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Massonnet P, Grifnée E, Farré-Segura J, Demeuse J, Huyghebaert L, Dubrowski T, Dufour P, Schoumacher M, Peeters S, Le Goff C, Cavalier E. Concise review on the combined use of immunocapture, mass spectrometry and liquid chromatography for clinical applications. Clin Chem Lab Med 2023; 61:1700-1707. [PMID: 37128992 DOI: 10.1515/cclm-2023-0253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/21/2023] [Indexed: 05/03/2023]
Abstract
Immunocapture is now a well-established method for sample preparation prior to quantitation of peptides and proteins in complex matrices. This short review will give an overview of some clinical applications of immunocapture methods, as well as protocols with and without enzymatic digestion in a clinical context. The advantages and limitations of both approaches are discussed in detail. Challenges related to the choice of mass spectrometer are also discussed. Top-down, middle-down, and bottom-up approaches are discussed. Even though immunocapture has its limitations, its main advantage is that it provides an additional dimension of separation and/or isolation when working with peptides and proteins. Overall, this short review demonstrates the potential of such techniques in the field of proteomics-based clinical medicine and paves the way for better personalized medicine.
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Affiliation(s)
- Philippe Massonnet
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Elodie Grifnée
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Jordi Farré-Segura
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Justine Demeuse
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Loreen Huyghebaert
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Thomas Dubrowski
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Patrice Dufour
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | | | - Stéphanie Peeters
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
| | - Caroline Le Goff
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Etienne Cavalier
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
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Gjorgjieva M, Ay AS, Correia de Sousa M, Delangre E, Dolicka D, Sobolewski C, Maeder C, Fournier M, Sempoux C, Foti M. MiR-22 Deficiency Fosters Hepatocellular Carcinoma Development in Fatty Liver. Cells 2022; 11:cells11182860. [PMID: 36139435 PMCID: PMC9496902 DOI: 10.3390/cells11182860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022] Open
Abstract
MiR-22 is mostly considered as a hepatic tumor-suppressor microRNA based on in vitro analyses. Yet, whether miR-22 exerts a tumor-suppressive function in the liver has not been investigated in vivo. Herein, in silico analyses of miR-22 expression were performed in hepatocellular carcinomas from human patient cohorts and different mouse models. Diethylnitrosamine-induced hepatocellular carcinomas were then investigated in lean and diet-induced obese miR-22-deficient mice. The proteome of liver tissues from miR-22-deficient mice prior to hepatocellular carcinoma development was further analyzed to uncover miR-22 regulated factors that impact hepatocarcinogenesis with miR-22 deficiency. MiR-22 downregulation was consistently observed in hepatocellular carcinomas from all human cohorts and mouse models investigated. The time of appearance of the first tumors was decreased and the number of tumoral foci induced by diethylnitrosamine was significantly increased by miR-22-deficiency in vivo, two features which were further drastically exacerbated with diet-induced obesity. At the molecular level, we provide evidence that the loss of miR-22 significantly affects the energetic metabolism and mitochondrial functions of hepatocytes, and the expression of tumor-promoting factors such as thrombospondin-1. Our study demonstrates that miR-22 acts as a hepatic tumor suppressor in vivo by restraining pro-carcinogenic metabolic deregulations through pleiotropic mechanisms and the overexpression of relevant oncogenes.
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Affiliation(s)
- Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Anne-Sophie Ay
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Etienne Delangre
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Dobrochna Dolicka
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Christine Sempoux
- Service of Clinical Pathology, Institute of Pathology, Lausanne University Hospital, University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Translational Research Centre in Onco-Haematology, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Correspondence:
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Glycomic and Glycoproteomic Techniques in Neurodegenerative Disorders and Neurotrauma: Towards Personalized Markers. Cells 2022; 11:cells11030581. [PMID: 35159390 PMCID: PMC8834236 DOI: 10.3390/cells11030581] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022] Open
Abstract
The proteome represents all the proteins expressed by a genome, a cell, a tissue, or an organism at any given time under defined physiological or pathological circumstances. Proteomic analysis has provided unparalleled opportunities for the discovery of expression patterns of proteins in a biological system, yielding precise and inclusive data about the system. Advances in the proteomics field opened the door to wider knowledge of the mechanisms underlying various post-translational modifications (PTMs) of proteins, including glycosylation. As of yet, the role of most of these PTMs remains unidentified. In this state-of-the-art review, we present a synopsis of glycosylation processes and the pathophysiological conditions that might ensue secondary to glycosylation shortcomings. The dynamics of protein glycosylation, a crucial mechanism that allows gene and pathway regulation, is described. We also explain how-at a biomolecular level-mutations in glycosylation-related genes may lead to neuropsychiatric manifestations and neurodegenerative disorders. We then analyze the shortcomings of glycoproteomic studies, putting into perspective their downfalls and the different advanced enrichment techniques that emanated to overcome some of these challenges. Furthermore, we summarize studies tackling the association between glycosylation and neuropsychiatric disorders and explore glycoproteomic changes in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington disease, multiple sclerosis, and amyotrophic lateral sclerosis. We finally conclude with the role of glycomics in the area of traumatic brain injury (TBI) and provide perspectives on the clinical application of glycoproteomics as potential diagnostic tools and their application in personalized medicine.
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Analysis of Multimerin 1 (MMRN1) expression in ovarian cancer. Mol Biol Rep 2020; 47:9459-9468. [PMID: 33263168 DOI: 10.1007/s11033-020-06027-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 11/20/2020] [Indexed: 12/31/2022]
Abstract
Ovarian cancer, the most lethal gynecological cancer, is the fifth most common cause of cancer-related deaths in women. A cost-effective and non-invasive early screening method for ovarian cancer is required to reduce the high mortality rate. Saliva is a clinically informative unique fluid, which is useful for novel approaches to prognosis, clinical diagnosis, and monitoring for non-invasive detection of disease. Multimerin1 (MMRN1) is a di-sulfide linked homo-polymeric glycoprotein from EMILIN family. Altered expression of MMRN1 has been reported in hepatocellular carcinoma, cervical cancer, and ovarian cancer. But, its role in epithelial ovarian cancer (EOC) is not clear and well documented. In this study, expression of Multimerin 1 was validated in saliva and tissues of EOC patients and age-matched controls by western blotting, ELISA, RT-PCR, and immunohistochemistry. Significant over expression of MMRN1 was observed by western blot and ELISA in saliva samples of EOC patients. The average concentration of MMRN1 in the saliva of healthy controls was 28.7 pg/ml (SE ± 1.76), 42.53 pg/ml (SE ± 4.06) in low grade and 52.91 pg/ml (SE ± 4.24) with p < 0.01 in high-grade EOC. Upregulated cytoplasmic expression of MMRN1 was observed in EOC tissue by immunohistochemistry. Our results suggest that MMRN1 expression is associated with EOC progression and MMRN1 may be potential biomarker candidates for early-stage EOC detection however further experiments are required in a large cohort to establish this proposition. Also, saliva can be explored as a novel medium for ovarian cancer diagnosis.
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Cao WQ, Jiang BY, Huang JM, Zhang L, Liu MQ, Yao J, Wu MX, Zhang LJ, Kong SY, Wang Y, Yang PY. Straightforward and Highly Efficient Strategy for Hepatocellular Carcinoma Glycoprotein Biomarker Discovery Using a Nonglycopeptide-Based Mass Spectrometry Pipeline. Anal Chem 2019; 91:12435-12443. [DOI: 10.1021/acs.analchem.9b03074] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Qin H, Dong X, Mao J, Chen Y, Dong M, Wang L, Guo Z, Liang X, Ye M. Highly Efficient Analysis of Glycoprotein Sialylation in Human Serum by Simultaneous Quantification of Glycosites and Site-Specific Glycoforms. J Proteome Res 2019; 18:3439-3446. [PMID: 31380653 DOI: 10.1021/acs.jproteome.9b00332] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aberrant sialylation of glycoproteins is closely related to many malignant diseases, and analysis of sialylation has great potential to reveal the status of these diseases. However, in-depth analysis of sialylation is still challenging because of the high microheterogeneity of protein glycosylation, as well as the low abundance of sialylated glycopeptides (SGPs). Herein, an integrated strategy was fabricated for the detailed characterization of glycoprotein sialylation on the levels of glycosites and site-specific glycoforms by employing the SGP enrichment method. This strategy enabled the identification of up to 380 glycosites, as well as 414 intact glycopeptides corresponding to 383 site-specific glycoforms from only initial 6 μL serum samples, indicating the high sensitivity of the method for the detailed analysis of glycoprotein sialylation. This strategy was further employed to the differential analysis of glycoprotein sialylation between hepatocellular carcinoma patients and control samples, leading to the quantification of 344 glycosites and 405 site-specific glycoforms, simultaneously. Among these, 43 glycosites and 55 site-specific glycoforms were found to have significant change on the glycosite and site-specific glycoform levels, respectively. Interestingly, several glycoforms attached onto the same glycosite were found with different change tendencies. This strategy was demonstrated to be a powerful tool to reveal subtle differences of the macro- and microheterogeneity of glycoprotein sialylation.
