1
|
Pongracz T, Biewenga M, Stoelinga AEC, Bladergroen MR, Nicolardi S, Trouw LA, Wuhrer M, de Haan N, van Hoek B. Autoimmune hepatitis displays distinctively high multi-antennary sialylation on plasma N-glycans compared to other liver diseases. J Transl Med 2024; 22:456. [PMID: 38745252 PMCID: PMC11092172 DOI: 10.1186/s12967-024-05173-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Changes in plasma protein glycosylation are known to functionally affect proteins and to associate with liver diseases, including cirrhosis and hepatocellular carcinoma. Autoimmune hepatitis (AIH) is a liver disease characterized by liver inflammation and raised serum levels of IgG, and is difficult to distinguish from other liver diseases. The aim of this study was to examine plasma and IgG-specific N-glycosylation in AIH and compare it with healthy controls and other liver diseases. METHODS In this cross-sectional cohort study, total plasma N-glycosylation and IgG Fc glycosylation analysis was performed by mass spectrometry for 66 AIH patients, 60 age- and sex-matched healthy controls, 31 primary biliary cholangitis patients, 10 primary sclerosing cholangitis patients, 30 non-alcoholic fatty liver disease patients and 74 patients with viral or alcoholic hepatitis. A total of 121 glycans were quantified per individual. Associations between glycosylation traits and AIH were investigated as compared to healthy controls and other liver diseases. RESULTS Glycan traits bisection (OR: 3.78 [1.88-9.35], p-value: 5.88 × 10- 3), tetraantennary sialylation per galactose (A4GS) (OR: 2.88 [1.75-5.16], p-value: 1.63 × 10- 3), IgG1 galactosylation (OR: 0.35 [0.2-0.58], p-value: 3.47 × 10- 5) and hybrid type glycans (OR: 2.73 [1.67-4.89], p-value: 2.31 × 10- 3) were found as discriminators between AIH and healthy controls. High A4GS differentiated AIH from other liver diseases, while bisection associated with cirrhosis severity. CONCLUSIONS Compared to other liver diseases, AIH shows distinctively high A4GS levels in plasma, with potential implications on glycoprotein function and clearance. Plasma-derived glycosylation has potential to be used as a diagnostic marker for AIH in the future. This may alleviate the need for a liver biopsy at diagnosis. Glycosidic changes should be investigated further in longitudinal studies and may be used for diagnostic and monitoring purposes in the future.
Collapse
Affiliation(s)
- Tamas Pongracz
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Maaike Biewenga
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Anna Eva Charlotte Stoelinga
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Marco René Bladergroen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Leendert Adrianus Trouw
- Department Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands.
| | - Bart van Hoek
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| |
Collapse
|
2
|
Park CS, Moon C, Kim M, Kim J, Yang S, Jang L, Jang JY, Jeong CM, Lee HS, Kim DK, Kim HH. Comparison of sialylated and fucosylated N-glycans attached to Asn 6 and Asn 41 with different roles in hyaluronan and proteoglycan link protein 1 (HAPLN1). Int J Biol Macromol 2024; 260:129575. [PMID: 38246450 DOI: 10.1016/j.ijbiomac.2024.129575] [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: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
Hyaluronan and proteoglycan link protein 1 (HAPLN1) is an extracellular matrix protein stabilizing interactions between hyaluronan and proteoglycan. Although HAPLN1 is being investigated for various biological roles, its N-glycosylation is poorly understood. In this study, the structure of N-glycopeptides of trypsin-treated recombinant human HAPLN1 (rhHAPLN1) expressed from CHO cells were identified by nano-liquid chromatography-tandem mass spectrometry. A total of 66 N-glycopeptides were obtained, including 16 and 12 N-glycans at sites Asn 6 (located in the N-terminal region) and Asn 41 (located in the Ig-like domain, which interacts with proteoglycan), respectively. The quantities (%) of each N-glycan relative to the totals (100 %) at each site were calculated. Tri- and tetra-sialylation (to resist proteolysis and extend half-life) were more abundant at Asn 6, and di- (core- and terminal-) fucosylation (to increase binding affinity and stability) and sialyl-Lewis X/a epitope (a major ligand for E-selectin) were more abundant at Asn 41. These results indicate that N-glycans attached to Asn 6 (protecting HAPLN1) and Asn 41 (supporting molecular interactions) play different roles in HAPLN1. This is the first study of site-specific N-glycosylation in rhHAPLN1, which will be useful for understanding its molecular interactions in the extracellular matrix.
Collapse
Affiliation(s)
- Chi Soo Park
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chulmin Moon
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Mirae Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Jieun Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Subin Yang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Leeseul Jang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Ji Yeon Jang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chang Myeong Jeong
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Han Seul Lee
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Dae Kyong Kim
- Department of Environmental & Health Chemistry, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Ha Hyung Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea.
| |
Collapse
|
3
|
Tudor L, Nedic Erjavec G, Nikolac Perkovic M, Konjevod M, Uzun S, Kozumplik O, Mimica N, Lauc G, Svob Strac D, Pivac N. The Association of the Polymorphisms in the FUT8-Related Locus with the Plasma Glycosylation in Post-Traumatic Stress Disorder. Int J Mol Sci 2023; 24:ijms24065706. [PMID: 36982780 PMCID: PMC10056189 DOI: 10.3390/ijms24065706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/04/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
The molecular underpinnings of post-traumatic stress disorder (PTSD) are still unclear due to the complex interactions of genetic, psychological, and environmental factors. Glycosylation is a common post-translational modification of proteins, and different pathophysiological states, such as inflammation, autoimmune diseases, and mental disorders including PTSD, show altered N-glycome. Fucosyltransferase 8 (FUT8) is the enzyme that catalyzes the addition of core fucose on glycoproteins, and mutations in the FUT8 gene are associated with defects in glycosylation and functional abnormalities. This is the first study that investigated the associations of plasma N-glycan levels with FUT8-related rs6573604, rs11621121, rs10483776, and rs4073416 polymorphisms and their haplotypes in 541 PTSD patients and control participants. The results demonstrated that the rs6573604 T allele was more frequent in the PTSD than in the control participants. Significant associations of plasma N-glycan levels with PTSD and FUT8-related polymorphisms were observed. We also detected associations of rs11621121 and rs10483776 polymorphisms and their haplotypes with plasma levels of specific N-glycan species in both the control and PTSD groups. In carriers of different rs6573604 and rs4073416 genotypes and alleles, differences in plasma N-glycan levels were only found in the control group. These molecular findings suggest a possible regulatory role of FUT8-related polymorphisms in glycosylation, the alternations of which could partially explain the development and clinical manifestation of PTSD.
Collapse
Affiliation(s)
- Lucija Tudor
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (L.T.); (G.N.E.); (M.N.P.); (M.K.)
| | - Gordana Nedic Erjavec
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (L.T.); (G.N.E.); (M.N.P.); (M.K.)
| | - Matea Nikolac Perkovic
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (L.T.); (G.N.E.); (M.N.P.); (M.K.)
| | - Marcela Konjevod
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (L.T.); (G.N.E.); (M.N.P.); (M.K.)
| | - Suzana Uzun
- Department for Biological Psychiatry and Psychogeriatrics, University Hospital Vrapce, 10000 Zagreb, Croatia; (S.U.); (O.K.); (N.M.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Faculty of Education and Rehabilitation Sciences, University of Zagreb, 10000 Zagreb, Croatia
| | - Oliver Kozumplik
- Department for Biological Psychiatry and Psychogeriatrics, University Hospital Vrapce, 10000 Zagreb, Croatia; (S.U.); (O.K.); (N.M.)
