thus paramount. Here we report our comparative N-glycomics study of cell-surface N-glycans of the hepatocellular carcinoma (HCC) HepG2 cells vs the normal liver LO2 cells. With sequential trypsin digestion of proteins, C18 depletion of peptides without glycosylation, PNGase F digestion of N-glycopeptides, PGC enrichment of N-glycans, CH3I permethylation of the enriched N-glycans, cell-surface N-glycomes of the HepG2 and LO2 cells were analyzed using C18-RPLC-MS/MS (HCD). With spectrum-level FDR no bigger than 1%, 351 and 310 N-glycans were identified for HepG2 and LO2, respectively, with comprehensive structural information (not only monosaccharide composition, but also sequence and linkage) by N-glycan database search engine GlySeeker. The percentage of hybrid N-glycans with tetra-antennary structures was substantially increased in the HepG2 cells. This comprehensive discovery study of differentially expressed cell-surface N-glycans in HepG2 vs LO2 serves as a solid reference for future validation study of glycosylation markers in HCC.
Collapse
Affiliation(s)
- Yuyin Han
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability , Tongji University , Shanghai 200092 , China
| | - Kaijie Xiao
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability , Tongji University , Shanghai 200092 , China
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability , Tongji University , Shanghai 200092 , China
| |
Collapse
|
11
|
Zhu R, Zhou S, Peng W, Huang Y, Mirzaei P, Donohoo K, Mechref Y. Enhanced Quantitative LC-MS/MS Analysis of N-linked Glycans Derived from Glycoproteins Using Sodium Deoxycholate Detergent. J Proteome Res 2018; 17:2668-2678. [PMID: 29745666 DOI: 10.1021/acs.jproteome.8b00127] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein glycosylation is a common protein post-translational modification (PTM) in living organisms and has been shown to associate with multiple diseases, and thus may potentially be a biomarker of such diseases. Efficient protein/glycoprotein extraction is a crucial step in the preparation of N-glycans derived from glycoproteins prior to LC-MS analysis. Convenient, efficient and unbiased sample preparation protocols are needed. Herein, we evaluated the use of sodium deoxycholate (SDC) acidic labile detergent to release N-glycans of glycoproteins derived from biological samples such as cancer cell lines. Compared to the filter-aided sample preparation approach, the sodium deoxycholate (SDC) assisted approach was determined to be more efficient and unbiased. SDC removal was determined to be more efficient when using acidic precipitation rather than ethyl acetate phase transfer. Efficient extraction of proteins/glycoproteins from biological samples was achieved by combining SDC lysis buffer and beads beating cell disruption. This was suggested by a significant overall increase in the intensities of N-glycans released from cancer cell lines. Additionally, the use of SDC approach was also shown to be more reproducible than those methods that do not use SDC.
Collapse
Affiliation(s)
- Rui Zhu
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Shiyue Zhou
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Wenjing Peng
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Yifan Huang
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Parvin Mirzaei
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Kaitlyn Donohoo
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| |
Collapse
|
12
|
de Oliveira RM, Ornelas Ricart CA, Araujo Martins AM. Use of Mass Spectrometry to Screen Glycan Early Markers in Hepatocellular Carcinoma. Front Oncol 2018; 7:328. [PMID: 29379771 PMCID: PMC5775512 DOI: 10.3389/fonc.2017.00328] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Association between altered glycosylation patterns and poor prognosis in cancer points glycans as potential specific tumor markers. Most proteins are glycosylated and functionally arranged on cell surface and extracellular matrix, mediating interactions and cellular signaling. Thereby, aberrant glycans may be considered a pathological phenotype at least as important as changes in protein expression for cancer and other complex diseases. As most serum glycoproteins have hepatic origin, liver disease phenotypes, such as hepatocellular carcinoma (HCC), may present altered glycan profile and display important modifications. One of the prominent obstacles in HCC is the diagnostic in advanced stages when patients have several liver dysfunctions, limiting treatment options and life expectancy. The characterization of glycomic profiles in pathological conditions by means of mass spectrometry (MS) may lead to the discovery of early diagnostic markers using non-invasive approaches. MS is a powerful analytical technique capable of elucidating many glycobiological issues and overcome limitations of the serological markers currently applied in clinical practice. Therefore, MS-based glycomics of tumor biomarkers is a promising tool to increase early detection and monitoring of disease.
Collapse
Affiliation(s)
- Raphaela Menezes de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
| | - Carlos Andre Ornelas Ricart
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
| | - Aline Maria Araujo Martins
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil.,University Hospital Walter Cantídeo, Surgery Department, Federal University of Ceara, Fortaleza, Brazil
| |
Collapse
|
13
|
Wang R, Liu Y, Wang C, Li H, Liu X, Cheng L, Zhou Y. Comparison of the methods for profiling N-glycans—hepatocellular carcinoma serum glycomics study. RSC Adv 2018; 8:26116-26123. [PMID: 35541959 PMCID: PMC9082735 DOI: 10.1039/c8ra02542h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/11/2018] [Indexed: 11/21/2022] Open
Abstract
Monitoring serum glycomics is one of the most important emerging approaches for diagnosis of various cancers, and the majority of previous studies were based on MALDI-MS or HPLC analysis. Considering the difference of these analytical methods employed for serum glycomics, it is necessary to compare the effectiveness of different analytical methods for monitoring the aberrant changes in serum glycomics. In this study, a strategy based on machine learning was firstly applied for comparing the analysis results of MALDI-MS and HPLC on the same serum glycomics of hepatocellular carcinoma (HCC) samples. The capability of these two analytical methods for identifying HCC is demonstrated by the classification results obtained from MALDI-MS and HPLC data. In addition, by comparing glycomics which were significantly correlated with HCC based on MALDI-MS and HPLC, some N-glycans which may be the potential biomarkers for HCC were identified, validating the capability of these two analytical methods for the differentiated identification in the analysis of glycomics. Meanwhile, it is noteworthy that various physiological and environmental factors may cause the aberrant changes in glycosylation, and all these interference factors may be minimized by analyzing the same sample sets of HCC. Overall, these results showed that MALDI-MS and HPLC are complementary in qualitative and quantitative analysis of serum glycomics. Monitoring serum glycomics is one of the most important emerging approaches for diagnosis of various cancers, and the majority of previous studies were based on MALDI-MS or HPLC analysis.![]()
Collapse
Affiliation(s)
- Ran Wang
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory
- Systems Biology Theme
- Department of Biomedical Engineering
- College of Life Science and Technology
- Huazhong University of Science and Technology
| | - Yufei Liu
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory
- Systems Biology Theme
- Department of Biomedical Engineering
- College of Life Science and Technology
- Huazhong University of Science and Technology
| | - Chang Wang
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory
- Systems Biology Theme
- Department of Biomedical Engineering
- College of Life Science and Technology
- Huazhong University of Science and Technology
| | - Henghui Li
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory
- Systems Biology Theme
- Department of Biomedical Engineering
- College of Life Science and Technology
- Huazhong University of Science and Technology
| | - Xin Liu
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory
- Systems Biology Theme
- Department of Biomedical Engineering
- College of Life Science and Technology
- Huazhong University of Science and Technology
| | - Liming Cheng
- Department of Laboratory Medicine
- Tongji Hospital
- Wuhan 430074
- China
| | - Yanhong Zhou
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory
- Systems Biology Theme
- Department of Biomedical Engineering
- College of Life Science and Technology
- Huazhong University of Science and Technology
| |
Collapse
|
14
|
Zhou S, Dong X, Veillon L, Huang Y, Mechref Y. LC-MS/MS analysis of permethylated N-glycans facilitating isomeric characterization. Anal Bioanal Chem 2017; 409:453-466. [PMID: 27796453 PMCID: PMC5444817 DOI: 10.1007/s00216-016-9996-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/23/2016] [Accepted: 09/29/2016] [Indexed: 12/18/2022]
Abstract
The biosynthesis of glycans is a template-free process; hence compositionally identical glycans may contain highly heterogeneous structures. Meanwhile, the functions of glycans in biological processes are significantly influenced by the glycan structure. Structural elucidation of glycans is an essential component of glycobiology. Although NMR is considered the most powerful approach for structural glycan studies, it suffers from low sensitivity and requires highly purified glycans. Although mass spectrometry (MS)-based methods have been applied in numerous glycan structure studies, there are challenges in preserving glycan structure during ionization. Permethylation is an efficient derivatization method that improves glycan structural stability. In this report, permethylated glycans are isomerically separated; thus facilitating structural analysis of a mixture of glycans by LC-MS/MS. Separation by porous graphitic carbon liquid chromatography at high temperatures in conjunction with tandem mass spectrometry (PGC-LC-MS/MS) was utilized for unequivocal characterization of glycan isomers. Glycan fucosylation sites were confidently determined by eliminating fucose rearrangement and assignment of diagnostic ions, achieved by permethylation and PGC-LC at high temperatures, respectively. Assigning monosaccharide residues to specific glycan antennae was also achieved. Galactose linkages were also distinguished from each other by CID/HCD tandem MS. This was attainable because of the different bond energies associated with monosaccharide linkages. Graphical Abstract LC-MS and tandem MS of terminal galactose isomers.