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Affiliation(s)
- Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , P. R. China
| | - Xuefang Dong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , P. R. China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yao Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Mingming Dong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , P. R. China
| | - Liming Wang
- The Second Affiliated Hospital of Dalian Medical University , Dalian 116027 , China
| | - Zhimou Guo
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , P. R. China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , P. R. China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , P. R. China
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7
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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
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Zhu J, Warner E, Parikh ND, Lubman DM. Glycoproteomic markers of hepatocellular carcinoma-mass spectrometry based approaches. MASS SPECTROMETRY REVIEWS 2019; 38:265-290. [PMID: 30472795 PMCID: PMC6535140 DOI: 10.1002/mas.21583] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/19/2018] [Indexed: 05/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is the third most-common cause of cancer-related death worldwide. Most cases of HCC develop in patients that already have liver cirrhosis and have been recommended for surveillance for an early onset of HCC. Cirrhosis is the final common pathway for several etiologies of liver disease, including hepatitis B and C, alcohol, and increasingly non-alcoholic fatty liver disease. Only 20-30% of patients with HCC are eligible for curative therapy due primarily to inadequate early-detection strategies. Reliable, accurate biomarkers for HCC early detection provide the highest likelihood of curative therapy and survival; however, current early-detection methods that use abdominal ultrasound and serum alpha fetoprotein are inadequate due to poor adherence and limited sensitivity and specificity. There is an urgent need for convenient and highly accurate validated biomarkers for HCC early detection. The theme of this review is the development of new methods to discover glycoprotein-based markers for detection of HCC with mass spectrometry approaches. We outline the non-mass spectrometry based methods that have been used to discover HCC markers including immunoassays, capillary electrophoresis, 2-D gel electrophoresis, and lectin-FLISA assays. We describe the development and results of mass spectrometry-based assays for glycan screening based on either MALDI-MS or ESI analysis. These analyses might be based on the glycan content of serum or on glycan screening for target molecules from serum. We describe some of the specific markers that have been developed as a result, including for proteins such as Haptoglobin, Hemopexin, Kininogen, and others. We discuss the potential role for other technologies, including PGC chromatography and ion mobility, to separate isoforms of glycan markers. Analyses of glycopeptides based on new technologies and innovative softwares are described and also their potential role in discovery of markers of HCC. These technologies include new fragmentation methods such as EThcD and stepped HCD, which can identify large numbers of glycopeptide structures from serum. The key role of lectin extraction in various assays for intact glycopeptides or their truncated versions is also described, where various core-fucosylated and hyperfucosylated glycopeptides have been identified as potential markers of HCC. Finally, we describe the role of LC-MRMs or lectin-FLISA MRMs as a means to validate these glycoprotein markers from patient samples. These technological advancements in mass spectrometry have the potential to lead to novel biomarkers to improve the early detection of HCC.
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Affiliation(s)
- Jianhui Zhu
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
| | - Elisa Warner
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
| | - Neehar D. Parikh
- Department of Internal Medicine, The University of Michigan, Ann Arbor 48109, Michigan
| | - David M. Lubman
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
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Qin H, Chen Y, Mao J, Cheng K, Sun D, Dong M, Wang L, Wang L, Ye M. Proteomics analysis of site-specific glycoforms by a virtual multistage mass spectrometry method. Anal Chim Acta 2019; 1070:60-68. [PMID: 31103168 DOI: 10.1016/j.aca.2019.04.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 01/08/2023]
Abstract
Determination of site-specific glycoforms is the key to reveal the micro-heterogeneity of protein glycosylation at proteome level. Herein, we presented an integrated virtual multistage MS strategy to identify intact glycopeptides, which allowed the determination of site-specific glycoforms. In this strategy, the enzymatically de-glycosylated peptides and intact glycopeptides were mixed and analyzed in the same LC-MS/MS run. The acquired MS2 spectra of intact glycopeptides allowed determination of the glycans, and the MS2 spectra of the de-glycosylated peptides enabled the identification of peptide backbone sequences. Compared with the conventional multistage strategy, the peptide backbones could be directly identified by the MS2 of the de-glycopeptides with higher sensitivity. This strategy was first validated by analyzing the glycosites and site-specific glycoforms of mouse liver tissues. Then, it was applied to differential analysis of the glycoproteomes of hepatocellular carcinoma (HCC) and adjacent liver tissues. Compared with the identification scheme using only MS2 spectra of intact glycopeptides or glycosites, this approach enabled quantitative analysis on two levels, i.e. glycosites and site-specific glycoforms, simultaneously. Thus, it could be a powerful tool to characterize the subtle differences in the macro- and micro-heterogeneity of protein glycosylation for different samples.
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Affiliation(s)
- Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yao Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Cheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Deguang Sun
- The Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, China
| | - Mingming Dong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lu Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Liming Wang
- The Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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Dahabiyeh LA, Tooth D, Barrett DA. Profiling of 54 plasma glycoproteins by label-free targeted LC-MS/MS. Anal Biochem 2019; 567:72-81. [DOI: 10.1016/j.ab.2018.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 01/02/2023]
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Portelli M, Baron B. Clinical Presentation of Preeclampsia and the Diagnostic Value of Proteins and Their Methylation Products as Biomarkers in Pregnant Women with Preeclampsia and Their Newborns. J Pregnancy 2018; 2018:2632637. [PMID: 30050697 PMCID: PMC6046127 DOI: 10.1155/2018/2632637] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
Preeclampsia (PE) is a disorder which affects 1-10% of pregnant women worldwide. It is characterised by hypertension and proteinuria in the later stages of gestation and can lead to maternal and perinatal morbidity and mortality. Other than the delivery of the foetus and the removal of the placenta, to date there are no therapeutic approaches to treat or prevent PE. It is thus only possible to reduce PE-related mortality through early detection, careful monitoring, and treatment of the symptoms. For these reasons the search for noninvasive, blood-borne, or urinary biochemical markers that could be used for the screening, presymptomatic diagnosis, and prediction of the development of PE is of great urgency. So far, a number of biomarkers have been proposed for predicting PE, based on pathophysiological observations, but these have mostly proven to be unreliable and inconsistent between different studies. The clinical presentation of PE and data gathered for the biochemical markers placental growth factor (PlGF), soluble Feline McDonough Sarcoma- (fms-) like tyrosine kinase-1 (sFlt-1), asymmetric dimethylarginine (ADMA), and methyl-lysine is being reviewed with the aim of providing both a clinical and biochemical understanding of how these biomarkers might assist in the diagnosis of PE or indicate its severity.
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Affiliation(s)
- Maria Portelli
- Centre for Molecular Medicine and Biobanking, Faculty of Medicine and Surgery, University of Malta, Msida MSD2080, Malta
| | - Byron Baron
- Centre for Molecular Medicine and Biobanking, Faculty of Medicine and Surgery, University of Malta, Msida MSD2080, Malta
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12
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Park J, Han D, Do M, Woo J, Wang JI, Han Y, Kwon W, Kim SW, Jang JY, Kim Y. Proteome characterization of human pancreatic cyst fluid from intraductal papillary mucinous neoplasm by liquid chromatography/tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1761-1772. [PMID: 28815810 DOI: 10.1002/rcm.7959] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/12/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE In recent years, the molecular components of pancreatic cyst fluid have been used for diagnosis and prognosis. Because the protein markers that are currently used in clinical tests are unreliable, proteomic studies to find new protein markers are being conducted. However, such researches have been limited due to the complexity of pancreatic cyst fluid and the immaturity of proteomic techniques. METHODS To overcome these limitations and provide a pancreatic cyst proteome dataset, we examined cyst fluid proteome with tandem mass spectrometry. The proteomic analysis was performed using a Orbitrap-based mass spectrometer (Q-Exactive) coupled with a 50-cm-long nano-liquid chromatography column. Protein mutations were identified using mutation sequence database search. RESULTS A total of 5850 protein groups were identified from microliters of cyst fluid. Among those, 3934 protein groups were reported for the first time in pancreatic cyst fluid. Although high-abundance proteins were not depleted in the experiment, our dataset detected almost all pancreatic tumor markers such as mucin family members, S100 proteins, and CEA-related proteins. In addition, 590 protein mutation marker candidates were discovered. CONCLUSIONS We provide a comprehensive cyst proteome dataset that includes cystic cellular proteins and mutated proteins. Our findings would serve as a rich resource for further IPMN studies and clinical applications. The MS data have been deposited in the ProteomeXchange with identifier PXD005671 (http://proteomecentral.proteomexchange.org/dataset/PXD005671).