- Faculty of Education and Rehabilitation Sciences, University of Zagreb, 10000 Zagreb, Croatia
| | - Ninoslav Mimica
- Department for Biological Psychiatry and Psychogeriatrics, University Hospital Vrapce, 10000 Zagreb, Croatia; (S.U.); (O.K.); (N.M.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Gordan Lauc
- Glycobiology Laboratory, Genos Ltd., 10000 Zagreb, Croatia;
| | - Dubravka Svob Strac
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (L.T.); (G.N.E.); (M.N.P.); (M.K.)
- Correspondence: (D.S.S.); (N.P.)
| | - Nela Pivac
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (L.T.); (G.N.E.); (M.N.P.); (M.K.)
- University of Applied Sciences Hrvatsko Zagorje Krapina, 49000 Krapina, Croatia
- Correspondence: (D.S.S.); (N.P.)
| |
Collapse
|
4
|
Meuskens I, Leva-Bueno J, Millner P, Schütz M, Peyman SA, Linke D. The Trimeric Autotransporter Adhesin YadA of Yersinia enterocolitica Serotype O:9 Binds Glycan Moieties. Front Microbiol 2022; 12:738818. [PMID: 35178035 PMCID: PMC8844515 DOI: 10.3389/fmicb.2021.738818] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/06/2021] [Indexed: 11/29/2022] Open
Abstract
Yersinia adhesin A (YadA) is a key virulence factor of Yersinia enterocolitica and Yersinia pseudotuberculosis. YadA is a trimeric autotransporter adhesin, a class of adhesins that have been shown to enable many Gram-negative pathogens to adhere to/interact with the host extracellular matrix proteins such as collagen, vitronectin, and fibronectin. Here, we show for the first time that YadA of Yersinia enterocolitica serotype O:9 not only interacts with proteinaceous surface molecules but can also attach directly to glycan moieties. We show that YadA from Y. enterocolitica serotype O:9 does not interact with the vitronectin protein itself but exclusively with its N-linked glycans. We also show that YadA can target other glycan moieties as found in heparin, for example. So far, little is known about specific interactions between bacterial autotransporter adhesins and glycans. This could potentially lead to new antimicrobial treatment strategies, as well as diagnostic applications.
Collapse
Affiliation(s)
- Ina Meuskens
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Juan Leva-Bueno
- Faculty of Biological Sciences, School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Paul Millner
- Faculty of Biological Sciences, School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Monika Schütz
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Sally A. Peyman
- Molecular and Nanoscale Physics Group, Department of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
5
|
Assessment of Plasma Vitronectin as Diagnostic and Prognostic Marker of Hepatocellular Carcinoma in Patients with Hepatitis C Virus Cirrhosis. GASTROENTEROLOGY INSIGHTS 2022. [DOI: 10.3390/gastroent13010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background: hepatitis C is an inflammatory liver disease caused by the hepatitis C infection (HCV), and without treatment, almost 50% will progress to liver cirrhosis. Hepatocellular carcinoma (HCC) is the most frequent type of primary liver cancer and the fourth leading cause of cancer-related mortality. Aim of the study: the objective of this study was to evaluate the serum level of vitronectin (VTN) compared to AFP and determine their role as diagnostic and prognostic markers of HCV-related liver diseases. Subject and Methods: this study involved 52 HCV patients from which 26 patients were cirrhotic, and 26 patients had HCC (on top of hepatitis C virus-related cirrhosis) plus 10 healthy people as a control group. It was carried out in Gastroenterology and Hepatology Unit, Internal Medicine Department, Zagazig University Hospitals, Egypt. All individuals in this study were subjected to physical examination, full history taking, liver function tests, assessment of serum levels of Vitronectin (VTN) and alpha-fetoprotein (AFP) before and after the intervention within three months. Results: serum level of vitronectin increased significantly in cirrhosis patients and HCC patients than controls (p = 0.0041), (p < 0.001), respectively, and in HCC than cirrhosis patients (p < 0.001). Significant positive correlations were observed between levels of serum VTN and AFP in all HCV patients as well as cirrhotic patients (p < 0.001, p = 0.011, respectively). On the contrary, VTN and AFP didn’t show a significant correlation in HCC patients’ group. Moreover, the median serum level of VTN decreased significantly after treatment in patients with HCC (p < 0.001). At cut-off 38.5 ng/mL for AFP it shows sensitivity 80.8%, specificity 76.9% to differentiate HCC from cirrhosis cases. While VTN shows 84.6% sensitivity, 96.2% specificity at cut-off 26.5 μg/mL. Regarding clinicopathological characteristics and VTN levels, half of patients were stage B, 63.9% had tumor size >3 cm, 84.6% had more than one focal lesion. Conclusions: these results may allow one to speculate a potential role of Vitronectin in diagnosis and prognosis of HCC on top of cirrhosis related to HCV infection in addition to AFP and US and CT.
Collapse
|
6
|
Identifying new molecular players in extracellular proteostasis. Biochem Soc Trans 2021; 50:321-334. [PMID: 34940856 DOI: 10.1042/bst20210369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 02/02/2023]
Abstract
Proteostasis refers to a delicately tuned balance between the processes of protein synthesis, folding, localization, and the degradation of proteins found inside and outside cells. Our understanding of extracellular proteostasis is rather limited and largely restricted to knowledge of 11 currently established extracellular chaperones (ECs). This review will briefly outline what is known of the established ECs, before moving on to discuss experimental strategies used to identify new members of this growing family, and an examination of a group of putative new ECs identified using one of these approaches. An observation that emerges from an analysis of the expanding number of ECs is that all of these proteins are multifunctional. Strikingly, the armory of activities each possess uniquely suit them as a group to act together at sites of tissue damage, infection, and inflammation to restore homeostasis. Lastly, we highlight outstanding questions to guide future research in this field.
Collapse
|
7
|
Lin Y, Zhu J, Pan L, Zhang J, Tan Z, Olivares J, Singal AG, Parikh ND, Lubman DM. A Panel of Glycopeptides as Candidate Biomarkers for Early Diagnosis of NASH Hepatocellular Carcinoma Using a Stepped HCD Method and PRM Evaluation. J Proteome Res 2021; 20:3278-3289. [PMID: 33929864 DOI: 10.1021/acs.jproteome.1c00175] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Changes in N-glycosylation on specific peptide sites of serum proteins have been investigated as potential markers for diagnosis of nonalcoholic steatohepatitis (NASH)-related HCC. To accomplish this work, a novel workflow involving broad-scale marker discovery in serum followed by targeted marker evaluation of these glycopeptides were combined. The workflow involved an LC-Stepped HCD-DDA-MS/MS method coupled with offline peptide fractionation for large-scale identification of N-glycopeptides directly from pooled serum samples (each n = 10) as well as differential determination of N-glycosylation changes between disease states. We then evaluated several potentially diagnostic N-glycopeptides among 78 individual patient samples (40 cirrhosis, 28 early stage NASH HCC, and 10 late-stage NASH HCC) by LC-Stepped HCD-PRM-MS/MS to quantitatively analyze 65 targeted glycopeptides from 7 glycoproteins. Of these targets, we found site-specific N-glycopeptides n169GSLFAFR_HexNAc(4)Hex(5)NeuAc(2) and n242ISDGFDGIPDNVDAALALPAHSYSGR_HexNAc(5)Hex(6)Fuc(1)NeuAc(3) from VTNC were significantly increased comparing samples from patients with NASH cirrhosis and NASH HCC (p < 0.05). When combining results of these 2 glycopeptides with AFP, the ROC curve analysis demonstrated the AUC value increased to 0.834 (95% CI, 0.748-0.921) and 0.847 (95% CI, 0.766-0.932), respectively, as compared to that of AFP alone (AUC = 0.791, 95% CI, 0.690-0.892). These 2 glycopeptides may serve as potential biomarkers for early HCC diagnosis in patients with NASH related cirrhosis.