Collapse
Affiliation(s)
- Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle & Boston, Box 41061, Lubbock, TX, 79409-1061, USA
| | - Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle & Boston, Box 41061, Lubbock, TX, 79409-1061, USA
| | - Lucas Veillon
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle & Boston, Box 41061, Lubbock, TX, 79409-1061, USA
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle & Boston, Box 41061, Lubbock, TX, 79409-1061, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle & Boston, Box 41061, Lubbock, TX, 79409-1061, USA.
| |
Collapse
|
15
|
Banazadeh A, Veillon L, Wooding KM, Zabet-Moghaddam M, Mechref Y. Recent advances in mass spectrometric analysis of glycoproteins. Electrophoresis 2016; 38:162-189. [PMID: 27757981 DOI: 10.1002/elps.201600357] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 12/13/2022]
Abstract
Glycosylation is one of the most common posttranslational modifications of proteins that plays essential roles in various biological processes, including protein folding, host-pathogen interaction, immune response, and inflammation and aberrant protein glycosylation is a well-known event in various disease states including cancer. As a result, it is critical to develop rapid and sensitive methods for the analysis of abnormal glycoproteins associated with diseases. Mass spectrometry (MS) in conjunction with different separation methods, such as capillary electrophoresis (CE), ion mobility (IM), and high performance liquid chromatography (HPLC) has become a popular tool for glycoprotein analysis, providing highly informative fragments for structural identification of glycoproteins. This review provides an overview of the developments and accomplishments in the field of glycomics and glycoproteomics reported between 2014 and 2016.
Collapse
Affiliation(s)
- Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Lucas Veillon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Kerry M Wooding
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.,Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
| |
Collapse
|
16
|
Dong X, Zhou S, Mechref Y. LC-MS/MS analysis of permethylated free oligosaccharides and N-glycans derived from human, bovine, and goat milk samples. Electrophoresis 2016; 37:1532-48. [PMID: 26959529 PMCID: PMC4963982 DOI: 10.1002/elps.201500561] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/28/2016] [Accepted: 02/28/2016] [Indexed: 11/10/2022]
Abstract
Oligosaccharides in milk not only provide nutrition to the infants but also have significant immune biofunctions such as inhibition of pathogen binding to the host cell. The main component in milk oligosaccharides is free oligosaccharides. Since the proteins in milk are highly glycosylated, N-glycans in milk also play an import role. In this study, we investigated the permethylated free oligosaccharides and N-glycans extracted from bovine, goat, and human milks using LC-MS/MS. Quantitation profiles of free oligosaccharides and N-glycans were reported. The number of free oligosaccharides observed in bovine, goat, and human milk samples (without isomeric consideration) were 11, 8, and 11, respectively. Human milk had more complex free oligosaccharides structures than the other two milk samples. Totally 58, 21, and 43 N-glycan structures (without isomeric consideration) were associated with whey proteins extracted from bovine, goat, and human milk samples, respectively. Bovine milk free oligosaccharides and N-glycans from whey proteins were highly sialylated and to a lesser extend fucosylated. Goat and human milk free oligosaccharides and N-glycans from whey proteins were both highly fucosylated. Also, the isomeric glycans in milk samples were determined by porous graphitic carbon LC at elevated temperatures. For example, separation of human milk free oligosaccharide Gal-GlcNAc-(Fuc)-Gal-Glc and Gal-GlcNAc-Gal-Glc-Fuc isomers was achieved using porous graphitic carbon column. Permethylation of the glycan structures facilitated the interpretation of MS/MS. For example, internal cleavage and glycosidic bond cleavage are readily distinguished in the tandem mass spectra of permethylated glycans. This feature resulted in the identification of several isomers.
Collapse
Affiliation(s)
- Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| |
Collapse
|
17
|
Tanaka-Okamoto M, Yabu M, Mukai M, Takahashi H, Fujiwara Y, Ohue M, Kamada Y, Miyoshi E, Miyamoto Y. Elevation of CA19-9-Related Novel Marker, Core 1 Sialyl Lewis A, in Sera of Adenocarcinoma Patients Verified by a SRM-Based Method. J Proteome Res 2015; 15:152-65. [PMID: 26641888 DOI: 10.1021/acs.jproteome.5b00893] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have attempted to identify a novel glycan tumor marker. Pyridylaminated (PA) O-glycans were prepared from sera, and the corresponding O-glycan profiles were constructed by HPLC separation. By comparing the serum O-glycan profiles from healthy controls with those of cancer patients, we identified a marker candidate, core 1 sialyl Lewis A (NeuAcα2-3Galβ1-3(Fucα1-4)GlcNAcβ1-3Gal) (abbreviated C1SLA), whose concentration appeared to be weakly correlated with CA19-9 values. To quantify this glycan, we developed a selected reaction monitoring (SRM) assay that used a stable isotope, tetradeuterium-labeled pyridylamino (d4-PA) glycan, as an internal standard. The analyte (d0-PA-C1SLA) and the internal standard (d4-PA-C1SLA) were subjected to SRM analyses after two types of HPLC separation. Serum levels of C1SLA, determined as the relative ratio to total O-glycans, were then measured. These analyses revealed that (i) C1SLA is a CA19-9-related glycan, (ii) the mean value of C1SLA in normal controls is 3.41 ppm, (iii) the level of C1SLA was significantly higher in samples of stages II-IV stomach cancers (P = 0.0036) as well as pancreatic cancers (P < 0.0001) compared to that of normal controls, (iv) the relationship between C1SLA and CA19-9 varies from poor to weak depending on the cancer, and (v) C1SLA could be valuable as a diagnostic adjunct for cancer.
Collapse
Affiliation(s)
- Miki Tanaka-Okamoto
- Department of Molecular Biology, Osaka Medical Center for Cancer and Cardiovascular Diseases , 1-3-2 Nakamichi, Higashinari-ku, Osaka 537-8511, Japan
| | - Masahiko Yabu
- Department of Molecular Biology, Osaka Medical Center for Cancer and Cardiovascular Diseases , 1-3-2 Nakamichi, Higashinari-ku, Osaka 537-8511, Japan
| | | | | | | | | | - Yoshihiro Kamada
- Department of Molecular Biochemistry and Clinical Investigation, Osaka University, Graduate School of Medicine , 1-7 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Eiji Miyoshi
- Department of Molecular Biochemistry and Clinical Investigation, Osaka University, Graduate School of Medicine , 1-7 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yasuhide Miyamoto
- Department of Molecular Biology, Osaka Medical Center for Cancer and Cardiovascular Diseases , 1-3-2 Nakamichi, Higashinari-ku, Osaka 537-8511, Japan
| |
Collapse
|
18
|
Cao L, Zhang Y, Chen L, Shen A, Zhang X, Ren S, Gu J, Yu L, Liang X. Sample preparation for mass spectrometric analysis of human serum N-glycans using hydrophilic interaction chromatography-based solid phase extraction. Analyst 2015; 139:4538-46. [PMID: 25068150 DOI: 10.1039/c4an00660g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Expression levels of N-linked glycans derived from human serum glycoproteins have been shown to change during the progression of many diseases. Generally, N-glycans released from human serum proteins co-exist with endogenous serum peptides, salts, and other contaminants. Effective removal of these contaminants is essential to obtain the glycan profile of human serum proteins. Here, we developed a sample preparation method for mass spectrometry (MS) analysis of N-linked glycans derived from human serum glycoproteins based on a zwitterionic hydrophilic material named Click TE-Cys. The high hydrophilicity of Click TE-Cys, resulting from its unique surface structure and charge distribution, facilitated removal of co-existing salts and endogenous serum peptides. Furthermore, the present enrichment approach was handled in parallel, thus saving time. Using this method, a total of 47 unique N-glycans released from human serum proteins were identified. The intrabatch and interbatch coefficients of variation for the 47 N-linked glycans were 8.57% ± 0.96% and 9.22% ± 1.03%, respectively. These results demonstrate that the present method is suitable for fast purification of N-linked glycans derived from human serum glycoproteins, and has potential for clinical application.
