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Sheta R, Woo CM, Roux-Dalvai F, Fournier F, Bourassa S, Droit A, Bertozzi CR, Bachvarov D. A metabolic labeling approach for glycoproteomic analysis reveals altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells. J Proteomics 2016; 145:91-102. [PMID: 27095597 PMCID: PMC5436706 DOI: 10.1016/j.jprot.2016.04.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/31/2016] [Accepted: 04/12/2016] [Indexed: 12/29/2022]
Abstract
UNLABELLED Epithelial ovarian cancer (EOC) is a disease responsible for more deaths among women in the Western world than all other gynecologic malignancies. There is urgent need for new therapeutic targets and a better understanding of EOC initiation and progression. We have previously identified the polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3) gene, a member of the GalNAc-transferases (GalNAc-Ts) gene family, as hypomethylated and overexpressed in high-grade serous EOC tumors, compared to low malignant potential EOC tumors and normal ovarian tissues. This data also suggested for a role of GALNT3 in aberrant EOC glycosylation, possibly implicated in disease progression. To evaluate differential glycosylation in EOC caused by modulations in GALNT3 expression, we used a metabolic labeling strategy for enrichment and mass spectrometry-based characterization of glycoproteins following GALNT3 gene knockdown (KD) in A2780s EOC cells. A total of 589 differentially expressed glycoproteins were identified upon GALNT3 KD. Most identified proteins were involved in mechanisms of cellular metabolic functions, post-translational modifications, and some have been reported to be implicated in EOC etiology. The GALNT3-dependent glycoproteins identified by this metabolic labeling approach support the oncogenic role of GALNT3 in EOC dissemination and may be pursued as novel EOC biomarkers and/or therapeutic targets. BIOLOGICAL SIGNIFICANCE Knowledge of the O-glycoproteome has been relatively elusive, and the functions of the individual polypeptide GalNAc-Ts have been poorly characterized. Alterations in GalNAc-Ts expression were shown to provide huge variability in the O-glycoproteome in various pathologies, including cancer. The application of a chemical biology approach for the metabolic labeling and subsequent characterization of O-glycoproteins in EOC using the Ac4GalNAz metabolite has provided a strategy allowing for proteomic discovery of GalNAc-Ts specific functions. Our study supports an essential role of one of the GalNAc-Ts - GALNT3, in EOC dissemination, including its implication in modulating PTMs and EOC metabolism. Our approach validates the use of the applied metabolic strategy to identify important functions of GalNAc-Ts in normal and pathological conditions.
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Affiliation(s)
- Razan Sheta
- Department of Molecular Medicine, Laval University, Québec, PQ, Canada; Centre de recherche du CHU de Québec, L'Hôtel-Dieu de Québec, Québec, PQ, Canada
| | - Christina M Woo
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | | | - Sylvie Bourassa
- Centre de recherche du CHU de Québec, CHUL, Québec, PQ, Canada
| | - Arnaud Droit
- Department of Molecular Medicine, Laval University, Québec, PQ, Canada; Centre de recherche du CHU de Québec, CHUL, Québec, PQ, Canada
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Dimcho Bachvarov
- Department of Molecular Medicine, Laval University, Québec, PQ, Canada; Centre de recherche du CHU de Québec, L'Hôtel-Dieu de Québec, Québec, PQ, Canada
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102
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Functional Consequences of Differential O-glycosylation of MUC1, MUC4, and MUC16 (Downstream Effects on Signaling). Biomolecules 2016; 6:biom6030034. [PMID: 27483328 PMCID: PMC5039420 DOI: 10.3390/biom6030034] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/18/2016] [Accepted: 07/21/2016] [Indexed: 12/12/2022] Open
Abstract
Glycosylation is one of the most abundant post-translational modifications that occur within the cell. Under normal physiological conditions, O-linked glycosylation of extracellular proteins is critical for both structure and function. During the progression of cancer, however, the expression of aberrant and truncated glycans is commonly observed. Mucins are high molecular weight glycoproteins that contain numerous sites of O-glycosylation within their extracellular domains. Transmembrane mucins also play a functional role in monitoring the surrounding microenvironment and transducing these signals into the cell. In cancer, these mucins often take on an oncogenic role and promote a number of pro-tumorigenic effects, including pro-survival, migratory, and invasive behaviors. Within this review, we highlight both the processes involved in the expression of aberrant glycan structures on mucins, as well as the potential downstream impacts on cellular signaling.