Collapse
Affiliation(s)
- Yu Lin
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Lingyun Pan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Jie Zhang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Zhijing Tan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Jocelyn Olivares
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Amit G Singal
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Neehar D Parikh
- Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
8
|
Jeong HK, Hwang H, Kang YM, Lee HK, Park GW, Lee JY, Kim DG, Lee JW, Lee SY, An HJ, Kim JY, Yoo JS. Computational classification of core and outer fucosylation of N-glycoproteins in human plasma using collision-induced dissociation in mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8917. [PMID: 32754952 DOI: 10.1002/rcm.8917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/23/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Glycoprotein fucosylation, one of the major posttranslational modifications, is known to be highly involved in proteins related to various cancers. Fucosylation occurs in the core and/or outer sites of N-glycopeptides. Elucidation of the fucosylation type of N-glycoproteins is therefore important. However, it has remained a challenge to classify the fucosylation types of N-glycopeptides using collision-induced dissociation (CID) tandem mass (MS/MS) spectra. METHODS The relative intensities of the Y1 F, Y2 F, Y3 F, and Y4 F product ions in the CID-MS/MS spectra of the IgG N-glycopeptides were measured for core fucosylation. The Core Fucose Index (CFI) was then calculated by multiplication of the relative intensities with a weight factor from logistic regression to differentiate between the core and none fucosylation. From the relative intensities of the B2 F and B3 SF ions of the MS/MS spectra of the AGP N-glycopeptides for outer fucosylation, the Outer Fucose Index (OFI) was calculated to differentiate between the outer and none fucosylation. RESULTS In order to classify core and/or outer fucosylation of N-glycoproteins, we defined the fucosylation score (F-score) by a sigmoidal equation using a combination of the CFI and the OFI. For application, we classified the fucosylation types of N-glycoproteins in human plasma with 99.7% accuracy from the F-score. Human plasma samples showed 54.4%, 33.3%, 10.3%, and 1.6% for none, core, outer, and dual fucosylated N-glycopeptides, respectively. Core fucosylation was abundant at mono- and bi-antennary N-glycopeptides. Outer fucosylation was abundant at tri- and tetra-antennary N-glycopeptides. In total, 113 N-glycopeptides of 29 glycoproteins from 3365 glycopeptide spectral matches (GPSMs) were classified for different types of fucosylation. CONCLUSIONS We established an F-score to classify three different fucosylation types: core, outer, and dual types of N-glycopeptides. The fucosylation types of 20 new N-glycopeptides from 11 glycoproteins in human plasma were classified using the F-score. Therefore, the F-score can be useful for the automatic classification of different types of fucosylation in N-glycoproteins of biological fluids including plasma, serum, and urine.
Collapse
Affiliation(s)
- Hoi Keun Jeong
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Heeyoun Hwang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Young-Mook Kang
- Drug Information Platform Center, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Hyun Kyoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Gun Wook Park
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Ju Yeon Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Dong Geun Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ji Won Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sang Yoon Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
- Asia-Pacific Glycomics Reference Site, Daejeon, 34134, Republic of Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Jong Shin Yoo
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| |
Collapse
|
9
|
Park GW, Lee JW, Lee HK, Shin JH, Kim JY, Yoo JS. Classification of Mucin-Type O-Glycopeptides Using Higher-Energy Collisional Dissociation in Mass Spectrometry. Anal Chem 2020; 92:9772-9781. [PMID: 32584546 DOI: 10.1021/acs.analchem.0c01218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Changes in mucin-type O-glycosylation of human proteins affect protein function, immune response, and cancer progression. Since O-glycoproteins are characterized by the microheterogeneity of diverse O-glycans with no conserved sequence and the macroheterogeneity of multiple glycosylation sites on serine and/or threonine in human proteins, the assessment of different mucin types, such as Tn-antigen, core 1, and core 2, and their extended core types in O-glycopeptides, is extremely challenging. Here, we present an O-GlycoProteome Analyzer (O-GPA) that automatically classifies mucin-type O-glycosylation using higher-energy collisional dissociation (HCD) in mass spectrometry. First, we estimated the number of GlcNAc residues using the intensity ratio of GlcNAc-specific fragment ions (HexNAc-CH6O3 and HexNAc-2H2O) over GalNAc-specific fragment ions (HexNAc-C2H6O3 and HexNAc-C2H4O2) in the HCD spectrum. Furthermore, we classified the different mucin types of O-glycopeptides from characteristic B2 (HexNAc2) or Y2α (PEP + HexNAc2), and Y2β (PEP + HexNAcHex) fragment ions, along with the number of GlcNAc. Furthermore, O-GPA automatically determined single or multiple O-glycosylation, regardless of the mucin types. The mucin type of O-glycopeptides from human urine and plasma was confirmed with an overall accuracy of 96%. We found 97 core 1, 56 core 2, 13 extended core 1, and 12 extended core 2 glycopeptides from urine; and 22 core 1, 13 core 2, 7 extended core 1, 1 extended core 2, and 1 Tn-antigen from plasma. Our strategy can be used to successfully characterize specific mucin types of O-glycoproteins in human biological samples.
Collapse
Affiliation(s)
- Gun Wook Park
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea
| | - Ji Won Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hyun Kyoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jong Hwan Shin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea
| | - Jong Shin Yoo
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| |
Collapse
|
10
|
Afroz A, Saleem S, Sughra K, Khan SA, Zeeshan N. Identification of Candidate Biomarkers for HCV Leading to Hepatocellular Carcinoma Differential Stages From Serum Samples. CURR PHARM ANAL 2020. [DOI: 10.2174/1573412914666180912111038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Hepatocellular carcinoma (HCC) is one of the most deadly liver malignancy
found and Hepatitis C virus (HCV) is a prominent risk factor for this disease. Prognosis of HCC is poor;
initiate the need of markers to discover therapeutic targets in HCC.
Introduction:
Clinical staging systems of HCC composed of tumor characteristics along with liver
function test are important in prognosis but they are not precise. Molecular profiling can lead to a better
understanding of the physiopathology of HCC and can help in the development of novel therapeutic
approaches.
Methods:
64 HCC serum samples (shifted from HCV) were graded into stage I- IV; along with +ive (3
Hepatitis C) and -ive control (2 healthy persons). Proteins were separated by sodium dodecyl sulfatepolyacrylamide
gel electrophoresis (SDS-PAGE) and differential mRNA expression from serum samples
of different HCC stages was confirmed by Real Time Polymerase Chain Reaction (qPCR).
Results:
HCC serum proteins displayed differential expression of glutathione s-transferase (GST),
glypican-3 (GPC3), vitronectin (VTN), and clusterin (CLU) by SDS-PAGE. GST was expressed in -ive
control, while GPC3 was found in both -ive and +ive control. The qPCR analysis, display more than
0.07 fold decrease in GST in I-IV HCC stages. The highest increase in HCC stages was observed by
GPC3; about 4 fold increase in I-IV stages. VTN show 1.7-3.4 fold; while CLU show 2-3.5 fold increase
in four stages of HCC.
Conclusion:
GPC3, VTN and CLU in combination can be good potential markers for differentiating
stages (I-IV) of HCC.
Collapse
Affiliation(s)
- Amber Afroz
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus Gujrat, Gujrat, Pakistan
| | - Saba Saleem
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus Gujrat, Gujrat, Pakistan
| | - Kalsoom Sughra
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus Gujrat, Gujrat, Pakistan
| | - Sabaz Ali Khan
- Biotechnology Program, Department of Environmental Sciences COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Nadia Zeeshan
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus Gujrat, Gujrat, Pakistan
| |
Collapse
|
11
|
Wang Y, Tian Z. New Energy Setup Strategy for Intact N-Glycopeptides Characterization Using Higher-Energy Collisional Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:651-657. [PMID: 31967800 DOI: 10.1021/jasms.9b00089] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
With the optional setting of multiple stepped collisional energies (NCEs), higher-energy collisional dissociation (HCD) as available on Orbitrap instruments is a widely adopted dissociation method for intact N-glycopeptides characterization, where peptide backbones and N-glycan moieties are selectively fragmented at high and low NCEs, respectively. Initially, a dependent setting of a central value plus minus a variation is available to the users to set up NCEs, and the combination of 30 ± 10% to give the energies 20%/30%/40% has been mostly adopted in the literature. With the recent availability of an independent NCEs setup, we found that the combination of 20%/30%/30% is better than 20%/30%/40%; in the analysis of complex intact N-glycopeptides enriched from gastric cancer tissues, total IDs with spectrum-level FDR ≤ 1%, site-specific IDs with site-determining fragment ions, and structure-specific IDs with structure-diagnostic fragment ions were increased by 42% (4,767 → 6,746), 57% (599 → 942), and 97% (1771 → 3495), respectively. This finding will benefit all the coming N-glycoproteomics studies using HCD as the dissociation method.