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MESH Headings
- Amino Acid Sequence
- Biomarkers, Tumor/analysis
- Carcinoma, Pancreatic Ductal/chemistry
- Carcinoma, Pancreatic Ductal/pathology
- Chromatography, Liquid/methods
- Cyst Fluid/chemistry
- Humans
- Neoplasms, Cystic, Mucinous, and Serous/chemistry
- Neoplasms, Cystic, Mucinous, and Serous/pathology
- Pancreas/chemistry
- Pancreas/pathology
- Pancreatic Cyst/chemistry
- Pancreatic Cyst/pathology
- Pancreatic Neoplasms/chemistry
- Pancreatic Neoplasms/pathology
- Proteome/analysis
- Proteomics/methods
- Tandem Mass Spectrometry/methods
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Affiliation(s)
- Joonho Park
- Department of Biomedical Engineering, Seoul National University College of Medicine, 103 Daehak-ro, Seoul, Korea
| | - Dohyun Han
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Seoul, Korea
| | - Misol Do
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Seoul, Korea
| | - Jongmin Woo
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Seoul, Korea
| | - Joseph I Wang
- Department of Biomedical Engineering, Seoul National University College of Medicine, 103 Daehak-ro, Seoul, Korea
| | - Youngmin Han
- Department of Surgery, Seoul National University College of Medicine, 103 Daehak-ro, Seoul, Korea
| | - Wooil Kwon
- Department of Surgery, Seoul National University College of Medicine, 103 Daehak-ro, Seoul, Korea
| | - Sun-Whe Kim
- Department of Surgery, Seoul National University College of Medicine, 103 Daehak-ro, Seoul, Korea
| | - Jin-Young Jang
- Department of Surgery, Seoul National University College of Medicine, 103 Daehak-ro, Seoul, Korea
| | - Youngsoo Kim
- Department of Biomedical Engineering, Seoul National University College of Medicine, 103 Daehak-ro, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Seoul, Korea
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13
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In-depth proteomic analysis of tissue interstitial fluid for hepatocellular carcinoma serum biomarker discovery. Br J Cancer 2017; 117:1676-1684. [PMID: 29024941 PMCID: PMC5729441 DOI: 10.1038/bjc.2017.344] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/25/2017] [Accepted: 09/01/2017] [Indexed: 12/12/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a primary malignancy of the liver. New serum biomarkers for HCC screening are needed, especially for alpha-fetoprotein (AFP) negative patients. As a proximal fluid between body fluids and intracellular fluid, tissue interstitial fluid (TIF) is a suitable source for serum biomarker discovery. Methods: Sixteen paired TIF samples from HCC tumour and adjacent non-tumour tissues were analysed by isobaric tags for relative and absolute quantitation (iTRAQ) method. Two proteins were selected for ELISA validation in serum samples. Results: Totally, 3629 proteins were identified and 3357 proteins were quantified in TIF samples. Among them, 232 proteins were significantly upregulated in HCC-TIF and 257 proteins down-regulated. Two overexpressed extracellular matrix proteins, SPARC and thrombospondin-2 (THBS2) were selected for further validation. ELISA result showed that the serum levels of SPARC and THBS2 in HCC patients were both significantly higher than those in healthy controls. The combination of serum SPARC and THBS2 could distinguish HCC (AUC=0.97, sensitivity=86%, specificity=100%) or AFP-negative HCC (AUC=0.95, sensitivity=91%, specificity=93%) from healthy controls. And the combination of serum SPARC and THBS2 could also distinguish HCC patients from benign liver disease patients (AUC=0.93, sensitivity=80%, specificity=94%). In addition, serum THBS2 was found to be a novel independent indicator for poor prognosis of HCC. Conclusions: Novel HCC candidate serum markers were found through in-depth proteomic analysis of TIF, which demonstrated the successful utility of TIF in cancer serum biomarker discovery.
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Kim H, Yu SJ, Yeo I, Cho YY, Lee DH, Cho Y, Cho EJ, Lee JH, Kim YJ, Lee S, Jun J, Park T, Yoon JH, Kim Y. Prediction of Response to Sorafenib in Hepatocellular Carcinoma: A Putative Marker Panel by Multiple Reaction Monitoring-Mass Spectrometry (MRM-MS). Mol Cell Proteomics 2017; 16:1312-1323. [PMID: 28550167 DOI: 10.1074/mcp.m116.066704] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/10/2017] [Indexed: 12/11/2022] Open
Abstract
Sorafenib is the only standard treatment for unresectable hepatocellular carcinoma (HCC), but it provides modest survival benefits over placebo, necessitating predictive biomarkers of the response to sorafenib. Serum samples were obtained from 115 consecutive patients with HCC before sorafenib treatment and analyzed by multiple reaction monitoring-mass spectrometry (MRM-MS) and ELISA to quantify candidate biomarkers. We verified a triple-marker panel to be predictive of the response to sorafenib by MRM-MS, comprising CD5 antigen-like (CD5L), immunoglobulin J (IGJ), and galectin-3-binding protein (LGALS3BP), in HCC patients. This panel was a significant predictor (AUROC > 0.950) of the response to sorafenib treatment, having the best cut-off value (0.4) by multivariate analysis. In the training set, patients who exceeded this cut-off value had significantly better overall survival (median, 21.4 months) than those with lower values (median, 8.6 months; p = 0.001). Further, a value that was lower than this cutoff was an independent predictor of poor overall survival [hazard ratio (HR), 2.728; 95% confidence interval (CI), 1.312-5.672; p = 0.007] and remained an independent predictive factor of rapid progression (HR, 2.631; 95% CI, 1.448-4.780; p = 0.002). When applied to the independent validation set, levels of the cut-off value for triple-marker panel maintained their prognostic value for poor clinical outcomes. On the contrast, the triple-marker panel was not a prognostic factor for patients who were treated with transarterial chemoembolization (TACE). The discriminatory signature of a triple-marker panel provides new insights into targeted proteomic biomarkers for individualized sorafenib therapy.
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Affiliation(s)
- Hyunsoo Kim
- From the ‡Department of Biomedical Engineering.,§Institute of Medical and Biological Engineering, Medical Research Center, and
| | - Su Jong Yu
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Injun Yeo
- From the ‡Department of Biomedical Engineering
| | - Young Youn Cho
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Dong Hyeon Lee
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Yuri Cho
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Eun Ju Cho
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Jeong-Hoon Lee
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Yoon Jun Kim
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | | | - Jongsoo Jun
- **Department of Statistics, Seoul National University, Daehak-dong, Seoul 151-742 Korea
| | - Taesung Park
- ‖Interdisciplinary program in Bioinformatics and.,**Department of Statistics, Seoul National University, Daehak-dong, Seoul 151-742 Korea
| | - Jung-Hwan Yoon
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea;
| | - Youngsoo Kim
- From the ‡Department of Biomedical Engineering; .,§Institute of Medical and Biological Engineering, Medical Research Center, and
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15
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Li Y, Turpin CP, Wang S. Role of thrombospondin 1 in liver diseases. Hepatol Res 2017; 47:186-193. [PMID: 27492250 PMCID: PMC5292098 DOI: 10.1111/hepr.12787] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/13/2016] [Accepted: 08/01/2016] [Indexed: 02/06/2023]
Abstract
Thrombospondin 1 (TSP1) is a matricellular glycoprotein that can be secreted by many cell types. Through binding to extracellular proteins and/or cell surface receptors, TSP1 modulates a variety of cellular functions. Since its discovery in 1971, TSP1 has been found to play important roles in multiple biological processes including angiogenesis, apoptosis, latent transforming growth factor-β activation, and immune regulation. Thrombospondin 1 is also involved in regulating many organ functions. However, the role of TSP1 in liver diseases has not been extensively addressed. In this review, we summarize the findings about the possible role that TSP1 plays in chronic liver diseases focusing on non-alcoholic fatty liver diseases, liver fibrosis, and hepatocellular carcinoma.
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Affiliation(s)
- Yanzhang Li
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
- Medical College of Henan University, Kaifeng, Henan 475004, China
| | - Courtney P Turpin
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Shuxia Wang
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
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16
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Abstract
Protein glycosylation is one of the most important posttranslational modifications. Numerous biological functions are related to protein glycosylation. However, analytical challenges remain in the glycoprotein analysis. To overcome the challenges associated with glycoprotein analysis, many analytical techniques were developed in recent years. Enrichment methods were used to improve the sensitivity of detection, while HPLC and mass spectrometry methods were developed to facilitate the separation of glycopeptides/proteins and enhance detection, respectively. Fragmentation techniques applied in modern mass spectrometers allow the structural interpretation of glycopeptides/proteins, while automated software tools started replacing manual processing to improve the reliability and throughput of the analysis. In this chapter, the current methodologies of glycoprotein analysis were discussed. Multiple analytical techniques are compared, and advantages and disadvantages of each technique are highlighted.
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17
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Discovering potential serological biomarker for chronic Hepatitis B Virus-related hepatocellular carcinoma in Chinese population by MAL-associated serum glycoproteomics analysis. Sci Rep 2017; 7:38918. [PMID: 28079114 PMCID: PMC5228127 DOI: 10.1038/srep38918] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/15/2016] [Indexed: 12/12/2022] Open
Abstract
The accuracy of current biomarkers for the diagnosis of hepatocellular carcinoma (HCC), especially chronic Hepatitis B Virus (HBV)-related HCC, is limited. Recent progress in glycoproteomics has provided a novel platform for screening novel serological biomarkers of HCC. In this study, lectin affinity chromatography by Maackia amurensis lectin (MAL) and iTRAQ combined with mass spectrometric analysis were performed to enrich and identify the glycoprotein fractions in serum samples from HBV-related HCC patients and from healthy controls. Seventeen differential MAL-associated glycoproteins were identified. Among them, Galectin 3 binding protein (Gal-3BP) was selected for further evaluated by ELISA analysis and showed a high diagnostic potential of HBV-related HCC, with the AUC of 0.898 and a sensitivity, specificity and accuracy of 80.00%, 93.75% and 86.88%, respectively. Moreover, we constructed a predictive model through the combined use of serum Gal-3BP and Alpha Fetoprotein (AFP), which improved the sensitivity (from 87.5% to 95%), specificity (from 93.75% to 95%) and accuracy (from 90.63% to 95%) of diagnosing early HCC. These data suggested serum Gal-3BP level is a promising biomarker to identify HBV-related HCC and the combined use of serum Gal-3BP and AFP improves the diagnostic potential of HBV-HCC compared with AFP alone in current clinical practice.