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103
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Cracking the Glycome Encoder: Signaling, Trafficking, and Glycosylation. Trends Cell Biol 2016; 26:379-388. [DOI: 10.1016/j.tcb.2015.12.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/08/2015] [Accepted: 12/18/2015] [Indexed: 01/22/2023]
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104
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Biochemical and functional characterization of glycosylation-associated mutational landscapes in colon cancer. Sci Rep 2016; 6:23642. [PMID: 27004849 PMCID: PMC4804330 DOI: 10.1038/srep23642] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/10/2016] [Indexed: 12/12/2022] Open
Abstract
The molecular basis of aberrant protein glycosylation, a pathological alteration widespread in colorectal cancers (CRC), and the mechanisms by which it contributes to tumor progression remain largely unknown. We performed targeted re-sequencing of 430 glycosylation-associated genes in a series of patient-derived CRC cell lines (N = 31) and matched primary tumor tissues, identifying 12 new significantly mutated glycosylation-associated genes in colon cancer. In particular, we observed an enrichment of mutations in genes (B3GNT2, B4GALT2, ST6GALNAC2) involved in the biosynthesis of N- and Cores 1–3 O-linked glycans in the colon, accounting for ~16% of the CRCs tested. Analysis of independent large-scale tumor tissue datasets confirmed recurrent mutations within these genes in colon and other gastrointestinal cancers. Systematic biochemical and phenotypic characterization of the candidate wild-type and mutant glycosyltransferases demonstrated these mutations as either markedly altering protein localization, post-translational modification, encoded enzymatic activities and/or the migratory potential of colon carcinoma cells. These findings suggest that functionally deleterious mutations in glycosyltransferase genes in part underlie aberrant glycosylation, and contribute to the pathogenesis of molecular subsets of colon and other gastrointestinal malignancies.
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105
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Mereiter S, Balmaña M, Gomes J, Magalhães A, Reis CA. Glycomic Approaches for the Discovery of Targets in Gastrointestinal Cancer. Front Oncol 2016; 6:55. [PMID: 27014630 PMCID: PMC4783390 DOI: 10.3389/fonc.2016.00055] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/24/2016] [Indexed: 12/22/2022] Open
Abstract
Gastrointestinal (GI) cancer is the most common group of malignancies and many of its types are among the most deadly. Various glycoconjugates have been used in clinical practice as serum biomarker for several GI tumors, however, with limited diagnose application. Despite the good accessibility by endoscopy of many GI organs, the lack of reliable serum biomarkers often leads to late diagnosis of malignancy and consequently low 5-year survival rates. Recent advances in analytical techniques have provided novel glycoproteomic and glycomic data and generated functional information and putative biomarker targets in oncology. Glycosylation alterations have been demonstrated in a series of glycoconjugates (glycoproteins, proteoglycans, and glycosphingolipids) that are involved in cancer cell adhesion, signaling, invasion, and metastasis formation. In this review, we present an overview on the major glycosylation alterations in GI cancer and the current serological biomarkers used in the clinical oncology setting. We further describe recent glycomic studies in GI cancer, namely gastric, colorectal, and pancreatic cancer. Moreover, we discuss the role of glycosylation as a modulator of the function of several key players in cancer cell biology. Finally, we address several state-of-the-art techniques currently applied in this field, such as glycomic and glycoproteomic analyses, the application of glycoengineered cell line models, microarray and proximity ligation assay, and imaging mass spectrometry, and provide an outlook to future perspectives and clinical applications.
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Affiliation(s)
- Stefan Mereiter
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Institute of Biomedical Sciences of Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Meritxell Balmaña
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona , Girona , Spain
| | - Joana Gomes
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Ana Magalhães
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Celso A Reis
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Institute of Biomedical Sciences of Abel Salazar (ICBAS), University of Porto, Porto, Portugal; Medical Faculty, University of Porto, Porto, Portugal
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106
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Chia J, Goh G, Bard F. Short O-GalNAc glycans: regulation and role in tumor development and clinical perspectives. Biochim Biophys Acta Gen Subj 2016; 1860:1623-39. [PMID: 26968459 DOI: 10.1016/j.bbagen.2016.03.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/03/2016] [Accepted: 03/03/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND While the underlying causes of cancer are genetic modifications, changes in cellular states mediate cancer development. Tumor cells display markedly changed glycosylation states, of which the O-GalNAc glycans called the Tn and TF antigens are particularly common. How these antigens get over-expressed is not clear. The expression levels of glycosylation enzymes fail to explain it. SCOPE OF REVIEW We describe the regulation of O-GalNAc glycosylation initiation and extension with emphasis on the initiating enzymes ppGalNAcTs (GALNTs), and introduce the GALA pathway--a change in GALNTs compartmentation within the secretory pathway that regulates Tn levels. We discuss the roles of O-GalNAc glycans and GALNTs in tumorigenic processes and finally consider diagnostic and therapeutic perspectives. MAJOR CONCLUSIONS Contrary to a common hypothesis, short O-glycans in tumors are not the result of an incomplete glycosylation process but rather reveal the activation of regulatory pathways. Surprisingly, high Tn levels reveal a major shift in the O-glycoproteome rather than a shortening of O-glycans. These changes are driven by membrane trafficking events. GENERAL SIGNIFICANCE Many attempts to use O-glycans for biomarker, antibody and therapeutic vaccine development have been made, but suffer limitations including poor sensitivity and/or specificity that may in part derive from lack of a mechanistic understanding. Deciphering how short O-GalNAc glycans are regulated would open new perspectives to exploit this biology for therapeutic usage. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.