Collapse
Affiliation(s)
- Liwei Cao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Li L, Liu Y, Ma C, Qu J, Calderon AD, Wu B, Wei N, Wang X, Guo Y, Xiao Z, Song J, Sugiarto G, Li Y, Yu H, Chen X, Wang PG. Efficient Chemoenzymatic Synthesis of an N-glycan Isomer Library. Chem Sci 2015; 6:5652-5661. [PMID: 26417422 PMCID: PMC4583208 DOI: 10.1039/c5sc02025e] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Quantification, characterization and biofunctional studies of N-glycans on proteins remain challenging tasks due to complexity, diversity and low abundance of these glycans. The availability of structurally defined N-glycans (especially isomers) libraries is essential to help on solving these tasks. We reported herein an efficient chemoenzymatic strategy, namely Core Synthesis/Enzymatic Extension (CSEE), for rapid production of diverse N-glycans. Starting with 5 chemically prepared building blocks, 8 N-glycan core structures containing one or two terminal N-acetyl-D-glucosamine (GlcNAc) residue(s) were chemically synthesized via consistent use of oligosaccharyl thioethers as glycosylation donors in the convergent fragment coupling strategy. Each of these core structures was then extended to 5 to 15 N-glycan sequences by enzymatic reactions catalyzed by 4 robust glycosyltransferases. Success in synthesizing N-glycans with Neu5Gc and core-fucosylation further expanded the ability of enzymatic extension. High performance liquid chromatography with an amide column enabled rapid and efficient purification (>98% purity) of N-glycans in milligram scales. A total of 73 N-glycans (63 isomers) were successfully prepared and characterized by MS2 and NMR. The CSEE strategy provides a practical approach for "mass production" of structurally defined N-glycans, which are important standards and probes for Glycoscience.
Collapse
Affiliation(s)
- Lei Li
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| | - Yunpeng Liu
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| | - Cheng Ma
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| | - Jingyao Qu
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| | - Angie D Calderon
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| | - Baolin Wu
- Chemily, LLC, 58 Edgewood Ave NE, Atlanta, GA 30303
| | - Na Wei
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| | - Xuan Wang
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| | - Yuxi Guo
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| | - Zhongying Xiao
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| | - Jing Song
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| | - Go Sugiarto
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616
| | - Yanhong Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616
| | - Hai Yu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616
| | - Xi Chen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616
| | - Peng George Wang
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, 50 Decatur St SE, Atlanta, GA 30303
| |
Collapse
|
20
|
Amin A, Bashir A, Zaki N, McCarthy D, Ahmed S, Lotfy M. Insights into glycan biosynthesis in chemically-induced hepatocellular carcinoma in rats: A glycomic analysis. World J Gastroenterol 2015; 21:6167-6179. [PMID: 26034352 PMCID: PMC4445094 DOI: 10.3748/wjg.v21.i20.6167] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/19/2015] [Accepted: 02/13/2015] [Indexed: 02/06/2023] Open
Abstract
AIM: To evaluate the qualitative and quantitative changes in N-linked glycosylation, which occurred in association with diethyl nitrosamine-induced hepatocellular carcinoma (HCC) in rodents.
METHODS: Liver tissues of (1) normal (non-tumor-bearing) rats; and (2) tumor-bearing rats; were collected and were used for histological and GlycanMap® analyses. Briefly, GlycanMap® analysis is a high-throughput assay that provides a structural and quantitative readout of protein-associated glycans using a unique, automated 96-well assay technology coupled to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and custom bioinformatics. Histopathological studies were carried out to ensure the development of HCC in the tested animals.
RESULTS: The N-glycomic analysis revealed 5 glycans; Glc1Man9GlcNAc2, Gal2Man3GlcNac4Fuc1Neu1, Man4GlcNac2, Gal2Man3GlcNac4Neu3OAc3, and Man3GlcNac5Fuc1, which showed significant changes in rat HCC tissues when compared with normal liver tissues. Four glycans were increased (P < 0.05) and Glc1Man9GlcNAc2 was decreased (5.89 ± 0.45 vs 3.54 ± 0.21, P < 0.01) in HCC tissues compared to normal liver tissues. An increase (66.5 ± 1.05 vs 62.7 ± 1.1, P < 0.05) in high-mannose structures in HCC rats was observed compared to normal rats. Importantly, HCC rats showed an increase (P < 0.05) in both tumor-associated carbohydrates and in branched glycans. The changes in glycans correlated well with glycan flow changes reported in the glycan biosynthetic pathway, which indicates the importance of enzyme activities involved in glycan synthesis at different subcellular localizations.
CONCLUSION: The reported HCC-associated changes in glycan flow and subcellular localization explain the increase in high mannose glycans and siayl Lewis glycans common in HCC liver tissues.
Collapse
|
21
|
Bults P, van de Merbel NC, Bischoff R. Quantification of biopharmaceuticals and biomarkers in complex biological matrices: a comparison of liquid chromatography coupled to tandem mass spectrometry and ligand binding assays. Expert Rev Proteomics 2015; 12:355-74. [DOI: 10.1586/14789450.2015.1050384] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
22
|
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.
Collapse
Affiliation(s)
- David J. Harvey
- Department of BiochemistryOxford Glycobiology InstituteUniversity of OxfordOxfordOX1 3QUUK
| |
Collapse
|
23
|
Chang CT, Liao HY, Huang WH, Lin SY, Tsai TY, Yang CY, Tsai FJ, Chen CJ. Early prediction of severe acute pancreatitis by urinary β-2 microglobulin/saposin B peak ratios on MALDI-TOF. Clin Chim Acta 2014; 440:115-22. [PMID: 25447703 DOI: 10.1016/j.cca.2014.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 10/18/2014] [Accepted: 11/10/2014] [Indexed: 01/01/2023]
Abstract
The current methods for predicting severe acute pancreatitis (severe AP) are either complicated or lack efficient sensitivity and specificity. In this study, a simple and practical approach was developed to predict severe AP by using peak intensity ratio of urinary β-2 microglobulin (B2M) to saposin B (SB) on MALDI-TOF MS. Patients with B2M/SB ratio higher than 1.127 present severe AP symptom with a higher Ranson score, computed tomography (CT) grade and longer hospitalization with a sensitivity of 83.7% and specificity of 74.3%. Label-free quantitative proteomics by nanoLC-MS/MS was applied to urine of severe AP patients and found that severe AP is accompanied with kidney injury and inflammation. The measurement of B2M/SB ratios by MALDI-TOF MS could be a simple, accurate and rapid method to diagnose severe AP as well as to monitor AP progression.