Collapse
Affiliation(s)
- Yue Wang
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| |
Collapse
|
12
|
Hwang H, Jeong HK, Lee HK, Park GW, Lee JY, Lee SY, Kang YM, An HJ, Kang JG, Ko JH, Kim JY, Yoo JS. Machine Learning Classifies Core and Outer Fucosylation of N-Glycoproteins Using Mass Spectrometry. Sci Rep 2020; 10:318. [PMID: 31941975 PMCID: PMC6962204 DOI: 10.1038/s41598-019-57274-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 12/27/2019] [Indexed: 12/14/2022] Open
Abstract
Protein glycosylation is known to be involved in biological progresses such as cell recognition, growth, differentiation, and apoptosis. Fucosylation of glycoproteins plays an important role for structural stability and function of N-linked glycoproteins. Although many of biological and clinical studies of protein fucosylation by fucosyltransferases has been reported, structural classification of fucosylated N-glycoproteins such as core or outer isoforms remains a challenge. Here, we report for the first time the classification of N-glycopeptides as core- and outer-fucosylated types using tandem mass spectrometry (MS/MS) and machine learning algorithms such as the deep neural network (DNN) and support vector machine (SVM). Training and test sets of more than 800 MS/MS spectra of N-glycopeptides from the immunoglobulin gamma and alpha 1-acid-glycoprotein standards were selected for classification of the fucosylation types using supervised learning models. The best-performing model had an accuracy of more than 99% against manual characterization and area under the curve values greater than 0.99, which were calculated by probability scores from target and decoy datasets. Finally, this model was applied to classify fucosylated N-glycoproteins from human plasma. A total of 82N-glycopeptides, with 54 core-, 24 outer-, and 4 dual-fucosylation types derived from 54 glycoproteins, were commonly classified as the same type in both the DNN and SVM. Specifically, outer fucosylation was dominant in tri- and tetra-antennary N-glycopeptides, while core fucosylation was dominant in the mono-, bi-antennary and hybrid types of N-glycoproteins in human plasma. Thus, the machine learning methods can be combined with MS/MS to distinguish between different isoforms of fucosylated N-glycopeptides.
Collapse
Affiliation(s)
- Heeyoun Hwang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Hoi Keun Jeong
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hyun Kyoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Gun Wook Park
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Ju Yeon Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Soo Youn Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Young-Mook Kang
- Drug Information Platform Center, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea.,Asia Glycomics Reference Site, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jeong Gu Kang
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jeong-Heon Ko
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,Department of Biomolecular Science, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea.
| | - Jong Shin Yoo
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea. .,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea.
| |
Collapse
|
13
|
Kim YC, Lee SE, Kim SK, Jang HD, Hwang I, Jin S, Hong EB, Jang KS, Kim HS. Toll-like receptor mediated inflammation requires FASN-dependent MYD88 palmitoylation. Nat Chem Biol 2019; 15:907-916. [PMID: 31427815 DOI: 10.1038/s41589-019-0344-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/11/2019] [Indexed: 12/24/2022]
Abstract
Toll-like receptor (TLR)/myeloid differentiation primary response protein (MYD88) signaling aggravates sepsis by impairing neutrophil migration to infection sites. However, the role of intracellular fatty acids in TLR/MYD88 signaling is unclear. Here, inhibition of fatty acid synthase by C75 improved neutrophil chemotaxis and increased the survival of mice with sepsis in cecal ligation puncture and lipopolysaccharide-induced septic shock models. C75 specifically blocked TLR/MYD88 signaling in neutrophils. Treatment with GSK2194069 that targets a different domain of fatty acid synthase, did not block TLR signaling or MYD88 palmitoylation. De novo fatty acid synthesis and CD36-mediated exogenous fatty acid incorporation contributed to MYD88 palmitoylation. The binding of IRAK4 to the MYD88 intermediate domain and downstream signal activation required MYD88 palmitoylation at cysteine 113. MYD88 was palmitoylated by ZDHHC6, and ZDHHC6 knockdown decreased MYD88 palmitoylation and TLR/MYD88 activation upon lipopolysaccharide stimulus. Thus, intracellular saturated fatty acid-dependent palmitoylation of MYD88 by ZDHHC6 is a therapeutic target of sepsis.
Collapse
Affiliation(s)
- Young-Chan Kim
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea
| | - Sang Eun Lee
- Cardiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Somi K Kim
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea
| | - Hyun-Duk Jang
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea
| | - Injoo Hwang
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea
| | - Sooryeonhwa Jin
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Eun-Byeol Hong
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea
| | - Kyoung-Soon Jang
- Biomedical Omics Center, Korea Basic Science Institute, Cheongju, South Korea
| | - Hyo-Soo Kim
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea. .,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea. .,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea. .,World Class University Program, Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul, Korea.
| |
Collapse
|
14
|
Kobayashi T, Ogawa K, Furukawa JI, Hanamatsu H, Hato M, Yoshinaga T, Morikawa K, Suda G, Sho T, Nakai M, Higashino K, Numata Y, Shinohara Y, Sakamoto N. Quantifying Protein-Specific N-Glycome Profiles by Focused Protein and Immunoprecipitation Glycomics. J Proteome Res 2019; 18:3133-3141. [DOI: 10.1021/acs.jproteome.9b00232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Takashi Kobayashi
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Sapporo, Japan
| | - Koji Ogawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Jun-ichi Furukawa
- Laboratory of Medical and Functional Glycomics, Graduate School of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Hisatoshi Hanamatsu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Megumi Hato
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Sapporo, Japan
| | - Tomoyo Yoshinaga
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Sapporo, Japan
| | - Kenichi Morikawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Goki Suda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Takuya Sho
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Masato Nakai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Kenichi Higashino
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Sapporo, Japan
| | - Yoshito Numata
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Sapporo, Japan
| | - Yasuro Shinohara
- Laboratory of Medical and Functional Glycomics, Graduate School of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Naoya Sakamoto
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| |
Collapse
|
15
|
Kim KH, Kim JY, Yoo JS. Mass spectrometry analysis of glycoprotein biomarkers in human blood of hepatocellular carcinoma. Expert Rev Proteomics 2019; 16:553-568. [DOI: 10.1080/14789450.2019.1626235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kwang Hoe Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| |
Collapse
|
16
|
Xiao K, Tian Z. GPSeeker Enables Quantitative Structural N-Glycoproteomics for Site- and Structure-Specific Characterization of Differentially Expressed N-Glycosylation in Hepatocellular Carcinoma. J Proteome Res 2019; 18:2885-2895. [DOI: 10.1021/acs.jproteome.9b00191] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kaijie Xiao
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Zhixin Tian
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| |
Collapse
|
17
|
Parallel reaction monitoring with multiplex immunoprecipitation of N-glycoproteins in human serum for detection of hepatocellular carcinoma. Anal Bioanal Chem 2019; 411:3009-3019. [DOI: 10.1007/s00216-019-01775-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/20/2019] [Accepted: 03/11/2019] [Indexed: 01/17/2023]
|
18
|