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18
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Chen R, Zou H, Figeys D. Detergent-Assisted Glycoprotein Capture: A Versatile Tool for In-Depth N-Glycoproteome Analysis. J Proteome Res 2016; 15:2080-6. [PMID: 27147131 DOI: 10.1021/acs.jproteome.6b00056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Large-scale N-glycoproteome studies have been hindered by poor solubility of hydrophobic membrane proteins and the complexity of proteome samples. Herein, we developed a detergent-assisted glycoprotein capture method to reduce these issues by conducting hydrazide chemistry-based glycoprotein capture in the presence of strong detergents such as sodium dodecyl sulfate and Triton X-100. The strong detergents helped to solubilize hydrophobic membrane proteins and then increased the access of hydrazide groups to oxidized glycoproteins, thus increasing the coverage of the N-glycoproteome. Compared with the conventional glycopeptide capture method, the detergent-assisted glycoprotein capture approach nearly doubled the number of N-glycosylation sites identified from HEK 293T cells with improved specificity. Application of this approach in the larger scale N-glycoproteomics analysis of the HEK 293T cell membrane led to the identification of 2253 unique N-glycosites from 953 proteins. Furthermore, the application of this approach to human serum resulted in the identification of 850 N-glycosylation sites without any immunodepletion or fractionation. Overall, the detergent-assisted glycoprotein capture method simplified the capture process, and it increased the number of sites observed on both hydrophobic membrane proteins and hydrophilic secreted proteins.
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Affiliation(s)
- Rui Chen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology and Department of Chemistry and Biomolecular Sciences, University of Ottawa , 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Hanfa Zou
- Key Lab of Separation Science for Analytical Chemistry, National Chromatography R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian 116023, China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology and Department of Chemistry and Biomolecular Sciences, University of Ottawa , 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
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19
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Integrated GlycoProteome Analyzer (I-GPA) for Automated Identification and Quantitation of Site-Specific N-Glycosylation. Sci Rep 2016; 6:21175. [PMID: 26883985 PMCID: PMC4756296 DOI: 10.1038/srep21175] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 01/19/2016] [Indexed: 01/01/2023] Open
Abstract
Human glycoproteins exhibit enormous heterogeneity at each N-glycosite, but few studies have attempted to globally characterize the site-specific structural features. We have developed Integrated GlycoProteome Analyzer (I-GPA) including mapping system for complex N-glycoproteomes, which combines methods for tandem mass spectrometry with a database search and algorithmic suite. Using an N-glycopeptide database that we constructed, we created novel scoring algorithms with decoy glycopeptides, where 95 N-glycopeptides from standard α1-acid glycoprotein were identified with 0% false positives, giving the same results as manual validation. Additionally automated label-free quantitation method was first developed that utilizes the combined intensity of top three isotope peaks at three highest MS spectral points. The efficiency of I-GPA was demonstrated by automatically identifying 619 site-specific N-glycopeptides with FDR ≤ 1%, and simultaneously quantifying 598 N-glycopeptides, from human plasma samples that are known to contain highly glycosylated proteins. Thus, I-GPA platform could make a major breakthrough in high-throughput mapping of complex N-glycoproteomes, which can be applied to biomarker discovery and ongoing global human proteome project.
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20
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Gao HJ, Chen YJ, Zuo D, Xiao MM, Li Y, Guo H, Zhang N, Chen RB. Quantitative proteomic analysis for high-throughput screening of differential glycoproteins in hepatocellular carcinoma serum. Cancer Biol Med 2015; 12:246-54. [PMID: 26487969 PMCID: PMC4607824 DOI: 10.7497/j.issn.2095-3941.2015.0010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths. Novel serum biomarkers are required to increase the sensitivity and specificity of serum screening for early HCC diagnosis. This study employed a quantitative proteomic strategy to analyze the differential expression of serum glycoproteins between HCC and normal control serum samples. METHODS Lectin affinity chromatography (LAC) was used to enrich glycoproteins from the serum samples. Quantitative mass spectrometric analysis combined with stable isotope dimethyl labeling and 2D liquid chromatography (LC) separations were performed to examine the differential levels of the detected proteins between HCC and control serum samples. Western blot was used to analyze the differential expression levels of the three serum proteins. RESULTS A total of 2,280 protein groups were identified in the serum samples from HCC patients by using the 2D LC-MS/MS method. Up to 36 proteins were up-regulated in the HCC serum, whereas 19 proteins were down-regulated. Three differential glycoproteins, namely, fibrinogen gamma chain (FGG), FOS-like antigen 2 (FOSL2), and α-1,6-mannosylglycoprotein 6-β-N-acetylglucosaminyltransferase B (MGAT5B) were validated by Western blot. All these three proteins were up-regulated in the HCC serum samples. CONCLUSION A quantitative glycoproteomic method was established and proven useful to determine potential novel biomarkers for HCC.
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Affiliation(s)
- Hua-Jun Gao
- 1 Research Center of Basic Medical Sciences & School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China ; 2 Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Ya-Jing Chen
- 1 Research Center of Basic Medical Sciences & School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China ; 2 Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Duo Zuo
- 1 Research Center of Basic Medical Sciences & School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China ; 2 Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Ming-Ming Xiao
- 1 Research Center of Basic Medical Sciences & School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China ; 2 Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Ying Li
- 1 Research Center of Basic Medical Sciences & School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China ; 2 Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Hua Guo
- 1 Research Center of Basic Medical Sciences & School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China ; 2 Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Ning Zhang
- 1 Research Center of Basic Medical Sciences & School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China ; 2 Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Rui-Bing Chen
- 1 Research Center of Basic Medical Sciences & School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China ; 2 Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
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21
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Song E, Mechref Y. Defining glycoprotein cancer biomarkers by MS in conjunction with glycoprotein enrichment. Biomark Med 2015; 9:835-44. [PMID: 26330015 DOI: 10.2217/bmm.15.55] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Protein glycosylation is an important and common post-translational modification. More than 50% of human proteins are believed to be glycosylated to modulate the functionality of proteins. Aberrant glycosylation has been correlated to several diseases, such as inflammatory skin diseases, diabetes mellitus, cardiovascular disorders, rheumatoid arthritis, Alzheimer's and prion diseases, and cancer. Many approved cancer biomarkers are glycoproteins which are not highly abundant proteins. Therefore, effective qualitative and quantitative assessment of glycoproteins entails enrichment methods. This chapter summarizes glycoprotein enrichment methods, including lectin affinity, immunoaffinity, hydrazide chemistry, hydrophilic interaction liquid chromatography, and click chemistry. The use of these enrichment approaches in assessing the qualitative and quantitative changes of glycoproteins in different types of cancers are presented and discussed. This chapter highlights the importance of glycoprotein enrichment techniques for the identification and characterization of new reliable cancer biomarkers.
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Affiliation(s)
- Ehwang Song
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Yehia Mechref
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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22
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Huang J, Kast J. Quantitative Glycoproteomic Analysis Identifies Platelet-Induced Increase of Monocyte Adhesion via the Up-Regulation of Very Late Antigen 5. J Proteome Res 2015; 14:3015-26. [PMID: 26159767 DOI: 10.1021/acs.jproteome.5b00407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Physiological stimuli, such as thrombin, or pathological stimuli, such as lysophosphatidic acid (LPA), activate platelets circulating in blood. Once activated, platelets bind to monocytes via P-selectin-PSGL-1 interactions but also release the stored contents of their granules. These platelet releasates, in addition to direct platelet binding, activate monocytes and facilitate their recruitment to atherosclerotic sites. Consequently, understanding the changes platelet releasates induce in monocyte membrane proteins is critical. We studied the glyco-proteome changes of THP-1 monocytic cells affected by LPA- or thrombin-induced platelet releasates. We employed lectin affinity chromatography combined with filter aided sample preparation to achieve high glyco- and membrane protein and protein sequence coverage. Using stable isotope labeling by amino acids in cell culture, we quantified 1715 proteins, including 852 membrane and 500 glycoproteins, identifying the up-regulation of multiple proteins involved in monocyte extracellular matrix binding and transendothelial migration. Flow cytometry indicated expression changes of integrin α5, integrin β1, PECAM-1, and PSGL-1. The observed increase in monocyte adhesion to fibronectin was determined to be mediated by the up-regulation of very late antigen 5 via a P-selectin-PSGL-1 independent mechanism. This novel aspect could be validated on CD14+ human primary monocytes, highlighting the benefits of the improved enrichment method regarding high membrane protein coverage and reliable quantification.