Collapse
Affiliation(s)
- Chiz-Tzung Chang
- College of Medicine, China Medical University, Taichung, Taiwan; Division of Nephrology, China Medical University Hospital, Taichung, Taiwan
| | - Hsin-Yi Liao
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 40402, Taiwan
| | - Wen-Hsin Huang
- College of Medicine, China Medical University, Taichung, Taiwan; Division of Gastroenterology, China Medical University Hospital, Taichung, Taiwan
| | - Shih-Yi Lin
- College of Medicine, China Medical University, Taichung, Taiwan; Division of Nephrology, China Medical University Hospital, Taichung, Taiwan
| | - Tsung-Yu Tsai
- Division of Gastroenterology, China Medical University Hospital, Taichung, Taiwan
| | - Chao-Yuh Yang
- L5 Research Center, China Medical University Hospital, Taichung, Taiwan; Section of Atherosclerosis and Lipoprotein Research, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, United States
| | - Fuu-Jen Tsai
- Department of Medical Genetics, Pediatrics and Medical Research, China Medical University Hospital, Taichung 40402, Taiwan
| | - Chao-Jung Chen
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 40402, Taiwan; Graduate Institute of Integrated Medicine, China Medical University, Taichung 40402, Taiwan.
| |
Collapse
|
24
|
Benicky J, Sanda M, Pompach P, Wu J, Goldman R. Quantification of fucosylated hemopexin and complement factor H in plasma of patients with liver disease. Anal Chem 2014; 86:10716-23. [PMID: 25302577 PMCID: PMC4222631 DOI: 10.1021/ac502727s] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Enhanced fucosylation has been suggested
as a marker for serologic
monitoring of liver disease and hepatocellular carcinoma (HCC). We
present a workflow for quantitative site-specific analysis of fucosylation
and apply it to a comparison of hemopexin (HPX) and complement factor
H (CFH), two liver-secreted glycoproteins, in healthy individuals
and patients with liver cirrhosis and HCC. Label-free LC-MS quantification
of glycopeptides derived from these purified glycoproteins was performed
on pooled samples (2 pools/group, 5 samples/pool) and complemented
by glycosidase assisted analysis using sialidase and endoglycosidase
F2/F3, respectively, to improve resolution of glycoforms. Our analysis,
presented as relative abundance of individual fucosylated glycoforms
normalized to the level of their nonfucosylated counterparts, revealed
a consistent increase in fucosylation in liver disease with significant
site- and protein-specific differences. We have observed the highest
microheterogeneity of glycoforms at the N187 site of HPX, absence
of core fucosylation at N882 and N911 sites of CFH, or a higher degree
of core fucosylation in CFH compared to HPX, but we did not identify
changes differentiating HCC from matched cirrhosis samples. Glycosidase
assisted LC-MS-MRM analysis of individual patient samples prepared
by a simplified protocol confirmed the quantitative differences. Transitions
specific to outer arm fucose document a disease-associated increase
in outer arm fucose on both bi- and triantennary glycans at the N187
site of HPX. Further verification is needed to confirm that enhanced
fucosylation of HPX and CFH may serve as an indicator of premalignant
liver disease. The analytical strategy can be readily adapted to analysis
of other proteins in the appropriate disease context.
Collapse
Affiliation(s)
- Julius Benicky
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University , LCCC Room S183, 3970 Reservoir Rd NW, Washington, D.C., 20057, United States
| | | | | | | | | |
Collapse
|
25
|
Tsai TH, Wang M, Di Poto C, Hu Y, Zhou S, Zhao Y, Varghese RS, Luo Y, Tadesse MG, Ziada DH, Desai CS, Shetty K, Mechref Y, Ressom HW. LC-MS profiling of N-Glycans derived from human serum samples for biomarker discovery in hepatocellular carcinoma. J Proteome Res 2014; 13:4859-68. [PMID: 25077556 PMCID: PMC4227556 DOI: 10.1021/pr500460k] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Defining
clinically relevant biomarkers for early stage hepatocellular
carcinoma (HCC) in a high-risk population of cirrhotic patients has
potentially far-reaching implications for disease management and patient
health. Changes in glycan levels have been associated with the onset
of numerous diseases including cancer. In the present study, we used
liquid chromatography coupled with electrospray ionization mass spectrometry
(LC–ESI-MS) to analyze N-glycans in sera from 183 participants
recruited in Egypt and the U.S. and identified candidate biomarkers
that distinguish HCC cases from cirrhotic controls. N-Glycans were
released from serum proteins and permethylated prior to the LC–ESI-MS
analysis. Through two complementary LC–ESI-MS quantitation
approaches, global profiling and targeted quantitation, we identified
11 N-glycans with statistically significant differences between HCC
cases and cirrhotic controls. These glycans can further be categorized
into four structurally related clusters, matching closely with the
implications of important glycosyltransferases in cancer progression
and metastasis. The results of this study illustrate the power of
the integrative approach combining complementary LC–ESI-MS
based quantitation approaches to investigate changes in N-glycan levels
between HCC cases and patients with liver cirrhosis.
Collapse
Affiliation(s)
- Tsung-Heng Tsai
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center , Washington, DC 20057, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Mayampurath A, Song E, Mathur A, Yu CY, Hammoud Z, Mechref Y, Tang H. Label-free glycopeptide quantification for biomarker discovery in human sera. J Proteome Res 2014; 13:4821-32. [PMID: 24946017 DOI: 10.1021/pr500242m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Glycan moieties of glycoproteins modulate many biological processes in mammals, such as immune response, inflammation, and cell signaling. Numerous studies show that many human diseases are correlated with quantitative alteration of protein glycosylation. In some cases, these changes can occur for certain types of glycans over specific sites in a glycoprotein rather than on the global abundance of the glycoprotein. Conventional analytical techniques that analyze the abundance of glycans cleaved from glycoproteins cannot reveal these subtle effects. Here we present a novel statistical method to quantify the site-specific glycosylation of glycoproteins in complex samples using label-free mass spectrometric techniques. Abundance variations between sites of a glycoprotein as well as different glycoforms, that is, glycopeptides with different glycans attached to the same site, can be detected using these techniques. We applied our method to an esophageal cancer study based on blood serum samples from cancer patients in an attempt to detect potential biomarkers of site-specific N-linked glycosylation. A few glycoproteins, including vitronectin, showed significantly different site-specific glycosylations within cancer/control samples, indicating that our method is ready to be used for the discovery of glycosylated biomarkers.
Collapse
Affiliation(s)
- Anoop Mayampurath
- School of Informatics & Computing, Indiana University , 901 East 10th Street, Bloomington, Indiana 47408, United States
| | | | | | | | | | | | | |
Collapse
|
27
|
Wang J, Zhou C, Zhang W, Yao J, Lu H, Dong Q, Zhou H, Qin L. An integrative strategy for quantitative analysis of the N-glycoproteome in complex biological samples. Proteome Sci 2014; 12:4. [PMID: 24428921 PMCID: PMC3923275 DOI: 10.1186/1477-5956-12-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/27/2013] [Indexed: 12/23/2022] Open
Abstract
Background The complexity of protein glycosylation makes it difficult to characterize glycosylation patterns on a proteomic scale. In this study, we developed an integrated strategy for comparatively analyzing N-glycosylation/glycoproteins quantitatively from complex biological samples in a high-throughput manner. This strategy entailed separating and enriching glycopeptides/glycoproteins using lectin affinity chromatography, and then tandem labeling them with 18O/16O to generate a mass shift of 6 Da between the paired glycopeptides, and finally analyzing them with liquid chromatography-mass spectrometry (LC-MS) and the automatic quantitative method we developed based on Mascot Distiller. Results The accuracy and repeatability of this strategy were first verified using standard glycoproteins; linearity was maintained within a range of 1:10–10:1. The peptide concentration ratios obtained by the self-build quantitative method were similar to both the manually calculated and theoretical values, with a standard deviation (SD) of 0.023–0.186 for glycopeptides. The feasibility of the strategy was further confirmed with serum from hepatocellular carcinoma (HCC) patients and healthy individuals; the expression of 44 glycopeptides and 30 glycoproteins were significantly different between HCC patient and control serum. Conclusions This strategy is accurate, repeatable, and efficient, and may be a useful tool for identification of disease-related N-glycosylation/glycoprotein changes.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Haijun Zhou
- Department of Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | | |
Collapse
|
28
|
Zhu J, Wang Y, Yu Y, Wang Z, Zhu T, Xu X, Liu H, Hawke D, Zhou D, Li Y. Aberrant fucosylation of glycosphingolipids in human hepatocellular carcinoma tissues. Liver Int 2014; 34:147-60. [PMID: 23902602 DOI: 10.1111/liv.12265] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 06/20/2013] [Indexed: 12/15/2022]
Abstract
BACKGROUNDS & AIMS Glycosylation promoting or inhibiting tumour cell invasion and metastasis is of crucial importance in current cancer research. Tumour-associated carbohydrate antigens are predominantly expressed on the tumour cell surface. Glycosphingolipids (GSLs) are members of the family. To perform glycosphingolipidomic assays on neutral GSLs obtained from solid hepatocellular carcinoma (HCC) tissues and paired peritumoural tissues by linear ion trap quadrupole-electrospray ionization mass spectrometry. METHODS Qualitative and quantitative analysis of fucosylated neutral GSLs was performed in the positive ion mode on the LTQ-XL mass spectrometer and MALDI-TOF-MS. RESULTS A group of fucosylated neutral GSLs in HCC was found to be expressed higher in the tumour tissues, as their proportion in total cellular GSLs was 3.3-fold higher in the tumour tissues than in the peritumoural tissues (P < 0.01). Moreover, qualitative analysis of the aberrant fucosylated GSLs were completed, and seven types of fucosylated GSLs that contained terminal Fuca2Gal- structure were identified by mass spectrometry. CONCLUSIONS Our results may lead to improved immunotherapy of HCC and contribute to understanding the role of aberrant fucosylated GSLs in the development and progress of HCC in following studies.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antigens, Tumor-Associated, Carbohydrate/analysis
- Carcinoma, Hepatocellular/chemistry
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/genetics
- Ceramides/analysis
- Ceramides/chemistry
- Female
- Fucosyltransferases/genetics
- Glycosylation
- Humans
- Liver Neoplasms/chemistry
- Liver Neoplasms/enzymology
- Liver Neoplasms/genetics
- Male
- Middle Aged
- Molecular Structure
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Up-Regulation
- Galactoside 2-alpha-L-fucosyltransferase
Collapse
Affiliation(s)
- Jian Zhu
- Laboratory of Cellular and Molecular Tumor Immunology, Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Di Girolamo F, Lante I, Muraca M, Putignani L. The Role of Mass Spectrometry in the "Omics" Era. CURR ORG CHEM 2013; 17:2891-2905. [PMID: 24376367 PMCID: PMC3873040 DOI: 10.2174/1385272817888131118162725] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/06/2013] [Accepted: 09/06/2013] [Indexed: 11/15/2022]
Abstract
Mass spectrometry (MS) is one of the key analytical technology on which the emerging ''-omics'' approaches are based. It may provide detection and quantization of thousands of proteins and biologically active metabolites from a tissue, body fluid or cell culture working in a ''global'' or ''targeted'' manner, down to ultra-trace levels. It can be expected that the high performance of MS technology, coupled to routine data handling, will soon bring fruit in the request for a better understanding of human diseases, leading to new molecular biomarkers, hence affecting drug targets and therapies. In this review, we focus on the main advances in the MS technologies, influencing genomics, transcriptomics, proteomics, lipidomics and metabolomics fields, up to the most recent MS applications to meta-omic studies.