Li Q, Kailemia MJ, Merleev AA, Xu G, Serie D, Danan LM, Haj FG, Maverakis E, Lebrilla CB. Site-Specific Glycosylation Quantitation of 50 Serum Glycoproteins Enhanced by Predictive Glycopeptidomics for Improved Disease Biomarker Discovery. Anal Chem 2019; 91:5433-5445. [DOI: 10.1021/acs.analchem.9b00776] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Qiongyu Li
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Muchena J. Kailemia
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Alexander A. Merleev
- Department of Dermatology, University of California Davis, School of Medicine, Sacramento, California 95817, United States
| | - Gege Xu
- Venn Biosciences Corporation, 800 Chesapeake Dr., Redwood City, California 94063, United States
| | - Daniel Serie
- Venn Biosciences Corporation, 800 Chesapeake Dr., Redwood City, California 94063, United States
| | - Lieza M. Danan
- Venn Biosciences Corporation, 800 Chesapeake Dr., Redwood City, California 94063, United States
| | - Fawaz G. Haj
- Department of Nutrition, University of California, One Shields Avenue, Davis, California 95616, United States
- Department of Internal Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of California Davis, Sacramento, California 95817, United States
| | - Emanual Maverakis
- Department of Dermatology, University of California Davis, School of Medicine, Sacramento, California 95817, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
19
|
Yuan W, Benicky J, Wei R, Goldman R, Sanda M. Quantitative Analysis of Sex-Hormone-Binding Globulin Glycosylation in Liver Diseases by Liquid Chromatography-Mass Spectrometry Parallel Reaction Monitoring. J Proteome Res 2018; 17:2755-2766. [PMID: 29972295 DOI: 10.1021/acs.jproteome.8b00201] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sex-hormone-binding globulin (SHBG) is a liver-secreted glycoprotein and a major regulator of steroid distribution. It has been reported that the serum concentration of SHBG changes in liver disease. To explore the involvement of SHBG in liver disease of different etiologies in greater detail, we developed a sensitive and selective liquid chromatography-mass spectrometry parallel reaction monitoring workflow to achieve quantitative analysis of SHBG glycosylation microheterogeneity. The method uses energy-optimized "soft" fragmentation to extract informative Y ions for maximal coverage of glycoforms and their quantitative comparisons. A total of 15 N-glycoforms of two N-glycosites and 3 O-glycoforms of 1 O-glycosite of this low-abundance serum protein were simultaneously analyzed in the complex samples. At the same time, we were able to partially resolve linkage isoforms of the fucosylated glycoforms and to identify and quantify SHBG N-glycoforms that were not previously reported. The results show that both core and outer-arm fucosylation of the N-glycoforms increases with liver cirrhosis but that a further increase of fucosylation is not observed with hepatocellular carcinoma (HCC). In contrast, the α-2-6 sialylated glycoform of the O-glycopeptide of SHBG increases in liver cirrhosis, and a significant 2-fold further increase is observed in HCC. In general, we do not find a significant contribution of different liver disease etiologies to the observed changes in glycosylation; however, elevation of the newly reported HexNAc(4)Hex(6) N-glycoform is associated with alcoholic liver disease.
Collapse
|
20
|
Ma J, Sanda M, Wei R, Zhang L, Goldman R. Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM. J Proteomics 2018; 189:67-74. [PMID: 29427759 DOI: 10.1016/j.jprot.2018.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/22/2022]
Abstract
Aberrant core fucosylation of proteins has been linked to liver diseases. In this study, we carried out multiple reaction monitoring (MRM) quantification of core fucosylated N-glycopeptides of serum proteins partially deglycosylated by a combination of endoglycosidases (endoF1, endoF2, and endoF3). To minimize variability associated with the preparatory steps, the analysis was performed without enrichment of glycopeptides or fractionation of serum besides the nanoRP chromatography. Specifically, we quantified core fucosylation of 22 N-glycopeptides derived from 17 proteins together with protein abundance of these glycoproteins in a cohort of 45 participants (15 disease-free control, 15 fibrosis and 15 cirrhosis patients) using a multiplex nanoUPLC-MS-MRM workflow. We find increased core fucosylation of 5 glycopeptides at the stage of liver fibrosis (i.e., N630 of serotransferrin, N107 of alpha-1-antitrypsin, N253 of plasma protease C1 inhibitor, N397 of ceruloplasmin, and N86 of vitronectin), increase of additional 6 glycopeptides at the stage of cirrhosis (i.e., N138 and N762 of ceruloplasmin, N354 of clusterin, N187 of hemopexin, N71 of immunoglobulin J chain, and N127 of lumican), while the degree of core fucosylation of 10 glycopeptides did not change. Interestingly, although we observe an increase in the core fucosylation at N86 of vitronectin in liver fibrosis, core fucosylation decreases on the N169 glycopeptide of the same protein. Our results demonstrate that the changes in core fucosylation are protein and site specific during the progression of fibrotic liver disease and independent of the changes in the quantity of N-glycoproteins. It is expected that the fully optimized multiplex LC-MS-MRM assay of core fucosylated glycopeptides will be useful for the serologic assessment of the fibrosis of liver. BIOLOGICAL SIGNIFICANCE: We have quantified the difference in core fucosylation among three comparison groups (healthy control, fibrosis and cirrhosis patients) using a sensitive and selective LC-MS-MRM method. Despite an overall increase in core fucosylation of many of the glycoproteins that we examined, core fucosylation changed in a protein- and site-specific manner. Moreover, increased and decreased fucosylation was observed on different N-glycopeptides of the same protein. Altered core fucosylation of N-glycopeptides might be used as an alternative serologic assay for the evaluation of fibrotic liver disease.
Collapse
Affiliation(s)
- Junfeng Ma
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Miloslav Sanda
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Renhuizi Wei
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Lihua Zhang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Radoslav Goldman
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA.
| |
Collapse
|
21
|
Benachour H, Leroy-Dudal J, Agniel R, Wilson J, Briand M, Carreiras F, Gallet O. Vitronectin (Vn) glycosylation patterned by lectin affinity assays-A potent glycoproteomic tool to discriminate plasma Vn from cancer ascites Vn. J Mol Recognit 2017; 31:e2690. [PMID: 29205553 DOI: 10.1002/jmr.2690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/27/2017] [Accepted: 10/28/2017] [Indexed: 11/10/2022]
Abstract
Changes in glycosylation have been associated with human cancer, but their complexity poses an analytical challenge. Ovarian cancer is a major cause of death in women because of an often late diagnosis. At least one-third of patients presents ascites fluid at diagnosis, and almost all have ascites at recurrence. Vitronectin (Vn) is a multifunctional glycoprotein that is suggested to be implicated in ovarian cancer metastasis and is found within ascites. The present study evaluated the potential of using lectin affinity for characterizing the glycosylation pattern of Vn. Human Vn was purified from 1 sample of ovarian cancer ascites or a pool of plasma samples. Consistent findings were observed with both dot blot and lectin array assays. Based on a panel of 40 lectins, the lectin array revealed discriminant patterns of lectin binding to Vn glycans. Interestingly, almost all the highlighted interactions were found to be higher with Vn from ascites relative to the plasma counterpart. Also, the lectin array was able to discriminate profiles of lectin interactions (ConA, SNA-I, PHA-E, PHA-L) between Vn samples that were not evident using dot blot, indicating its high sensitivity. The model of ConA binding during thermal unfolding of Vn confirmed the higher accessibility of mannosylated glycans in Vn from ascites as monitored by turbidimetry. Thus, this study demonstrated the usefulness of lectins and the lectin array as a glycoproteomic tool for high throughput and sensitive analysis of glycosylation patterns. Our data provide novel insights concerning Vn glycosylation patterns in clinical specimens, paving the way for further investigations regarding their functional impact and clinical interest.