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Affiliation(s)
- Jiqing Huang
- †The Biomedical Research Centre, ‡Department of Chemistry, and §Centre for Blood Research, University of British Columbia, Vancouver, B. C. V6T 1Z3, Canada
| | - Juergen Kast
- †The Biomedical Research Centre, ‡Department of Chemistry, and §Centre for Blood Research, University of British Columbia, Vancouver, B. C. V6T 1Z3, Canada
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23
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Revealing Glycoproteins in the Secretome of MCF-7 Human Breast Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2015; 2015:453289. [PMID: 26167486 PMCID: PMC4488092 DOI: 10.1155/2015/453289] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/07/2015] [Indexed: 01/30/2023]
Abstract
Breast cancer is one of the major issues in the field of oncology, reported with a higher prevalence rate in women worldwide. In attempt to reveal the potential biomarkers for breast cancer, the findings of differentially glycosylated haptoglobin and osteonectin in previous study have drawn our attention towards glycoproteins of secretome from the MCF-7 cancer cell line. In the present study, further analyses were performed on the medium of MCF-7 cells by subjecting it to two-dimensional analyses followed by image analysis in contrast to the medium of human mammary epithelial cells (HMEpC) as a negative control. Carboxypeptidase A4 (CPA4), alpha-1-antitrypsin (AAT), haptoglobin (HP), and HSC70 were detected in the medium of MCF-7, while only CPA4 and osteonectin (ON) were detected in HMEpC medium. In addition, CPA4 was detected as upregulated in the MCF-7 medium. Further analysis by lectin showed that CPA4, AAT, HP, and HSC70 were secreted as N-glycan in the medium of MCF-7, with HP also showing differentially N-glycosylated isoforms. For the HMEpC, only CPA4 was detected as N-glycan. No O-glycan was detected in the medium of HMEpC but MCF-7 expressed O-glycosylated CPA4 and HSC70. All these revealed that glycoproteins could be used as glycan-based biomarkers for the prognosis of breast cancer.
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Ahn YH, Kim JY, Yoo JS. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods. MASS SPECTROMETRY REVIEWS 2015; 34:148-65. [PMID: 24889823 PMCID: PMC4340049 DOI: 10.1002/mas.21428] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/20/2013] [Indexed: 05/12/2023]
Abstract
Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies.
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Affiliation(s)
- Yeong Hee Ahn
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
| | - Jin Young Kim
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
| | - Jong Shin Yoo
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
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25
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Tan AA, Mu AKW, Kiew LV, Chen Y. Comparative secretomic and N-glycoproteomic profiling in human MCF-7 breast cancer and HMEpC normal epithelial cell lines using a gel-based strategy. Cancer Cell Int 2014; 14:120. [PMID: 25484625 PMCID: PMC4258303 DOI: 10.1186/s12935-014-0120-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 10/30/2014] [Indexed: 11/26/2022] Open
Abstract
Background Concurrent study of secretomic and glycoproteomic profiles in cancer cell lines represents an excellent approach for investigating cancer progression and identifying novel biomarker candidates. In this study, we performed a comparative secretomic and N-glycoprotein profiling from the secretions of normal human mammary epithelial cells (HMEpC) and the MCF-7 human breast cancer cell line. Method We analyzed these cell lines using a combined methodology involving glycan-binding lectins and two-dimensional electrophoresis and identified several differentially secreted factors, including osteonectin and haptoglobin. Result Notably, comparative analyses also revealed that MCF-7 cells produced differentially N-glycosylated forms of haptoglobin. Conclusion The present data suggested that osteonectin and haptoglobin might have potential to be served as potential biomarkers for breast cancer. However, further investigation is needed to validate the findings.
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Affiliation(s)
- Aik-Aun Tan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, 11800 Malaysia
| | - Alan Kang-Wai Mu
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603 Malaysia
| | - Lik-Voon Kiew
- Department of Pharmacology, Faculty of Medicine Building, University of Malaya, Kuala Lumpur, 50603 Malaysia
| | - Yeng Chen
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603 Malaysia ; Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603 Malaysia
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26
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In-depth analysis of site-specific N-glycosylation in vitronectin from human plasma by tandem mass spectrometry with immunoprecipitation. Anal Bioanal Chem 2014; 406:7999-8011. [DOI: 10.1007/s00216-014-8226-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/11/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022]
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27
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Song E, Zhu R, Hammoud ZT, Mechref Y. LC-MS/MS quantitation of esophagus disease blood serum glycoproteins by enrichment with hydrazide chemistry and lectin affinity chromatography. J Proteome Res 2014; 13:4808-20. [PMID: 25134008 PMCID: PMC4227547 DOI: 10.1021/pr500570m] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Changes
in glycosylation have been shown to have a profound correlation
with development/malignancy in many cancer types. Currently, two major
enrichment techniques have been widely applied in glycoproteomics,
namely, lectin affinity chromatography (LAC)-based and hydrazide chemistry
(HC)-based enrichments. Here we report the LC–MS/MS quantitative
analyses of human blood serum glycoproteins and glycopeptides associated
with esophageal diseases by LAC- and HC-based enrichment. The separate
and complementary qualitative and quantitative data analyses of protein
glycosylation were performed using both enrichment techniques. Chemometric
and statistical evaluations, PCA plots, or ANOVA test, respectively,
were employed to determine and confirm candidate cancer-associated
glycoprotein/glycopeptide biomarkers. Out of 139, 59 common glycoproteins
(42% overlap) were observed in both enrichment techniques. This overlap
is very similar to previously published studies. The quantitation
and evaluation of significantly changed glycoproteins/glycopeptides
are complementary between LAC and HC enrichments. LC–ESI–MS/MS
analyses indicated that 7 glycoproteins enriched by LAC and 11 glycoproteins
enriched by HC showed significantly different abundances between disease-free
and disease cohorts. Multiple reaction monitoring quantitation resulted
in 13 glycopeptides by LAC enrichment and 10 glycosylation sites by
HC enrichment to be statistically different among disease cohorts.
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Affiliation(s)
- Ehwang Song
- Department of Chemistry and Biochemistry, Texas Tech University , Memorial Circle & Boston, Lubbock, Texas 79409, United States
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Uversky VN. Wrecked regulation of intrinsically disordered proteins in diseases: pathogenicity of deregulated regulators. Front Mol Biosci 2014; 1:6. [PMID: 25988147 PMCID: PMC4428494 DOI: 10.3389/fmolb.2014.00006] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/06/2014] [Indexed: 12/14/2022] Open
Abstract
Biologically active proteins without stable tertiary structure are common in all known proteomes. Functions of these intrinsically disordered proteins (IDPs) are typically related to regulation, signaling, and control. Cellular levels of these important regulators are tightly regulated by a variety mechanisms ranging from firmly controlled expression to precisely targeted degradation. Functions of IDPs are controlled by binding to specific partners, alternative splicing, and posttranslational modifications among other means. In the norm, right amounts of precisely activated IDPs have to be present in right time at right places. Wrecked regulation brings havoc to the ordered world of disordered proteins, leading to protein misfolding, misidentification, and missignaling that give rise to numerous human diseases, such as cancer, cardiovascular disease, neurodegenerative diseases, and diabetes. Among factors inducing pathogenic transformations of IDPs are various cellular mechanisms, such as chromosomal translocations, damaged splicing, altered expression, frustrated posttranslational modifications, aberrant proteolytic degradation, and defective trafficking. This review presents some of the aspects of deregulated regulation of IDPs leading to human diseases.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida Tampa, FL, USA ; Biology Department, Faculty of Science, King Abdulaziz University Jeddah, Saudi Arabia ; Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences Moscow, Russia
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29
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Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LCJ, Wollscheid B, Zhang H, Aebersold R. Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics 2014; 13:1753-68. [PMID: 24741114 PMCID: PMC4083113 DOI: 10.1074/mcp.m114.038273] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/04/2014] [Indexed: 12/31/2022] Open
Abstract
The identification of biomarkers indicating the level of aggressiveness of prostate cancer (PCa) will address the urgent clinical need to minimize the general overtreatment of patients with non-aggressive PCa, who account for the majority of PCa cases. Here, we isolated formerly N-linked glycopeptides from normal prostate (n = 10) and from non-aggressive (n = 24), aggressive (n = 16), and metastatic (n = 25) PCa tumor tissues and analyzed the samples using SWATH mass spectrometry, an emerging data-independent acquisition method that generates a single file containing fragment ion spectra of all ionized species of a sample. The resulting datasets were searched using a targeted data analysis strategy in which an a priori spectral reference library representing known N-glycosites of the human proteome was used to identify groups of signals in the SWATH mass spectrometry data. On average we identified 1430 N-glycosites from each sample. Out of those, 220 glycoproteins showed significant quantitative changes associated with diverse biological processes involved in PCa aggressiveness and metastasis and indicated functional relationships. Two glycoproteins, N-acylethanolamine acid amidase and protein tyrosine kinase 7, that were significantly associated with aggressive PCa in the initial sample cohort were further validated in an independent set of patient tissues using tissue microarray analysis. The results suggest that N-acylethanolamine acid amidase and protein tyrosine kinase 7 may be used as potential tissue biomarkers to avoid overtreatment of non-aggressive PCa.