Collapse
Affiliation(s)
- Francesco Di Girolamo
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Isabella Lante
- Laboratory Medicine, San Camillo Hospital, Viale Vittorio Veneto 18, 31100, Treviso, Italy
| | - Maurizio Muraca
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Lorenza Putignani
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
- Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| |
Collapse
|
30
|
Comunale MA, Wang M, Anbarasan N, Betesh L, Karabudak A, Moritz E, Devarajan K, Marrero J, Block TM, Mehta A. Total serum glycan analysis is superior to lectin-FLISA for the early detection of hepatocellular carcinoma. Proteomics Clin Appl 2013; 7:690-700. [PMID: 23857719 DOI: 10.1002/prca.201200125] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/22/2013] [Accepted: 03/30/2013] [Indexed: 12/25/2022]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is a primary cancer of the liver that is predominantly the result of infection with a hepatotropic virus such as hepatitis B virus or hepatitis C virus. As liver cancer is often asymptomatic, the development of sensitive noninvasive biomarkers is needed for early detection and improved survival. EXPERIMENTAL DESIGN We have previously identified alterations in the N-linked glycosylation of serum proteins with the development of HCC and identified many of the proteins that contained the altered glycosylation. In the current study, we compared the ability of the identified proteins to diagnose HCC with the total serum glycan analysis. RESULTS Surprisingly, glycan analysis of total serum had the greatest ability to distinguish HCC from cirrhosis with an AUROC of 0.851, a sensitivity of 73% at a specificity of 88%. When total glycan sequencing was combined with alpha-fetoprotein (AFP), the sensitivity increased to 95% at a specificity of 90%. CONCLUSION AND CLINICAL RELEVANCE Changes in glycosylation as detected in whole serum could be used to diagnose HCC with greater sensitivity and specificity than that observed through the analysis of specific protein glycoforms or protein levels. Such an assay could have value in the management of those at risk for the development of HCC.
Collapse
Affiliation(s)
- Mary Ann Comunale
- Department of Microbiology and Immunology, Drexel Institute for Biotechnology and Virology, Drexel University College of Medicine, Doylestown, PA 18901, USA
| | - Mengjun Wang
- Department of Microbiology and Immunology, Drexel Institute for Biotechnology and Virology, Drexel University College of Medicine, Doylestown, PA, USA
| | | | - Lucy Betesh
- Department of Microbiology and Immunology, Drexel Institute for Biotechnology and Virology, Drexel University College of Medicine, Doylestown, PA, USA
| | - Aykan Karabudak
- Institute for Hepatitis and Virus Research, Doylestown, PA, USA
| | - Ethan Moritz
- Institute for Hepatitis and Virus Research, Doylestown, PA, USA
| | | | - Jorge Marrero
- Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Timothy M Block
- Department of Microbiology and Immunology, Drexel Institute for Biotechnology and Virology, Drexel University College of Medicine, Doylestown, PA, USA
| | - Anand Mehta
- Department of Microbiology and Immunology, Drexel Institute for Biotechnology and Virology, Drexel University College of Medicine, Doylestown, PA, USA
| |
Collapse
|
31
|
Mitra I, Alley WR, Goetz JA, Vasseur JA, Novotny MV, Jacobson SC. Comparative profiling of N-glycans isolated from serum samples of ovarian cancer patients and analyzed by microchip electrophoresis. J Proteome Res 2013; 12:4490-6. [PMID: 23984816 DOI: 10.1021/pr400549e] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ovarian cancer is the fifth leading cause of cancer-related mortalities for women in the United States and the most lethal gynecological cancer. Aberrant glycosylation has been linked to several human diseases, including ovarian cancer, and accurate measurement of changes in glycosylation may provide relevant diagnostic and prognostic information. In this work, we used microchip electrophoresis coupled with laser-induced fluorescence detection to determine quantitative differences among the N-glycan profiles of control individuals and late-stage recurrent ovarian cancer patients prior to and after an experimental drug treatment that combined docetaxel and imatinib mesylate. N-Glycans were enzymatically released from 5-μL aliquots of serum samples, labeled with the anionic fluorescent tag, 8-aminopyrene-1,3,6-trisulfonic acid, and analyzed on microfluidic devices. A 22-cm long separation channel, operated at 1250 V/cm, generated analysis times less than 100 s, separation efficiencies up to 8 × 10(5) plates (3.6 × 10(6) plates/m), and migration time reproducibilities better than 0.1% relative standard deviation after peak alignment. Principal component analysis (PCA) and analysis of variance (ANOVA) tests showed significant differences between the control and both pre- and post-treatment cancer samples and subtle differences between the pre- and post-treatment cancer samples. Area-under-the-curve (AUC) values from receiver operating characteristics (ROC) tests were used to evaluate the diagnostic merit of N-glycan peaks, and specific N-glycan peaks used in combination provided AUCs > 0.90 (highly accurate test) when the control and pretreatment cancer samples and control and post-treatment samples were compared.