Collapse
Affiliation(s)
- H Benachour
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122), Université de Cergy-Pontoise, Neuville Sur Oise Cedex, France
| | - J Leroy-Dudal
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122), Université de Cergy-Pontoise, Neuville Sur Oise Cedex, France
| | - R Agniel
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122), Université de Cergy-Pontoise, Neuville Sur Oise Cedex, France
| | - J Wilson
- RayBiotech, Inc., Norcross, GA, USA
| | - M Briand
- Normandie Univ, UNICAEN, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment, BioTICLA axis "Biology and Innovative Therapeutics for Ovarian Cancers"), Caen, France.,UNICANCER, Comprehensive Cancer Center François Baclesse, CRB Biological Resources Centre « OvaRessources », Caen, France
| | - F Carreiras
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122), Université de Cergy-Pontoise, Neuville Sur Oise Cedex, France
| | - O Gallet
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122), Université de Cergy-Pontoise, Neuville Sur Oise Cedex, France
| |
Collapse
|
22
|
Sensitive and fast characterization of site-specific protein glycosylation with capillary electrophoresis coupled to mass spectrometry. Talanta 2017; 179:22-27. [PMID: 29310225 DOI: 10.1016/j.talanta.2017.10.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/06/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022]
Abstract
Glycoproteomic analysis requires efficient separation and sensitive detection to enable the comprehensive characterization of glycan heterogeneity. Here, we report the use of capillary zone electrophoresis-electrospray ionization-mass spectrometry (CZE-ESI-MS) with an electrokinetically-pumped nanospray interface for the study of protein glycosylation microheterogeneity. A fast separation was developed that resolved intact glycopeptides generated from standard proteins within ~9min. Differentially terminal-galactosylated and sialylated species with the same glycosylation sites were well resolved. The concentration detection limits for CZE were three times higher than for nanoLC methods; however, a 200-fold smaller injection volume was used in CZE, which reflects the use of an extremely efficient electrospray interface in our CZE-ESI-MS setup. The resulting glycopeptide mass detection limit was two orders of magnitude superior to a nanoLC method. We also observed a 1.5% and 7% average relative standard deviation in peak migration time and glycopeptide relative abundance, and a four order of magnitude linear dynamic range in signal intensity. With CZE-ESI-MS, 40 haptoglobin glycopeptides were identified from roughly 40 fmol of digest.
Collapse
|
23
|
Direct analysis of site-specific N-glycopeptides of serological proteins in dried blood spot samples. Anal Bioanal Chem 2017; 409:4971-4981. [DOI: 10.1007/s00216-017-0438-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/22/2017] [Accepted: 05/29/2017] [Indexed: 10/19/2022]
|
24
|
Yang XP, Zhou LX, Yang QJ, Liu L, Cai Y, Ma SL. Diagnostic and prognostic roles of serum vitronectin in hepatitis B-related hepatocellular carcinoma. Cancer Biomark 2017; 17:271-279. [PMID: 27802203 DOI: 10.3233/cbm-160639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Vitronectin (VN) might be involved in the progression of hepatocellular carcinoma (HCC). OBJECTIVE This study was designed to evaluate the diagnostic and prognostic value of serum vitronectin among HCC patients. METHODS A total of 105 patients with HCC, 91 with liver cirrhosis, 102 with chronic hepatitis, and 100 healthy subjects were recruited. Serum VN and alpha-fetoprotein (AFP) levels were measured. RESULTS Serum VN levels were significantly higher in HCC patients than in the other groups. Based on area under receiver operating characteristic curve, serum VN had similar diagnostic value, compared with serum AFP, in distinguishing HCC from the groups, and also improved the diagnostic value of AFP alone. Serum VN levels were associated with the degree of histological differentiation, multiple foci, vascular tumor thrombosis and tumor node metastasis stage. Serum VN was an independent predictor for early recurrence and disease-free survival. Moreover, serum VN possessed similar prognostic predictive performance as compared to serum AFP and also significantly enhanced the prognostic value of AFP alone. CONCLUSIONS Elevated serum VN levels represented high diagnostic value and had close relation to clinicopathological factors and early recurrence, suggesting that serum VN might be a useful diagnostic and prognostic marker for HCC.
Collapse
Affiliation(s)
- Xiao-Ping Yang
- Department of Hepatopancreatobiliary Surgery, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou, Zhejiang, China
| | - Li-Xing Zhou
- Department of Hepatopancreatobiliary Surgery, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou, Zhejiang, China
| | - Qi-Jun Yang
- Department of Hepatopancreatobiliary Surgery, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou, Zhejiang, China
| | - Ling Liu
- Department of Hepatopancreatobiliary Surgery, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou, Zhejiang, China
| | - Yang Cai
- Department of Hepatopancreatobiliary Surgery, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou, Zhejiang, China
| | - Sheng-Lin Ma
- Department of Oncology, Cancer Institute, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou, Zhejiang, China
| |
Collapse
|
25
|
Mass spectrometric identification of phenol-soluble modulins in the ATCC® 43300 standard strain of methicillin-resistant Staphylococcus aureus harboring two distinct phenotypes. Eur J Clin Microbiol Infect Dis 2017; 36:1151-1157. [PMID: 28091797 DOI: 10.1007/s10096-017-2902-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/04/2017] [Indexed: 01/06/2023]
Abstract
Staphylococcus aureus subsp. aureus Rosenbach (ATCC® 43300™) is a representative methicillin-resistant S. aureus (MRSA) strain that is used as a quality control strain for testing the methicillin susceptibility of clinical isolates. It has been consistently observed that colonies with two different colors (golden yellow and white) grow from the ATCC stock on blood agar plates. In this study, staphylococcal peptide and protein profiling was performed using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. From the extract of the potentially hemolytic 43300 strain, we identified a single significant peak at an observed mass-to-charge (m/z) value of 2306.9, which correlates well with the predicted mass of formylated phenol-soluble modulin α2, a major staphylococcal virulence factor. Subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed that the hemolytic 43300 cells predominantly produced various phenol-soluble modulins (PSMs) and their export proteins, including four α type PSM peptides, PSMβ1, PSM-mec, PmtC and PmtD. However, none of the PSM peptides was detected in the presumably non-hemolytic 43300 strain, but the export proteins PmtC and PmtD. We found that this MRSA standard strain expresses two distinct phenotypes and that their phenotypic features are more likely associated with PSM toxin production. Therefore, careful attention is needed when MRSA reference strains are utilized for the diagnosis and susceptibility testing of MRSA in clinical settings.
Collapse
|
26
|
Banazadeh A, Veillon L, Wooding KM, Zabet-Moghaddam M, Mechref Y. Recent advances in mass spectrometric analysis of glycoproteins. Electrophoresis 2016; 38:162-189. [PMID: 27757981 DOI: 10.1002/elps.201600357] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 12/13/2022]
Abstract
Glycosylation is one of the most common posttranslational modifications of proteins that plays essential roles in various biological processes, including protein folding, host-pathogen interaction, immune response, and inflammation and aberrant protein glycosylation is a well-known event in various disease states including cancer. As a result, it is critical to develop rapid and sensitive methods for the analysis of abnormal glycoproteins associated with diseases. Mass spectrometry (MS) in conjunction with different separation methods, such as capillary electrophoresis (CE), ion mobility (IM), and high performance liquid chromatography (HPLC) has become a popular tool for glycoprotein analysis, providing highly informative fragments for structural identification of glycoproteins. This review provides an overview of the developments and accomplishments in the field of glycomics and glycoproteomics reported between 2014 and 2016.