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Affiliation(s)
- Yansheng Liu
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jing Chen
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231
| | - Atul Sethi
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Qing K Li
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231
| | - Lijun Chen
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231
| | - Ben Collins
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ludovic C J Gillet
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Bernd Wollscheid
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Hui Zhang
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231;
| | - Ruedi Aebersold
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; **Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
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30
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Zhang Y, Jiao J, Yang P, Lu H. Mass spectrometry-based N-glycoproteomics for cancer biomarker discovery. Clin Proteomics 2014; 11:18. [PMID: 24872809 PMCID: PMC4017703 DOI: 10.1186/1559-0275-11-18] [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] [Received: 09/30/2013] [Accepted: 03/20/2014] [Indexed: 02/04/2023] Open
Abstract
Glycosylation is estimated to be found in over 50% of human proteins. Aberrant protein glycosylation and alteration of glycans are closely related to many diseases. More than half of the cancer biomarkers are glycosylated-proteins, and specific glycoforms of glycosylated-proteins may serve as biomarkers for either the early detection of disease or the evaluation of therapeutic efficacy for treatment of diseases. Glycoproteomics, therefore, becomes an emerging field that can make unique contributions to the discovery of biomarkers of cancers. The recent advances in mass spectrometry (MS)-based glycoproteomics, which can analyze thousands of glycosylated-proteins in a single experiment, have shown great promise for this purpose. Herein, we described the MS-based strategies that are available for glycoproteomics, and discussed the sensitivity and high throughput in both qualitative and quantitative manners. The discovery of glycosylated-proteins as biomarkers in some representative diseases by employing glycoproteomics was also summarized.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Glycoconjuates Research Ministry of Public Health and Institutes of Biomedical Sciences, Fudan University Shanghai, 200032, China
| | - Jing Jiao
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Pengyuan Yang
- Key Laboratory of Glycoconjuates Research Ministry of Public Health and Institutes of Biomedical Sciences, Fudan University Shanghai, 200032, China
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Haojie Lu
- Key Laboratory of Glycoconjuates Research Ministry of Public Health and Institutes of Biomedical Sciences, Fudan University Shanghai, 200032, China
- Department of Chemistry, Fudan University, Shanghai 200433, China
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An integrated sample pretreatment platform for quantitative N-glycoproteome analysis with combination of on-line glycopeptide enrichment, deglycosylation and dimethyl labeling. Anal Chim Acta 2014; 833:1-8. [PMID: 24909767 DOI: 10.1016/j.aca.2014.04.037] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 11/22/2022]
Abstract
Relative quantification of N-glycoproteomes shows great promise for the discovery of candidate biomarkers and therapeutic targets. The traditional protocol for quantitative analysis of glycoproteomes is usually off-line performed, and suffers from long sample preparation time, and the risk of sample loss or contamination due to manual manipulation. In this study, a novel integrated sample preparation platform for quantitative N-glycoproteome analysis was established, with combination of online N-glycopeptide capture by a HILIC column, sample buffer exchange by a N2-assisted HILIC-RPLC interface, deglycosylation by a hydrophilic PNGase F immobilized enzymatic reactor (hIMER) and solid dimethyl labeling on a C18 precolumn. To evaluate the performance of such a platform, two equal aliquots of immunoglobulin G (IgG) digests were sequentially pretreated, followed by MALDI-TOF MS analysis. The signal intensity ratio of heavy/light (H/L) labeled deglycosylated peptides with the equal aliquots was 1.00 (RSD=6.2%, n=3), much better than those obtained by the offline protocol, with H/L ratio as 0.76 (RSD=11.6%, n=3). Additionally, the total on-line sample preparation time was greatly shortened to 160 min, much faster than that of offline approach (24h). Furthermore, such an integrated pretreatment platform was successfully applied to analyze the two kinds of hepatocarcinoma ascites syngeneic cell lines with high (Hca-F) and low (Hca-P) lymph node metastasis rates. For H/L labeled Hca-P lysates with the equal aliquots, 99.6% of log2 ratios (H/L) of quantified glycopeptides ranged from -1 to 1, demonstrating high accuracy of the developed sample preparation strategy. By triplicated analysis of glycopeptides and non-glycopeptides of Hca-F and Hca-P lysates, 43 up-regulated and 30 down-regulated (Hca-F/P) N-glycosylation sites, and 11 significantly changed N-glycoproteins were successfully quantified, and most of them were related to tumorigenesis and tumor metastasis. All these results demonstrate the developed integrated N-glycoprotein pretreatment platform is of great power for the accurate, precise and high-throughput analysis of N-glycoproteomes.
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Liu H, Zhang N, Wan D, Cui M, Liu Z, Liu S. Mass spectrometry-based analysis of glycoproteins and its clinical applications in cancer biomarker discovery. Clin Proteomics 2014; 11:14. [PMID: 24722010 PMCID: PMC3984494 DOI: 10.1186/1559-0275-11-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/19/2014] [Indexed: 02/08/2023] Open
Abstract
Glycosylation is one of the most important posttranslational modifications of proteins and plays essential roles in various biological processes. Aberration in the glycan moieties of glycoproteins is associated with many diseases. It is especially critical to develop the rapid and sensitive methods for analysis of aberrant glycoproteins associated with diseases. Mass spectrometry (MS) has become a powerful tool for glycoprotein analysis. Especially, tandem mass spectrometry can provide highly informative fragments for structural identification of glycoproteins. This review provides an overview of the development of MS technologies and their applications in identification of abnormal glycoproteins and glycans in human serum to screen cancer biomarkers in recent years.
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Affiliation(s)
| | | | | | - Meng Cui
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P, R, China.
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Ferrín G, Ranchal I, Llamoza C, Rodríguez-Perálvarez ML, Romero-Ruiz A, Aguilar-Melero P, López-Cillero P, Briceño J, Muntané J, Montero-Álvarez JL, De la Mata M. Identification of candidate biomarkers for hepatocellular carcinoma in plasma of HCV-infected cirrhotic patients by 2-D DIGE. Liver Int 2014; 34:438-46. [PMID: 23944848 DOI: 10.1111/liv.12277] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 06/23/2013] [Indexed: 12/22/2022]
Abstract
BACKGROUND The current methods available for screening and detecting hepatocellular carcinoma (HCC) have insufficient sensitivity and specificity, and only a low percentage of diagnosis of small tumours is based on these assays. Because HCC is usually asymptomatic at potentially curative stages, identification of biomarkers for the early detection of HCC is essential to improve patient survival. AIM The aim of this study was to identify candidate markers for HCC development in the plasma from hepatitis C virus (HCV)-infected cirrhotic patients. METHODS We compared protein expression profiles of plasma samples from HCV-infected cirrhotic patients with and without HCC, using two-dimensional fluorescence difference gel electrophoresis (2-D DIGE) coupled with MALDI-TOF/TOF mass spectrometry. The 2-D DIGE results were analysed statistically using Decyder™ software, and verified by western blot and enzyme-linked immunosorbent assay (ELISA). RESULTS In the plasma of HCV-infected HCC patients, we observed decreased expression of complement component 9, ficolin-3 (FCN3), serum amyloid P component (SAP), fibrinogen-gamma and immunoglobulin gamma-1 chain, and increased expression of vitronectin (VTN) and galectin-3 binding protein (G3BP) by DIGE analysis. ELISA confirmed DIGE results for VTN and G3BP but not for SAP or FCN3 in a larger patient population. CONCLUSIONS The proteins VTN and SAP are candidate biomarkers for HCC development in HCV-infected cirrhotic patients.
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Affiliation(s)
- Gustavo Ferrín
- Maimónides Institute for Biomedical Research in Córdoba (IMBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Networked Biomedical Research Center, Hepatic and Digestive Diseases (CIBERehd), Barcelona, Spain
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Aberrant glycosylation as biomarker for cancer: focus on CD43. BIOMED RESEARCH INTERNATIONAL 2014; 2014:742831. [PMID: 24689054 PMCID: PMC3943294 DOI: 10.1155/2014/742831] [Citation(s) in RCA: 278] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/10/2013] [Indexed: 11/23/2022]
Abstract
Glycosylation is a posttranslational modification of proteins playing a major role in cell signalling, immune recognition, and cell-cell interaction because of their glycan branches conferring structure variability and binding specificity to lectin ligands. Aberrant expression of glycan structures as well as occurrence of truncated structures, precursors, or novel structures of glycan may affect ligand-receptor interactions and thus interfere with regulation of cell adhesion, migration, and proliferation. Indeed, aberrant glycosylation represents a hallmark of cancer, reflecting cancer-specific changes in glycan biosynthesis pathways such as the altered expression of glycosyltransferases and glycosidases. Most studies have been carried out to identify changes in serum glycan structures. In most cancers, fucosylation and sialylation are significantly modified. Thus, aberrations in glycan structures can be used as targets to improve existing serum cancer biomarkers. The ability to distinguish differences in the glycosylation of proteins between cancer and control patients emphasizes glycobiology as a promising field for potential biomarker identification. In this review, we discuss the aberrant protein glycosylation associated with human cancer and the identification of protein glycoforms as cancer biomarkers. In particular, we will focus on the aberrant CD43 glycosylation as cancer biomarker and the potential to exploit the UN1 monoclonal antibody (UN1 mAb) to identify aberrant CD43 glycoforms.