Collapse
Affiliation(s)
- Indranil Mitra
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | | | | | | | | | | |
Collapse
|
32
|
Kamiyama T, Yokoo H, Furukawa JI, Kurogochi M, Togashi T, Miura N, Nakanishi K, Kamachi H, Kakisaka T, Tsuruga Y, Fujiyoshi M, Taketomi A, Nishimura SI, Todo S. Identification of novel serum biomarkers of hepatocellular carcinoma using glycomic analysis. Hepatology 2013; 57:2314-25. [PMID: 23322672 DOI: 10.1002/hep.26262] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 12/19/2012] [Indexed: 02/05/2023]
Abstract
UNLABELLED The altered N-glycosylation of glycoproteins has been suggested to play an important role in the behavior of malignant cells. Using glycomics technology, we attempted to determine the specific and detailed N-glycan profile for hepatocellular carcinoma (HCC) and investigate the prognostic capabilities. From 1999 to 2011, 369 patients underwent primary curative hepatectomy in our facility and were followed up for a median of 60.7 months. As normal controls, 26 living Japanese related liver transplantation donors were selected not infected by hepatitis B and C virus. Their mean age was 40.0 and 15 (57.7%) were male. We used a glycoblotting method to purify N-glycans from preoperative blood samples from this cohort (10 μL serum) which were then identified and quantified using mass spectrometry (MS). Correlations between the N-glycan levels and the clinicopathologic characteristics and outcomes for these patients were evaluated. Our analysis of the relative areas of all the sugar peaks identified by MS, totaling 67 N-glycans, revealed that a proportion had higher relative areas in the HCC cases compared with the normal controls. Fourteen of these molecules had an area under the curve of greater than 0.80. Analysis of the correlation between these 14 N-glycans and surgical outcomes by univariate and multivariate analysis identified G2890 (m/z value, 2890.052) as a significant recurrence factor and G3560 (m/z value, 3560.295) as a significant prognostic factor. G2890 and G3560 were found to be strongly correlated with tumor number, size, and vascular invasion. CONCLUSION Quantitative glycoblotting based on whole serum N-glycan profiling is an effective approach to screening for new biomarkers. The G2890 and G3560 N-glycans determined by tumor glycomics appear to be promising biomarkers for malignant behavior in HCCs. (HEPATOLOGY 2013;).
Collapse
Affiliation(s)
- Toshiya Kamiyama
- Department of Gastroenterological Surgery I, Hokkaido University Graduate School of Medicine, Hokkaido, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Hua S, Williams CC, Dimapasoc LM, Ro GS, Ozcan S, Miyamoto S, Lebrilla CB, An HJ, Leiserowitz GS. Isomer-specific chromatographic profiling yields highly sensitive and specific potential N-glycan biomarkers for epithelial ovarian cancer. J Chromatogr A 2013; 1279:58-67. [PMID: 23380366 PMCID: PMC5628020 DOI: 10.1016/j.chroma.2012.12.079] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 12/17/2012] [Accepted: 12/26/2012] [Indexed: 12/13/2022]
Abstract
Aberrant glycosylation has been observed for decades in essentially all types of cancer, and is now well established as an indicator of carcinogenesis. Mining the glycome for biomarkers, however, requires analytical methods that can rapidly separate, identify, and quantify isomeric glycans. We have developed a rapid-throughput method for chromatographic glycan profiling using microfluidic chip-based nanoflow liquid chromatography (nano-LC)/mass spectrometry. To demonstrate the utility of this method, we analyzed and compared serum samples from epithelial ovarian cancer cases (n=46) and healthy control individuals (n=48). Over 250 N-linked glycan compound peaks with over 100 distinct N-linked glycan compositions were identified. Statistical testing identified 26 potential glycan biomarkers based on both compositional and structure-specific analyses. Using these results, an optimized model was created incorporating the combined abundances of seven potential glycan biomarkers. The receiver operating characteristic (ROC) curve of this optimized model had an area under the curve (AUC) of 0.96, indicating robust discrimination between cancer cases and healthy controls. Rapid-throughput chromatographic glycan profiling was found to be an effective platform for structure-specific biomarker discovery.
Collapse
Affiliation(s)
- Serenus Hua
- Department of Chemistry, University of California, Davis, CA, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Frisch E, Schwedler C, Kaup M, Iona Braicu E, Gröne J, Lauscher JC, Sehouli J, Zimmermann M, Tauber R, Berger M, Blanchard V. Endo-β-N-acetylglucosaminidase H de-N-glycosylation in a domestic microwave oven: Application to biomarker discovery. Anal Biochem 2013; 433:65-9. [DOI: 10.1016/j.ab.2012.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/05/2012] [Accepted: 10/11/2012] [Indexed: 11/29/2022]
|
35
|
Serum biomarkers identification by mass spectrometry in high-mortality tumors. INTERNATIONAL JOURNAL OF PROTEOMICS 2013; 2013:125858. [PMID: 23401773 PMCID: PMC3562576 DOI: 10.1155/2013/125858] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 11/16/2012] [Accepted: 12/11/2012] [Indexed: 02/08/2023]
Abstract
Cancer affects millions of people worldwide. Tumor mortality is substantially due to diagnosis at stages that are too late for therapies to be effective. Advances in screening methods have improved the early diagnosis, prognosis, and survival for some cancers. Several validated biomarkers are currently used to diagnose and monitor the progression of cancer, but none of them shows adequate specificity, sensitivity, and predictive value for population screening. So, there is an urgent need to isolate novel sensitive, specific biomarkers to detect the disease early and improve prognosis, especially in high-mortality tumors. Proteomic techniques are powerful tools to help in diagnosis and monitoring of treatment and progression of the disease. During the last decade, mass spectrometry has assumed a key role in most of the proteomic analyses that are focused on identifying cancer biomarkers in human serum, making it possible to identify and characterize at the molecular level many proteins or peptides differentially expressed. In this paper we summarize the results of mass spectrometry serum profiling and biomarker identification in high mortality tumors, such as ovarian, liver, lung, and pancreatic cancer.
Collapse
|
36
|
Abstract
We introduce three software tools, Cartoonist, GlycoWorkbench, and MultiGlycan, for N-glycan profiling of complex biological samples. Detailed instructions for using these tools are provided, and their performances are demonstrated by using real glycan profiling data.
Collapse
Affiliation(s)
| | | | - Haixu Tang
- Corresponding author: Haixu Tang, Informatics 225, Informatics Building, 901 E. 10th St. Bloomington, IN 47408-3912, , Phone: (812)-856-1859, Fax: (812)-856-4764
| |
Collapse
|
37
|
Serum protein N-glycan alterations of diethylnitrosamine-induced hepatocellular carcinoma mice and their evolution after inhibition of the placental growth factor. Mol Cell Biochem 2012; 372:199-210. [PMID: 23001868 DOI: 10.1007/s11010-012-1461-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/14/2012] [Indexed: 12/17/2022]
Abstract
Placental growth factor (PlGF) inhibition produced promising results in reducing tumor burden in a diethylnitrosamine (DEN)-induced mouse model for hepatocellular carcinoma (HCC). The aim of this study was to non-invasively assess the improved histology by performing a serum glycomic analysis. To elucidate the molecular mechanism underlying the observed glycomic effects, we investigated the transcription and expression of E26 transformation-specific sequence 1 (Ets-1), a transcription factor essential for the glycomic and angiogenic changes in malignant transformation, including its different phosphorylated forms that result from activation of the MAP kinase and a Ca(2+)-dependent pathway. In addition, three Ets-1-dependent glycosyltransferase genes, Mgat4a, Mgat4b, and Mgat5, were also evaluated. HCC was induced in mice by weekly injections with DEN for 16, 20, 25, and 30 w. In the treatment study, mice were injected with DEN for 25 w and subsequently treated with PlGF antibodies (5D11D4) for 5 w. Finally, PlGF-/- mice were injected with DEN for 20, 25, and 30 w. Serum N-glycans were analyzed with DNA sequencer-assisted fluorophore-assisted capillary electrophoresis and compared with histology. Maximum altered N-glycan phenotype was reached after 20 w of DEN-injections, i.e., when the first neoplastic lesions started to appear. 5D11D4-treatment improved the glycomic phenotype in that 7 of the 11 altered glycans tended to normalize. The PlGF-/- mice also showed a normalization trend, although not to the same extent of the treatment group. Number of Ets1, Mgat4a, Mgat4b, and Mgat5 transcripts increased considerably in DEN-injected mice, however, a non-significant decrease was observed after 5D11D4-treatment. On the protein level, 5D11D4-treatment had a prominent effect on the MAP kinase pathway with a significant p38 activation, yet independent of Ets-1 function.