Collapse
Affiliation(s)
- Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Lucas Veillon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Kerry M Wooding
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.,Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
| |
Collapse
|
27
|
Lee JY, Lee HK, Park GW, Hwang H, Jeong HK, Yun KN, Ji ES, Kim KH, Kim JS, Kim JW, Yun SH, Choi CW, Kim SI, Lim JS, Jeong SK, Paik YK, Lee SY, Park J, Kim SY, Choi YJ, Kim YI, Seo J, Cho JY, Oh MJ, Seo N, An HJ, Kim JY, Yoo JS. Characterization of Site-Specific N-Glycopeptide Isoforms of α-1-Acid Glycoprotein from an Interlaboratory Study Using LC-MS/MS. J Proteome Res 2016; 15:4146-4164. [PMID: 27760464 DOI: 10.1021/acs.jproteome.5b01159] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glycoprotein conformations are complex and heterogeneous. Currently, site-specific characterization of glycopeptides is a challenge. We sought to establish an efficient method of N-glycoprotein characterization using mass spectrometry (MS). Using alpha-1-acid glycoprotein (AGP) as a model N-glycoprotein, we identified its tryptic N-glycopeptides and examined the data reproducibility in seven laboratories running different LC-MS/MS platforms. We used three test samples and one blind sample to evaluate instrument performance with entire sample preparation workflow. 165 site-specific N-glycopeptides representative of all N-glycosylation sites were identified from AGP 1 and AGP 2 isoforms. The glycopeptide fragmentations by collision-induced dissociation or higher-energy collisional dissociation (HCD) varied based on the MS analyzer. Orbitrap Elite identified the greatest number of AGP N-glycopeptides, followed by Triple TOF and Q-Exactive Plus. Reproducible generation of oxonium ions, glycan-cleaved glycopeptide fragment ions, and peptide backbone fragment ions was essential for successful identification. Laboratory proficiency affected the number of identified N-glycopeptides. The relative quantities of the 10 major N-glycopeptide isoforms of AGP detected in four laboratories were compared to assess reproducibility. Quantitative analysis showed that the coefficient of variation was <25% for all test samples. Our analytical protocol yielded identification and quantification of site-specific N-glycopeptide isoforms of AGP from control and disease plasma sample.
Collapse
Affiliation(s)
- Ju Yeon Lee
- Biomedical Omics Group, Korea Basic Science Institute , Ochang 28119, Republic of Korea
| | - Hyun Kyoung Lee
- Biomedical Omics Group, Korea Basic Science Institute , Ochang 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Gun Wook Park
- Biomedical Omics Group, Korea Basic Science Institute , Ochang 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Heeyoun Hwang
- Biomedical Omics Group, Korea Basic Science Institute , Ochang 28119, Republic of Korea
| | - Hoi Keun Jeong
- Biomedical Omics Group, Korea Basic Science Institute , Ochang 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Ki Na Yun
- Biomedical Omics Group, Korea Basic Science Institute , Ochang 28119, Republic of Korea.,Department of Chemistry, Sogang University , Seoul 04107, Republic of Korea
| | - Eun Sun Ji
- Biomedical Omics Group, Korea Basic Science Institute , Ochang 28119, Republic of Korea.,Department of Chemistry, Hannam University , Daejeon 34430, Republic of Korea
| | - Kwang Hoe Kim
- Biomedical Omics Group, Korea Basic Science Institute , Ochang 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Jun Seok Kim
- Department of Biomedical Systems Engineering, Korea Polytechnics , Gyeonggi 13590, Republic of Korea
| | - Jong Won Kim
- New Drug Development Center, Osong Medical Innovation Foundation , Cheongju 28160, Republic of Korea
| | - Sung Ho Yun
- Drug & Disease Target Group, Korea Basic Science Institute , Daejeon 34133, Republic of Korea
| | - Chi-Won Choi
- Drug & Disease Target Group, Korea Basic Science Institute , Daejeon 34133, Republic of Korea
| | - Seung Il Kim
- Drug & Disease Target Group, Korea Basic Science Institute , Daejeon 34133, Republic of Korea
| | - Jong-Sun Lim
- Yonsei Proteome Research Center, Yonsei University , Seoul 03722, Republic of Korea
| | - Seul-Ki Jeong
- Yonsei Proteome Research Center, Yonsei University , Seoul 03722, Republic of Korea
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University , Seoul 03722, Republic of Korea
| | - Soo-Youn Lee
- Department of Laboratory & Genetics, Samsung Medical Center, Sungkyunkwan University of Medicine , Seoul 06351, Republic of Korea.,Department of Clinical Pharmacology and Therapeutics, Samsung Medical Center , Seoul 06351, Republic of Korea
| | - Jisook Park
- Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul 06351, Republic of Korea
| | - Su Yeon Kim
- Department of Clinical Research Supporting Team, Clinical Research Institute, Samsung Medical Center , Seoul 06351, Republic of Korea
| | - Young-Jin Choi
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, Republic of Korea
| | - Yong-In Kim
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, Republic of Korea
| | - Jawon Seo
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, Republic of Korea
| | - Myoung Jin Oh
- Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Nari Seo
- Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute , Ochang 28119, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute , Ochang 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea
| |
Collapse
|
28
|
Kim JW, Hwang H, Lim JS, Lee HJ, Jeong SK, Yoo JS, Paik YK. gFinder: A Web-Based Bioinformatics Tool for the Analysis of N-Glycopeptides. J Proteome Res 2016; 15:4116-4125. [PMID: 27573070 DOI: 10.1021/acs.jproteome.6b00772] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Glycoproteins influence numerous indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to the development of proteome informatics tools that facilitate the MS analysis of glycans and glycopeptides. Here we report on the development of gFinder, a web-based bioinformatics tool that analyzes mixtures of native N-glycopeptides that have been profiled by tandem MS. gFinder not only enables the simultaneous integration of collision-induced dissociation (CID) and high-energy collisional dissociation (HCD) fragmentation but also merges the spectra for high-throughput analysis. These merged spectra expedite the identification of both glycans and N-glycopeptide backbones in tandem MS data using the glycan database and a proteomic search tool (e.g., Mascot). These data can be used to simultaneously characterize peptide backbone sequences and possible N-glycan structures using assigned scores. gFinder also provides many convenient functions that make it easy to perform manual calculations while viewing the spectrum on-screen. We used gFinder to detect an additional protein (Q8N9B8) that was missed from the previously published data set containing N-linked glycosylation. For N-glycan analysis, we used the GlycomeDB glycan structure database, which integrates the structural and taxonomic data from all of the major carbohydrate databases available in the public domain. Thus, gFinder is a convenient, high-throughput analytical tool for interpreting the tandem mass spectra of N-glycopeptides, which can then be used for identification of potential missing proteins having glycans. gFinder is available publicly at http://gFinder.proteomix.org/ .
Collapse
Affiliation(s)
- Ju-Wan Kim
- Graduate Program in Functional Genomics, College of Life Sciences and Biotechnology, Yonsei University , Seoul 03722, Korea.,Yonsei Proteome Research Center , Seoul 03722, Korea
| | - Heeyoun Hwang
- Korea Basic Science Institute , Ochang 28199, Chungbuk, Korea
| | - Jong-Sun Lim
- Yonsei Proteome Research Center , Seoul 03722, Korea
| | | | - Seul-Ki Jeong
- Yonsei Proteome Research Center , Seoul 03722, Korea
| | - Jong Shin Yoo
- Korea Basic Science Institute , Ochang 28199, Chungbuk, Korea
| | - Young-Ki Paik
- Graduate Program in Functional Genomics, College of Life Sciences and Biotechnology, Yonsei University , Seoul 03722, Korea.,Yonsei Proteome Research Center , Seoul 03722, Korea
| |
Collapse
|
29
|
Ji ES, Hwang H, Park GW, Lee JY, Lee HK, Choi NY, Jeong HK, Kim KH, Kim JY, Lee S, Ahn YH, Yoo JS. Analysis of fucosylation in liver-secreted N-glycoproteins from human hepatocellular carcinoma plasma using liquid chromatography with tandem mass spectrometry. Anal Bioanal Chem 2016; 408:7761-7774. [PMID: 27565792 DOI: 10.1007/s00216-016-9878-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/01/2016] [Accepted: 08/12/2016] [Indexed: 12/11/2022]
Abstract
Fucosylation of N-glycoproteins has been implicated in various diseases, such as hepatocellular carcinoma (HCC). However, few studies have performed site-specific analysis of fucosylation in liver-secreted proteins. In this study, we characterized the fucosylation patterns of liver-secreted proteins in HCC plasma using a workflow to identify site-specific N-glycoproteins, where characteristic B- and/or Y-ion series with and without fucose in collision-induced dissociation were used in tandem mass spectrometry. In total, 71 fucosylated N-glycopeptides from 13 major liver-secreted proteins in human plasma were globally identified by LC-MS/MS. Additionally, 37 fucosylated N-glycopeptides were newly identified from nine liver-secreted proteins, including alpha-1-antichymotrypsin, alpha-1-antitrypsin, alpha-2-HS-glycoprotein, ceruloplasmin, alpha-1-acid glycoprotein 1/2, alpha-2-macroglobulin, serotransferrin, and beta-2-glycoprotein 1. Of the fucosylated N-glycopeptides, bi- and tri-antennary glycoforms were the most common ones identified in liver-secreted proteins from HCC plasma. Therefore, we suggest that this analytical method is effective for characterizing fucosylation in liver-secreted proteins. Graphical abstract A global map of fucosylated and non-fucosylated glycopeptides from 13 liver-secreted glycoproteins in hepatocellular carcinoma plasma.