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Affiliation(s)
- Joanne Chia
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Germaine Goh
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Frederic Bard
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, 138673, Singapore; Department of Biochemistry, National University of Singapore, 21 Lower Kent Ridge, Road, 119077, Singapore.
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107
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Recent structural and mechanistic insights into protein O-GalNAc glycosylation. Biochem Soc Trans 2016; 44:61-7. [DOI: 10.1042/bst20150178] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein O-GalNAcylation is an abundant post-translational modification and predicted to occur in over 80% of the proteins passing through the Golgi apparatus. This modification is driven by 20 polypeptide GaINAc (N-acetylgalactosamine)-transferases (GalNAc-Ts), which are unique in that they possess both catalytic and lectin domains. The peptide substrate specificities of GalNAc-Ts are still poorly defined and our understanding of the sequence and structural features that direct O-glycosylation of proteins is limited. Part of this may be attributed to the complex regulation by coordinated action of multiple GalNAc-T isoforms, and part of this may also be attributed to the two functional domains of GalNAc-Ts that both seems to be involved in directing the substrate specificities. Recent studies have resulted in 3D structures of GalNAc-Ts and determination of the reaction mechanism of this family of enzymes. Key advances include the trapping of binary/ternary complexes in combination with computational simulations and AFM/small-SAXS experiments, which have allowed for the dissection of the reaction coordinates and the mechanism by which the lectin domains modulate the glycosylation. These studies not only broaden our knowledge of the modes-of-action of this family of enzymes but also open up potential avenues for the rational design of effective and selective inhibitors of O-glycosylation.
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108
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Stone JA, Nicola AV, Baum LG, Aguilar HC. Multiple Novel Functions of Henipavirus O-glycans: The First O-glycan Functions Identified in the Paramyxovirus Family. PLoS Pathog 2016; 12:e1005445. [PMID: 26867212 PMCID: PMC4750917 DOI: 10.1371/journal.ppat.1005445] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/19/2016] [Indexed: 01/13/2023] Open
Abstract
O-linked glycosylation is a ubiquitous protein modification in organisms belonging to several kingdoms. Both microbial and host protein glycans are used by many pathogens for host invasion and immune evasion, yet little is known about the roles of O-glycans in viral pathogenesis. Reportedly, there is no single function attributed to O-glycans for the significant paramyxovirus family. The paramyxovirus family includes many important pathogens, such as measles, mumps, parainfluenza, metapneumo- and the deadly Henipaviruses Nipah (NiV) and Hendra (HeV) viruses. Paramyxoviral cell entry requires the coordinated actions of two viral membrane glycoproteins: the attachment (HN/H/G) and fusion (F) glycoproteins. O-glycan sites in HeV G were recently identified, facilitating use of the attachment protein of this deadly paramyxovirus as a model to study O-glycan functions. We mutated the identified HeV G O-glycosylation sites and found mutants with altered cell-cell fusion, G conformation, G/F association, viral entry in a pseudotyped viral system, and, quite unexpectedly, pseudotyped viral F protein incorporation and processing phenotypes. These are all important functions of viral glycoproteins. These phenotypes were broadly conserved for equivalent NiV mutants. Thus our results identify multiple novel and pathologically important functions of paramyxoviral O-glycans, paving the way to study O-glycan functions in other paramyxoviruses and enveloped viruses.
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Affiliation(s)
- Jacquelyn A. Stone
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, United States of America
| | - Anthony V. Nicola
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, United States of America
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Linda G. Baum
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California, United States of America
| | - Hector C. Aguilar
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, United States of America
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
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109
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Liquid chromatography-tandem mass spectrometry-based fragmentation analysis of glycopeptides. Glycoconj J 2016; 33:261-72. [PMID: 26780731 DOI: 10.1007/s10719-016-9649-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/23/2015] [Accepted: 01/04/2016] [Indexed: 02/08/2023]
Abstract
The use of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS(n)) for the glycoproteomic characterization of glycopeptides is a growing field of research. The N- and O-glycosylated peptides (N- and O-glycopeptides) analyzed typically originate from protease-digested glycoproteins where many of them are expected to be biomedically important. Examples of LC-MS(2) and MS(3) fragmentation strategies used to pursue glycan structure, peptide identity and attachment-site identification analyses of glycopeptides are described in this review. MS(2) spectra, using the CID and HCD fragmentation techniques of a complex biantennary N-glycopeptide and a core 1 O-glycopeptide, representing two examples of commonly studied glycopeptide types, are presented. A few practical tips for accomplishing glycopeptide analysis using reversed-phase LC-MS(n) shotgun proteomics settings, together with references to the latest glycoproteomic studies, are presented.