Collapse
|
38
|
Fogli A, Merle C, Roussel V, Schiffmann R, Ughetto S, Theisen M, Boespflug-Tanguy O. CSF N-glycan profiles to investigate biomarkers in brain developmental disorders: application to leukodystrophies related to eIF2B mutations. PLoS One 2012; 7:e42688. [PMID: 22952606 PMCID: PMC3430715 DOI: 10.1371/journal.pone.0042688] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/10/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Primary or secondary abnormalities of glycosylation have been reported in various brain diseases. Decreased asialotransferrin to sialotransferrin ratio in cerebrospinal fluid (CSF) is a diagnostic marker of leukodystrophies related to mutations of genes encoding translation initiation factor, EIF2B. We investigated the CSF glycome of eIF2B-mutated patients and age-matched normal individuals in order to further characterize the glycosylation defect for possible use as a biomarker. METHODOLOGY/PRINCIPAL FINDINGS We conducted a differential N-glycan analysis using MALDI-TOF/MS of permethylated N-glycans in CSF and plasma of controls and eIF2B-mutated patients. We found in control CSF that tri-antennary/bisecting and high mannose structures were highly represented in samples obtained between 1 to 5 years of age, whereas fucosylated, sialylated structures were predominant at later age. In CSF, but not in plasma, of eIF2B-mutated patient samples, we found increased relative intensity of bi-antennary structures and decreased tri-antennary/bisecting structures in N-glycan profiles. Four of these structures appeared to be biomarker candidates of glycomic profiles of eIF2B-related disorders. CONCLUSION Our results suggest a dynamic development of normal CSF N-glycan profiles from high mannose type structures to complex sialylated structures that could be correlated with postnatal brain maturation. CSF N-glycome analysis shows relevant quantitative changes associated with eIF2B related disorders. This approach could be applied to other neurological disorders involving developmental gliogenesis/synaptogenesis abnormalities.
Collapse
Affiliation(s)
- Anne Fogli
- Laboratoire GReD UMR INSERM U931 CNRS 6247, Faculté de Médecine, Clermont-Ferrand, France.
| | | | | | | | | | | | | |
Collapse
|
39
|
Kuzmanov U, Smith CR, Batruch I, Soosaipillai A, Diamandis A, Diamandis EP. Separation of kallikrein 6 glycoprotein subpopulations in biological fluids by anion-exchange chromatography coupled to ELISA and identification by mass spectrometry. Proteomics 2012; 12:799-809. [PMID: 22539431 DOI: 10.1002/pmic.201100371] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Kallikrein 6 (KLK6) has been shown to be aberrantly glycosylated in ovarian cancer. Here, we report a novel HPLC anion exchange method, coupled to a KLK6-specific ELISA, capable of differentiating KLK6 glycoform subgroups in biological fluids. Biological fluids were fractionated using anion exchange and resulting fractions were analyzed for KLK6 content by ELISA producing a four-peak elution profile. Using this assay, the KLK6 elution profile and distribution across peaks of a set (n = 7) of ovarian cancer patient matched serum and ascites fluid samples was found to be different than the profile of serum and cerebrospinal fluid (CSF) of normal individuals (n = 7). Glycosylation patterns of recombinant KLK6 (rKLK6) were characterized using tandem mass spectrometry (MS/MS), and found to consist of a highly heterogeneous KLK6 population. This protein was found to contain all of the four diagnostic KLK6 peaks present in the previously assayed biological fluids. The rKLK6 glycoform composition of each peak was assessed by lectin affinity and MS/MS based glycopeptide quantification by product ion monitoring. The combined results showed an increase in terminal alpha 2-6 linked sialic acid in the N-glycans found on KLK6 from ovarian cancer serum and ascites, as opposed to CSF and serum of normal individuals.
Collapse
Affiliation(s)
- Uros Kuzmanov
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | | |
Collapse
|
40
|
Dallas DC, Martin WF, Hua S, German JB. Automated glycopeptide analysis--review of current state and future directions. Brief Bioinform 2012; 14:361-74. [PMID: 22843980 DOI: 10.1093/bib/bbs045] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycosylation of proteins is involved in immune defense, cell-cell adhesion, cellular recognition and pathogen binding and is one of the most common and complex post-translational modifications. Science is still struggling to assign detailed mechanisms and functions to this form of conjugation. Even the structural analysis of glycoproteins-glycoproteomics-remains in its infancy due to the scarcity of high-throughput analytical platforms capable of determining glycopeptide composition and structure, especially platforms for complex biological mixtures. Glycopeptide composition and structure can be determined with high mass-accuracy mass spectrometry, particularly when combined with chromatographic separation, but the sheer volume of generated data necessitates computational software for interpretation. This review discusses the current state of glycopeptide assignment software-advances made to date and issues that remain to be addressed. The various software and algorithms developed so far provide important insights into glycoproteomics. However, there is currently no freely available software that can analyze spectral data in batch and unambiguously determine glycopeptide compositions for N- and O-linked glycopeptides from relevant biological sources such as human milk and serum. Few programs are capable of aiding in structural determination of the glycan component. To significantly advance the field of glycoproteomics, analytical software and algorithms are required that: (i) solve for both N- and O-linked glycopeptide compositions, structures and glycosites in biological mixtures; (ii) are high-throughput and process data in batches; (iii) can interpret mass spectral data from a variety of sources and (iv) are open source and freely available.
Collapse
|
41
|
Vasseur JA, Goetz JA, Alley WR, Novotny MV. Smoking and lung cancer-induced changes in N-glycosylation of blood serum proteins. Glycobiology 2012; 22:1684-708. [PMID: 22781126 DOI: 10.1093/glycob/cws108] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Glycosylation is a key post-translational protein modification which appears important in malignant transformation and tumor metastasis. Abnormal glycosylation of different proteins can often be measured in the blood serum. In this study, we extend our serum-based structural investigations to samples provided by patients diagnosed with lung cancer, paying particular attention to the effects of smoking on the serum glycomic traces. Following a battery of glycomic tests, we find that several fucosylated tetra-antennary structures with varying degrees of sialylation are increased in their abundances in control samples provided by the former smokers, with further elevations in the lung cancer patients who were former smokers. Further detailed investigations demonstrated that the level of outer-arm fucosylation was elevated in the control samples of the former smokers and again in the lung cancer samples provided by the former smokers. This trend was particularly noticeable for the tri- and tetra-antennary structures. Different ratios of sialylation linkages were also observed that could be correlated with the different states of health and smoking status. Decreases in the abundance levels of isomers with two and three α2,3-linked sialic acids and an increased abundance of an isomer with two α2,6-linked sialic acids were noted for a fucosylated tri-sialylated tri-antennary glycan. These results demonstrate the long-term effects of smoking on glycomic profiles and that this factor needs to be considered in these and other serum-based analyses.
Collapse
|
42
|
Abstract
The glycome, that is, the glycan components of a biological source, has been widely reported to change with disease states. However, mining the glycome for biomarkers is complicated by glycan structural heterogeneity. Nanoflow LC, or nano-LC, significantly addresses the problem by providing a highly sensitive and quantitative method of separating and profiling glycans. This review summarizes recent advances in analytical technology and methodology that enhance and augment the advantages offered by nano-LC. (e.g., reversed phase, hydrophilic interaction and porous graphitized carbon chromatography, as well as associated derivatization strategies), detectors (e.g., fluorescence and MS), and technology platforms (particularly chip-based nano-LC) are examined in detail, along with their application to biomarker discovery. Particular emphasis is placed on methods and technologies that allow structure-specific glycan profiling.
Collapse
|
43
|
Pompach P, Chandler KB, Lan R, Edwards N, Goldman R. Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC-MS/MS, and glycan database search. J Proteome Res 2012; 11:1728-40. [PMID: 22239659 DOI: 10.1021/pr201183w] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glycoproteins fulfill many indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. Improved analytical methods are needed to allow a complete characterization of this complex and common post-translational modification. In this study, we present a workflow for the analysis of the microheterogeneity of N-glycoproteins that couples hydrophilic interaction and nanoreverse-phase C18 chromatography to tandem QTOF mass spectrometric analysis. A glycan database search program, GlycoPeptideSearch, was developed to match N-glycopeptide MS/MS spectra with the glycopeptides comprised of a glycan drawn from the GlycomeDB glycan structure database and a peptide from a user-specified set of potentially glycosylated peptides. Application of the workflow to human haptoglobin and hemopexin, two microheterogeneous N-glycoproteins, identified a total of 57 distinct site-specific glycoforms in the case of haptoglobin and 14 site-specific glycoforms of hemopexin. Using glycan oxonium ions and peptide-characteristic glycopeptide fragment ions and by collapsing topologically redundant glycans, the search software was able to make unique N-glycopeptide assignments for 51% of assigned spectra, with the remaining assignments primarily representing isobaric topological rearrangements. The optimized workflow, coupled with GlycoPeptideSearch, is expected to make high-throughput semiautomated glycopeptide identification feasible for a wide range of users.