Collapse
Affiliation(s)
- Eun Sun Ji
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju, Chungbuk, 28119, Republic of Korea
| | - Heeyoun Hwang
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju, Chungbuk, 28119, Republic of Korea
| | - Gun Wook Park
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju, Chungbuk, 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764, Republic of Korea
| | - Ju Yeon Lee
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju, Chungbuk, 28119, Republic of Korea
| | - Hyun Kyoung Lee
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju, Chungbuk, 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764, Republic of Korea
| | - Na Young Choi
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju, Chungbuk, 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764, Republic of Korea
| | - Hoi Keun Jeong
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju, Chungbuk, 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764, Republic of Korea
| | - Kwang Hoe Kim
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju, Chungbuk, 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju, Chungbuk, 28119, Republic of Korea
| | - Seungho Lee
- Department of Chemistry, Hannam University, Daejeon, 306-791, Republic of Korea
| | - Yeong Hee Ahn
- Department of Biomedical Science, Cheongju University, Cheongju, 28503, Republic of Korea.
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongju, Chungbuk, 28119, Republic of Korea. .,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764, Republic of Korea.
| |
Collapse
|
30
|
Gudelj I, Baciarello M, Ugrina I, De Gregori M, Napolioni V, Ingelmo PM, Bugada D, De Gregori S, Đerek L, Pučić-Baković M, Novokmet M, Gornik O, Saccani Jotti G, Meschi T, Lauc G, Allegri M. Changes in total plasma and serum N-glycome composition and patient-controlled analgesia after major abdominal surgery. Sci Rep 2016; 6:31234. [PMID: 27501865 PMCID: PMC4977520 DOI: 10.1038/srep31234] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/15/2016] [Indexed: 12/21/2022] Open
Abstract
Systemic inflammation participates to the complex healing process occurring after major surgery, thus directly affecting the surgical outcome and patient recovery. Total plasma N-glycome might be an indicator of inflammation after major surgery, as well as an anti-inflammatory therapy response marker, since protein glycosylation plays an essential role in the inflammatory cascade. Therefore, we assessed the effects of surgery on the total plasma N-glycome and the association with self-administration of postoperative morphine in two cohorts of patients that underwent major abdominal surgery. We found that plasma N-glycome undergoes significant changes one day after surgery and intensifies one day later, thus indicating a systemic physiological response. In particular, we observed the increase of bisialylated biantennary glycan, A2G2S[3,6]2, 12 hours after surgery, which progressively increased until 48 postoperative hours. Most changes occurred 24 hours after surgery with the decrease of most core-fucosylated biantennary structures, as well as the increase in sialylated tetraantennary and FA3G3S[3,3,3]3 structures. Moreover, we observed a progressive increase of sialylated triantennary and tetraantennary structures two days after surgery, with a concomitant decrease of the structures containing bisecting N-acetylglucosamine along with bi- and trisialylated triantennary glycans. We did not find any statistically significant association between morphine consumption and plasma N-glycome.
Collapse
Affiliation(s)
- Ivan Gudelj
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Marco Baciarello
- Department of Anesthesia, ICU and Pain Therapy, University Hospital of Parma, Parma, Italy.,SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Department of Surgical Sciences, University of Parma, Parma, Italy
| | - Ivo Ugrina
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Manuela De Gregori
- SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Pain Therapy Service, Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy.,YAP (Young Against Pain) group, Parma, Italy
| | - Valerio Napolioni
- SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Pablo M Ingelmo
- SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Department of Anesthesia, Montreal Children's Hospital, Canada
| | - Dario Bugada
- Department of Anesthesia, ICU and Pain Therapy, University Hospital of Parma, Parma, Italy.,SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Department of Surgical Sciences, University of Parma, Parma, Italy
| | - Simona De Gregori
- Clinical and Experimental Pharmacokinetics Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Lovorka Đerek
- Department of Medical Biochemistry and Laboratory Medicine, Clinical Hospital Merkur, Zagreb, Croatia
| | | | | | - Olga Gornik
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Gloria Saccani Jotti
- Department of Biomedical, Biotechnological and Translational Science (S.Bi.Bi.T.), University of Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Clinical and Experimental Medicine, University of Parma, Italy
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Massimo Allegri
- Department of Anesthesia, ICU and Pain Therapy, University Hospital of Parma, Parma, Italy.,SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Department of Surgical Sciences, University of Parma, Parma, Italy
| |
Collapse
|
31
|
Clerc F, Reiding KR, Jansen BC, Kammeijer GSM, Bondt A, Wuhrer M. Human plasma protein N-glycosylation. Glycoconj J 2015; 33:309-43. [PMID: 26555091 PMCID: PMC4891372 DOI: 10.1007/s10719-015-9626-2] [Citation(s) in RCA: 293] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 09/30/2015] [Accepted: 10/05/2015] [Indexed: 01/09/2023]
Abstract
Glycosylation is the most abundant and complex protein modification, and can have a profound structural and functional effect on the conjugate. The oligosaccharide fraction is recognized to be involved in multiple biological processes, and to affect proteins physical properties, and has consequentially been labeled a critical quality attribute of biopharmaceuticals. Additionally, due to recent advances in analytical methods and analysis software, glycosylation is targeted in the search for disease biomarkers for early diagnosis and patient stratification. Biofluids such as saliva, serum or plasma are of great use in this regard, as they are easily accessible and can provide relevant glycosylation information. Thus, as the assessment of protein glycosylation is becoming a major element in clinical and biopharmaceutical research, this review aims to convey the current state of knowledge on the N-glycosylation of the major plasma glycoproteins alpha-1-acid glycoprotein, alpha-1-antitrypsin, alpha-1B-glycoprotein, alpha-2-HS-glycoprotein, alpha-2-macroglobulin, antithrombin-III, apolipoprotein B-100, apolipoprotein D, apolipoprotein F, beta-2-glycoprotein 1, ceruloplasmin, fibrinogen, immunoglobulin (Ig) A, IgG, IgM, haptoglobin, hemopexin, histidine-rich glycoprotein, kininogen-1, serotransferrin, vitronectin, and zinc-alpha-2-glycoprotein. In addition, the less abundant immunoglobulins D and E are included because of their major relevance in immunology and biopharmaceutical research. Where available, the glycosylation is described in a site-specific manner. In the discussion, we put the glycosylation of individual proteins into perspective and speculate how the individual proteins may contribute to a total plasma N-glycosylation profile determined at the released glycan level.
Collapse
Affiliation(s)
- Florent Clerc
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Karli R Reiding
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Bas C Jansen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Guinevere S M Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Albert Bondt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.,Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands. .,Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|