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35
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Sun Z, Dong J, Zhang S, Hu Z, Cheng K, Li K, Xu B, Ye M, Nie Y, Fan D, Zou H. Identification of chemoresistance-related cell-surface glycoproteins in leukemia cells and functional validation of candidate glycoproteins. J Proteome Res 2014; 13:1593-601. [PMID: 24467213 DOI: 10.1021/pr4010822] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemoresistance remains the most significant obstacle to successful chemotherapy for leukemia, and its exact mechanism is still unknown. In this work, we used the cell-surface capturing method together with quantitative proteomics to investigate differences in the glycoproteomes of adriamycin-sensitive and adriamycin-resistant leukemia cells. Two quantitative methods, isotopic dimethyl labeling and SWATH, were used to quantify glycoproteins, and 35 glycoproteins were quantified by both methods. High correlation was observed between the glycoproteins quantified by the above two methods, and 15 glycoproteins displayed a consistent significant change trend in both sets of quantitative results. These 15 proteins included classical multidrug resistance-related glycoproteins such as ABCB1 as well as a set of novel glycoproteins that have not previously been reported to be associated with chemoresistance in leukemia cells. Further validation with quantitative real-time PCR and Western blotting confirmed the proteomic screening results. Subsequent functional experiments based on RNA interference technology showed that CTSD, FKBP10, and SLC2A1 are novel genes that participate in the acquisition and maintenance of the adriamycin-resistant phenotype in leukemia cells.
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Affiliation(s)
- Zhen Sun
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, China
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36
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MRM validation of targeted nonglycosylated peptides from N-glycoprotein biomarkers using direct trypsin digestion of undepleted human plasma. J Proteomics 2014; 98:206-17. [PMID: 24434586 DOI: 10.1016/j.jprot.2014.01.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/19/2013] [Accepted: 01/02/2014] [Indexed: 12/11/2022]
Abstract
UNLABELLED A rapid, simple, and reproducible MRM-based validation method for serological glycoprotein biomarkers in clinical use was developed by targeting the nonglycosylated tryptic peptides adjacent to N-glycosylation sites. Since changes in protein glycosylation are known to be associated with a variety of diseases, glycoproteins have been major targets in biomarker discovery. We previously found that nonglycosylated tryptic peptides adjacent to N-glycosylation sites differed in concentration between normal and hepatocellular carcinoma (HCC) plasma due to differences in steric hindrance of the glycan moiety in N-glycoproteins to tryptic digestion (Lee et al., 2011). To increase the feasibility and applicability of clinical validation of biomarker candidates (nonglycosylated tryptic peptides), we developed a method to effectively monitor nonglycosylated tryptic peptides from a large number of plasma samples and to reduce the total analysis time with maximizing the effect of steric hindrance by the glycans during digestion of glycoproteins. The AUC values of targeted nonglycosylated tryptic peptides were excellent (0.955 for GQYCYELDEK, 0.880 for FEDGVLDPDYPR and 0.907 for TEDTIFLR), indicating that these could be effective biomarkers for hepatocellular carcinoma. This method provides the necessary throughput required to validate glycoprotein biomarkers, as well as quantitative accuracy for human plasma analysis, and should be amenable to clinical use. BIOLOGICAL SIGNIFICANCE Difficulties in verifying and validating putative protein biomarkers are often caused by complex sample preparation procedures required to determine their concentrations in a large number of plasma samples. To solve the difficulties, we developed MRM-based protein biomarker assays that greatly reduce complex, time-consuming, and less reproducible sample pretreatment steps in plasma for clinical implementation. First, we used undepleted human plasma samples without any enrichment procedures. Using nanoLC/MS/MS, we targeted nonglycosylated tryptic peptides adjacent to N-linked glycosylation sites in N-linked glycoprotein biomarkers, which could be detected in human plasma samples without depleting highly abundant proteins. Second, human plasma proteins were digested with trypsin without reduction and alkylation procedures to minimize sample preparation. Third, trypsin digestion times were shortened so as to obtain reproducible results with maximization of the steric hindrance effect of the glycans during enzyme digestion. Finally, this rapid and simple sample preparation method was applied to validate targeted nonglycosylated tryptic peptides as liver cancer biomarker candidates for diagnosis in 40 normal and 41 hepatocellular carcinoma (HCC) human plasma samples. This strategy provided the necessary throughput required to monitor protein biomarkers, as well as quantitative accuracy in human plasma analysis. From biomarker discovery to clinical implementation, our method will provide a biomarker study platform that is suitable for clinical deployment, and can be applied to high-throughput approaches.
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Mayne J, Starr AE, Ning Z, Chen R, Chiang CK, Figeys D. Fine Tuning of Proteomic Technologies to Improve Biological Findings: Advancements in 2011–2013. Anal Chem 2013; 86:176-95. [DOI: 10.1021/ac403551f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Zhibin Ning
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Rui Chen
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Daniel Figeys
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
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Liu Y, Hüttenhain R, Collins B, Aebersold R. Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Rev Mol Diagn 2013; 13:811-25. [PMID: 24138574 PMCID: PMC3833812 DOI: 10.1586/14737159.2013.845089] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Among the wide range of proteomic technologies, targeted mass spectrometry (MS) has shown great potential for biomarker studies. To extend the degree of multiplexing achieved by selected reaction monitoring (SRM), we recently developed SWATH MS. SWATH MS is a variant of the emerging class of data-independent acquisition (DIA) methods and essentially converts the molecules in a physical sample into perpetually re-usable digital maps. The thus generated SWATH maps are then mined using a targeted data extraction strategy, allowing us to profile disease-related proteomes at a high degree of reproducibility. The successful application of both SRM and SWATH MS requires the a priori generation of reference spectral maps that provide coordinates for quantification. Herein, we demonstrate that the application of the mass spectrometric reference maps and the acquisition of personalized SWATH maps hold a particular promise for accelerating the current process of biomarker discovery.
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Affiliation(s)
- Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli-Str.16, 8093 Zurich, Switzerland
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Wang F, Shi Z, Wang P, You W, Liang G. Comparative proteome profile of human placenta from normal and preeclamptic pregnancies. PLoS One 2013; 8:e78025. [PMID: 24205073 PMCID: PMC3799759 DOI: 10.1371/journal.pone.0078025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/09/2013] [Indexed: 12/17/2022] Open
Abstract
To better understand the molecular mechanisms involved in pathological development of placenta in preeclampsia, we used LC-MS/MS to construct a large-scale comparative proteome profile of human placentas from normal and preeclamptic pregnancies. A total of 2636 proteins were detected in human placentas, and 171 different proteins were definitively identified between control and preeclamptic placentas. Further bioinformatics analysis indicated that these differentially expressed proteins correlate with several specific cellular processes which occur during pathological changes of preeclamptic placenta. 6 proteins were randomly selected to verify their expression patterns with Western blotting. Of which, 3 proteins’ cellular localizations were validated with immunohistochemistry. Elucidation of how protein-expression changes coordinate the pathological development would provide researchers with a better understanding of the critical biological processes of preeclampsia and potential targets for therapeutic agents to regulate placenta function, and eventually benefit the treatment of preeclampsia.
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Affiliation(s)
- Fuqiang Wang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, China
- State Key Laboratory of Reproductive Medicine, Analysis Center, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhonghua Shi
- State Key Laboratory of Reproductive Medicine, Analysis Center, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ping Wang
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China;
| | - Wei You
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China;
- * E-mails: (GL); (WY)
| | - Gaolin Liang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, China
- * E-mails: (GL); (WY)
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40
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Imperlini E, Colavita I, Caterino M, Mirabelli P, Pagnozzi D, Vecchio LD, Noto RD, Ruoppolo M, Orrù S. The secretome signature of colon cancer cell lines. J Cell Biochem 2013; 114:2577-87. [DOI: 10.1002/jcb.24600] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/29/2013] [Indexed: 01/09/2023]
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41
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Tian Y, Zhang H. Characterization of disease-associated N-linked glycoproteins. Proteomics 2013; 13:504-11. [PMID: 23255236 DOI: 10.1002/pmic.201200333] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/20/2012] [Accepted: 10/13/2012] [Indexed: 12/14/2022]
Abstract
N-linked glycoproteins play important roles in biological processes, including cell-to-cell recognition, growth, differentiation, and programmed cell death. Specific N-linked glycoprotein changes are associated with disease progression and identification of these N-linked glycoproteins has potential for use in disease diagnosis, prognosis, and prediction of treatments. In this review, we summarize common strategies for N-linked glycoprotein characterization and applications of these strategies to identification of glycoprotein changes associated with disease states. We also review the N-linked glycoproteins altered in diseases such as breast cancer, lung cancer, and prostate cancer. Although assays for these glycoproteins have potential clinical utility, research is needed to translate these glycoproteins to clinical biomarkers.