Collapse
Affiliation(s)
- Petr Pompach
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University , 3970 Reservoir Road NW, Washington, DC 20057-1465, United States
| | | | | | | | | |
Collapse
|
44
|
N-glycans in liver-secreted and immunoglogulin-derived protein fractions. J Proteomics 2012; 75:2216-24. [PMID: 22326963 DOI: 10.1016/j.jprot.2012.01.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/17/2012] [Accepted: 01/20/2012] [Indexed: 02/01/2023]
Abstract
N-glycosylation of proteins provides a rich source of information on liver disease progression because majority of serum glycoproteins, with the exception of immunoglobulins, are secreted by the liver. In this report, we present results of an optimized workflow for MALDI-TOF analysis of permethylated N-glycans detached from serum proteins and separated into liver secreted and immunoglobulin fractions. We have compared relative intensities of N-glycans in 23 healthy controls and 23 cirrhosis patients. We were able to detect 82 N-glycans associated primarily with liver secreted glycoproteins, 54 N-glycans in the protein G bound fraction and 52 N-glycans in the fraction bound to protein A. The N-glycan composition of the fractions differed substantially, independent of liver disease. The relative abundance of approximately 53% N-glycans in all fractions was significantly altered in the cirrhotic liver. The removal of immunoglobulins allowed detection of an increase in a series of high mannose and hybrid N-glycans associated with the liver secreted protein fraction.
Collapse
|
45
|
Frisch E, Kaup M, Egerer K, Weimann A, Tauber R, Berger M, Blanchard V. Profiling of Endo H-released serum N-glycans using CE-LIF and MALDI-TOF-MS - Application to rheumatoid arthritis. Electrophoresis 2011; 32:3510-5. [DOI: 10.1002/elps.201100250] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
46
|
Hua S, An HJ, Ozcan S, Ro GS, Soares S, DeVere-White R, Lebrilla CB. Comprehensive native glycan profiling with isomer separation and quantitation for the discovery of cancer biomarkers. Analyst 2011; 136:3663-71. [PMID: 21776491 PMCID: PMC3331797 DOI: 10.1039/c1an15093f] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Glycosylation is highly sensitive to the biochemical environment and has been implicated in many diseases including cancer. Glycan compositional profiling of human serum with mass spectrometry has already identified potential biomarkers for several types of cancer and diseases; however, composition alone does not fully describe glycan stereo- and regioisomeric diversity. The vast structural heterogeneity of glycans presents a formidable analytical challenge. We have developed a method to identify and quantify isomeric native glycans using nanoflow liquid chromatography (nano-LC)/mass spectrometry. A microfluidic chip packed with graphitized carbon was used to chromatographically separate the glycans. To determine the utility of this method for structure-specific biomarker discovery, we analyzed serum samples from two groups of prostate cancer patients with different prognoses. More than 300 N-glycan species (including isomeric structures) were identified, corresponding to over 100 N-glycan compositions. Statistical tests established significant differences in glycan abundances between patient groups. This method provides comprehensive, selective, and quantitative glycan profiling.
Collapse
Affiliation(s)
- Serenus Hua
- Department of Chemistry, University of California, Davis, 95616
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Sureyya Ozcan
- Department of Chemistry, University of California, Davis, 95616
| | - Grace S. Ro
- Department of Chemistry, University of California, Davis, 95616
| | | | | | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, 95616
- Department of Biochemistry and Molecular Medicine, University of California, Davis, 95616
| |
Collapse
|
47
|
Kang P, Madera M, Alley WR, Goldman R, Mechref Y, Novotny MV. Glycomic Alterations in the Highly-abundant and Lesser-abundant Blood Serum Protein Fractions for Patients Diagnosed with Hepatocellular Carcinoma. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 305:185-198. [PMID: 23788846 PMCID: PMC3685172 DOI: 10.1016/j.ijms.2010.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Hepatocellular cancer is a serious human disease with an unfortunately low survival rate. It further poses a significant epidemic threat to our society through its viral vectors associated with cirrhosis conditions preceding the cancer. A search for biomarkers of these diseases enlists analytical glycobiology, in general, and quantitative biomolecular mass spectrometry (MS), in particular, as valuable approaches to cancer research. The recent advances in quantitative glycan permethylation prior to MALDI-MS oligosaccharide profiling has enabled us to compare the glycan quantitative proportions in the small serum samples of cancer and cirrhotic patients against control individuals. We were further able to fractionate the major serum proteins from the minor components and compare statistically their differential glycosylation, elucidating some causes of quantitatively unusual glycosylation events. Numerous glycan structures were tentatively identified and connected with the origin proteins, with a particular emphasis on sialylated and fucosylated glycans.
Collapse
Affiliation(s)
- Pilsoo Kang
- National Center for Glycomics and Glycoproteomics
- Department of Chemistry, Bloomington, IN, USA, 47405
| | - Milan Madera
- National Center for Glycomics and Glycoproteomics
- Department of Chemistry, Bloomington, IN, USA, 47405
| | - William R. Alley
- National Center for Glycomics and Glycoproteomics
- Department of Chemistry, Bloomington, IN, USA, 47405
| | - Radoslav Goldman
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., USA, 20057
| | - Yehia Mechref
- National Center for Glycomics and Glycoproteomics
- Department of Chemistry, Bloomington, IN, USA, 47405
| | - Milos V. Novotny
- National Center for Glycomics and Glycoproteomics
- Department of Chemistry, Bloomington, IN, USA, 47405
| |
Collapse
|
48
|
The application of SELDI-TOF-MS in clinical diagnosis of cancers. J Biomed Biotechnol 2011; 2011:245821. [PMID: 21687541 PMCID: PMC3114543 DOI: 10.1155/2011/245821] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 03/30/2011] [Indexed: 12/24/2022] Open
Abstract
Cancer diagnosis is important, and the early diagnosis of cancers could predict a more successful treatment. The proteomic studies emerged to be useful in combined analyses of samples from patients and provide more accurate diagnosis when compared to the single-factor-based diagnosis. In recent years, cancer detection with surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF MS) is flourishing and brought significant progress in this area. This paper summarizes some recent results with this technique for cancer diagnosis.
Collapse
|
49
|
Tsai HY, Boonyapranai K, Sriyam S, Yu CJ, Wu SW, Khoo KH, Phutrakul S, Chen ST. Glycoproteomics analysis to identify a glycoform on haptoglobin associated with lung cancer. Proteomics 2011; 11:2162-70. [PMID: 21538882 DOI: 10.1002/pmic.201000319] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 12/21/2010] [Accepted: 02/19/2011] [Indexed: 11/10/2022]
Abstract
Glycosylation is a common protein modification that is of interest in current cancer research because altered carbohydrate moieties are often found during cancer progress. A search for biomarkers in human lung cancer serum samples using glycoproteomic approaches identified fucosylated haptoglobin (Hp) significantly increased in serum of each subtype of lung cancer compared to normal donors. In addition, MS provided evidence of an increase of Hp fucosylation; the glycan structure was determined to be an α 2,6-linked tri-sialylated triantennary glycan containing α1,3-linked fucose attached to the four-linked position of the three-arm mannose of N-linked core pentasaccharide. These preliminary findings suggest that the specific glycoform of Hp may be useful as a marker to monitor lung cancer progression.
Collapse
Affiliation(s)
- Hsien-Yu Tsai
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Masuda T, Miyoshi E. Cancer biomarkers for hepatocellular carcinomas: from traditional markers to recent topics. Clin Chem Lab Med 2011; 49:959-66. [PMID: 21428856 DOI: 10.1515/cclm.2011.152] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hepatocellular carcinomas (HCC) are the fifth most common tumor type and the third most common cause of cancer-related death worldwide. Some tumor markers for HCC, such as α-fetoprotein and des-γ-carboxyprothrombin, are used clinically. Recent advances in proteomics and glyco-proteomics might provide various types of novel tumor markers for HCC. While the clinical availability of these tumor markers is important, the molecular mechanisms underlying the production of tumor markers requires further clarification. Our group has investigated the glycobiology of tumor markers. In this review, we describe the impact of novel HCC markers and their possible implications for clinical use.
Collapse
Affiliation(s)
- Tomomi Masuda
- Department of Molecular Biochemistry and Clinical Investigation, Osaka University Graduate School of Medicine, Suita, Japan
| | | |
Collapse
|