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Affiliation(s)
- Yuan Tian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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42
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Liu Y, Hüttenhain R, Surinova S, Gillet LCJ, Mouritsen J, Brunner R, Navarro P, Aebersold R. Quantitative measurements of N
-linked glycoproteins in human plasma by SWATH-MS. Proteomics 2013; 13:1247-56. [DOI: 10.1002/pmic.201200417] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 10/16/2012] [Accepted: 10/25/2012] [Indexed: 12/24/2022]
Affiliation(s)
- Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology; Zurich Switzerland
| | - Ruth Hüttenhain
- Department of Biology, Institute of Molecular Systems Biology; Zurich Switzerland
- Competence Center for Systems Physiology and Metabolic Diseases; Zurich Switzerland
| | - Silvia Surinova
- Department of Biology, Institute of Molecular Systems Biology; Zurich Switzerland
- Competence Center for Systems Physiology and Metabolic Diseases; Zurich Switzerland
| | - Ludovic CJ Gillet
- Department of Biology, Institute of Molecular Systems Biology; Zurich Switzerland
| | - Jeppe Mouritsen
- Department of Biology, Institute of Molecular Systems Biology; Zurich Switzerland
| | - Roland Brunner
- Department of Biology, Institute of Molecular Systems Biology; Zurich Switzerland
| | - Pedro Navarro
- Department of Biology, Institute of Molecular Systems Biology; Zurich Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology; Zurich Switzerland
- Competence Center for Systems Physiology and Metabolic Diseases; Zurich Switzerland
- Faculty of Science, University of Zurich; Zurich Switzerland
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43
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Li K, Sun Z, Zheng J, Lu Y, Bian Y, Ye M, Wang X, Nie Y, Zou H, Fan D. In-depth research of multidrug resistance related cell surface glycoproteome in gastric cancer. J Proteomics 2013; 82:130-40. [PMID: 23470797 DOI: 10.1016/j.jprot.2013.02.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 02/20/2013] [Accepted: 02/22/2013] [Indexed: 12/13/2022]
Abstract
UNLABELLED Human gastric cancer is a big public health problem. Multidrug resistance is a main obstacle to successful chemotherapeutic treatment in gastric cancers and the underlying mechanism is not clear. Glycosylation, one of the most important post translational modifications of proteins, plays a vital role in diverse aspects of tumor progression. In the present study, we applied two multidrug resistance cell lines and their parental drug sensitive gastric cancer cell line to a modified cell surface capturing strategy with triplex labeling to characterize MDR related cell surface glycoproteome. Finally, 56 cell membrane glycoproteins were successfully identified via combination of identification by glycopeptides and quantitation by non-glycopeptides, and 11 of them were found to be differentially expressed with the same trend in both drug resistant cell lines compared with that in sensitive cell line. The further analysis by western blot and in vitro drug sensitivity assay demonstrated that our approach is reliable and accurate and suggested that these glycoproteins may represent as biomarkers for multidrug resistance in gastric cancer. BIOLOGICAL SIGNIFICANCE In this study, we performed a cell surface glycoproteomics research of multidrug resistance in gastric cancer using a modified CSC approach. Totally we identified and quantified 11 membrane N-glycoproteins which were significantly changed in MDR gastric cancer cells. These glycoproteins are quite possible to be biomarkers for predicting MDR or key regulators for targeted therapy, and are also helpful for better interpreting the sophisticated mechanisms of MDR in gastric cancer. In addition to that, this approach used in this study can be well applied to screen aberrantly glycosylated biomarkers associated with other malignant phenotypes of various kinds of cancers.
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Affiliation(s)
- Kai Li
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, the Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
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44
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Qin X, Chen Q, Sun C, Wang C, Peng Q, Xie L, Liu Y, Li S. High-throughput screening of tumor metastatic-related differential glycoprotein in hepatocellular carcinoma by iTRAQ combines lectin-related techniques. Med Oncol 2013; 30:420. [PMID: 23292873 DOI: 10.1007/s12032-012-0420-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/05/2012] [Indexed: 02/06/2023]
Abstract
Glycoproteomics is an important aspect in the research of cancer biomarker discovery. The objective of our study is to screen the profile of serum glycoproteins in hepatocellular carcinoma (HCC) patients and to discover differentially expressed glycoproteins in HCC with or without metastasis. We collected serum from HCC patients and divided them into two groups (non-metastatic HCC group and metastatic HCC group) according to 2002 UICC TNM staging system. Wheat germ agglutinin (WGA) lectin was used to enrich the serum glycoproteins by lectin affinity chromatography. The enriched glycoproteins were labeled with mass-balanced isobaric tags (iTRAQ) and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Two differential glycoproteins were validated by Western blot and biochemical methods, respectively. Fifteen differential serum glycoproteins with WGA affinity were identified (p < 0.05). Among them, nine proteins were up-regulated (>1.5-folds) and six were down-regulated (<0.5-folds) in HCC patients with metastasis. Expression of alpha-1-antitrypsin (SERPINA1) and apolipoprotein A-I (APOA1) was validated by Western blot and biochemical methods, respectively (p < 0.05). Our study has obtained a set of HCC metastasis-associated glycoproteins which may serve as novel prognostic candidates and potential therapeutic targets for HCC metastasis. SERPINA1 might act as a potential glycoprotein biomarker of HCC metastasis.
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Affiliation(s)
- Xue Qin
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, NO. 22, Shuangyong Road, Nanning 530021, Guangxi, China
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Lazar IM, Lee W, Lazar AC. Glycoproteomics on the rise: established methods, advanced techniques, sophisticated biological applications. Electrophoresis 2012; 34:113-25. [PMID: 23161435 DOI: 10.1002/elps.201200445] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 10/07/2012] [Accepted: 10/07/2012] [Indexed: 02/05/2023]
Abstract
Glycosylation is the most complex form of protein PTMs. Affected proteins may carry dozens of glycosylation sites with tens to hundreds of glycan residues attached to every site. Glycosylated proteins have many important functions in biology, from cellular to organismal levels, being involved in cell-cell signaling, cell adhesion, immune response, host-pathogen interactions, and development and growth. Glycosylation, however, expands the biological functional diversity of proteins at the expense of a tremendous increase in structural heterogeneity. Aberrant glycosylation of cell surface proteins, as well as their detectable fingerprint in plasma samples, has been associated with cancer, inflammatory and degenerative diseases, and congenital disorders of glycosylation. Therefore, there are on-going efforts directed toward developing new technologies and approaches for glycan sequencing and high-throughput analysis of glycosylated proteins in complex samples with simultaneous characterization of both the protein and glycan moieties. This work is aimed primarily at pinpointing the challenges associated with the large-scale analysis of glycoproteins and the latest developments in glycoproteomic research, with focus on recent advancements (2011-2012) in microcolumn separations and MS detection.
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Affiliation(s)
- Iulia M Lazar
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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46
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Zhang Y, Hu Z, Qin H, Wei X, Cheng K, Liu F, Wu R, Zou H. Highly Efficient Extraction of Cellular Nucleic Acid Associated Proteins in Vitro with Magnetic Oxidized Carbon Nanotubes. Anal Chem 2012; 84:10454-62. [DOI: 10.1021/ac302695u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Yi Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengyan Hu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoluan Wei
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Kai Cheng
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangjie Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Ren’an Wu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Pan S, Tamura Y, Chen R, May D, McIntosh MW, Brentnall TA. Large-scale quantitative glycoproteomics analysis of site-specific glycosylation occupancy. MOLECULAR BIOSYSTEMS 2012; 8:2850-6. [PMID: 22892896 PMCID: PMC3463725 DOI: 10.1039/c2mb25268f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Disease-associated aberrant glycosylation may be protein specific and glycosylation site specific. Quantitative assessment of glycosylation changes at a site-specific molecular level may represent one of the initial steps for systematically revealing the glycosylation abnormalities associated with a disease or biological state. Comparative quantitative profiling of glycoproteome to provide accurate quantification of site-specific glycosylation occupancy has been a challenging task, requiring a concerted approach drawing from a variety of techniques. In this report, we present a quantitative glycoproteomics method that allows global scale identification and comparative quantification of glycosylation site occupancy using mass spectrometry. We further demonstrated this approach by quantitatively characterizing the N-glycoproteome of human pancreas.
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Affiliation(s)
- Sheng Pan
- Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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Sun Z, Chen R, Cheng K, Liu H, Qin H, Ye M, Zou H. A new method for quantitative analysis of cell surface glycoproteome. Proteomics 2012; 12:3328-37. [DOI: 10.1002/pmic.201200150] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/10/2012] [Accepted: 09/10/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Zhen Sun
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Rui Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Kai Cheng
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Hongwei Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Hongqiang Qin
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Mingliang Ye
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Hanfa Zou
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
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Kikuchi T, Hassanein M, Amann JM, Liu Q, Slebos RJC, Rahman SMJ, Kaufman JM, Zhang X, Hoeksema MD, Harris BK, Li M, Shyr Y, Gonzalez AL, Zimmerman LJ, Liebler DC, Massion PP, Carbone DP. In-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers. Mol Cell Proteomics 2012; 11:916-32. [PMID: 22761400 DOI: 10.1074/mcp.m111.015370] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Advances in proteomic analysis of human samples are driving critical aspects of biomarker discovery and the identification of molecular pathways involved in disease etiology. Toward that end, in this report we are the first to use a standardized shotgun proteomic analysis method for in-depth tissue protein profiling of the two major subtypes of nonsmall cell lung cancer and normal lung tissues. We identified 3621 proteins from the analysis of pooled human samples of squamous cell carcinoma, adenocarcinoma, and control specimens. In addition to proteins previously shown to be implicated in lung cancer, we have identified new pathways and multiple new differentially expressed proteins of potential interest as therapeutic targets or diagnostic biomarkers, including some that were not identified by transcriptome profiling. Up-regulation of these proteins was confirmed by multiple reaction monitoring mass spectrometry. A subset of these proteins was found to be detectable and differentially present in the peripheral blood of cases and matched controls. Label-free shotgun proteomic analysis allows definition of lung tumor proteomes, identification of biomarker candidates, and potential targets for therapy.
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Affiliation(s)
- Takefumi Kikuchi
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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50
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Kim YJ, Zaidi-Ainouch Z, Gallien S, Domon B. Mass spectrometry–based detection and quantification of plasma glycoproteins using selective reaction monitoring. Nat Protoc 2012; 7:859-71. [DOI: 10.1038/nprot.2012.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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