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110
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Arend P. ABO (histo) blood group phenotype development and human reproduction as they relate to ancestral IgM formation: A hypothesis. Immunobiology 2016; 221:116-27. [DOI: 10.1016/j.imbio.2015.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 03/18/2015] [Accepted: 07/07/2015] [Indexed: 10/23/2022]
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111
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Niang B, Jin L, Chen X, Guo X, Zhang H, Wu Q, Padhiar AA, Xiao M, Fang D, Zhang J. GalNAc-T4 putatively modulates the estrogen regulatory network through FOXA1 glycosylation in human breast cancer cells. Mol Cell Biochem 2016; 411:393-402. [PMID: 26541755 DOI: 10.1007/s11010-015-2601-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/29/2015] [Indexed: 12/31/2022]
Abstract
GALNT4 belongs to a family of N-acetylgalactosaminyltransferases, which catalyze the transfer of GalNAc to Serine or Threonine residues in the initial step of mucin-type O-linked protein glycosylation. This glycosylation type is the most complex post-translational modification of proteins, playing important roles during cellular differentiation and in pathological disorders. Most of the breast cancer subtypes are estrogen receptor positive, and hence, the estrogen pathway represents a key regulatory network. We investigated the expression of GalNAc-T4 in a panel of mammary epithelial cell lines and found its expression is associated with the estrogen status of the cells. FOXA1, a key transcription factor, functions to promote estrogen responsive gene expression by acting as a cofactor to estrogen receptor alpha (ERα), but all the aspects of this regulatory mechanism are not fully explored. This study found that knockdown of GALNT4 expression in human breast cancer cells attenuated the protein expression of ERα, FOXA1, and Cyclin D1. Further, our immunoprecipitation assays depicted the possibility of FOXA1 to undergo O-GalNAc modifications with a decrease of GalNAc residues in the GALNT4 knockdown cells and also impairment in the FOXA1-ERα association. Rescuing GALNT4 expression could restore the interaction as well as the glycosylation of FOXA1. Together, these findings suggest a key role for GalNAc-T4 in the estrogen pathway through FOXA1 glycosylation.
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Affiliation(s)
- Bachir Niang
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, 9 South Lvshun Road Western Section, Dalian, 116044, China
| | - Liyuan Jin
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, 9 South Lvshun Road Western Section, Dalian, 116044, China
| | - Xixi Chen
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, 9 South Lvshun Road Western Section, Dalian, 116044, China
| | - Xiaohan Guo
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, 9 South Lvshun Road Western Section, Dalian, 116044, China
| | - Hongshuo Zhang
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, 9 South Lvshun Road Western Section, Dalian, 116044, China
| | - Qiong Wu
- School of Life Science and Medicine, Dalian University of Technology, 2 Linggong Road, Dalian, 116024, China
| | - Arshad Ahmed Padhiar
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, 9 South Lvshun Road Western Section, Dalian, 116044, China
| | - Min Xiao
- National Glycoengineering Research Center and State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave, Chicago, IL, 60611, USA
| | - Jianing Zhang
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, 9 South Lvshun Road Western Section, Dalian, 116044, China.
- School of Life Science and Medicine, Dalian University of Technology, 2 Linggong Road, Dalian, 116024, China.
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112
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Schjoldager KT, Joshi HJ, Kong Y, Goth CK, King SL, Wandall HH, Bennett EP, Vakhrushev SY, Clausen H. Deconstruction of O-glycosylation--GalNAc-T isoforms direct distinct subsets of the O-glycoproteome. EMBO Rep 2015; 16:1713-22. [PMID: 26566661 PMCID: PMC4693523 DOI: 10.15252/embr.201540796] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/05/2015] [Accepted: 10/16/2015] [Indexed: 12/20/2022] Open
Abstract
GalNAc-type O-glycosylation is found on most proteins trafficking through the secretory pathway in metazoan cells. The O-glycoproteome is regulated by up to 20 polypeptide GalNAc-Ts and the contributions and biological functions of individual GalNAc-Ts are poorly understood. Here, we used a zinc-finger nuclease (ZFN)-directed knockout strategy to probe the contributions of the major GalNAc-Ts (GalNAc-T1 and GalNAc-T2) in liver cells and explore how the GalNAc-T repertoire quantitatively affects the O-glycoproteome. We demonstrate that the majority of the O-glycoproteome is covered by redundancy, whereas distinct subsets of substrates are modified by non-redundant functions of GalNAc-T1 and GalNAc-T2. The non-redundant O-glycoproteome subsets and specific transcriptional responses for each isoform are related to different cellular processes; for the GalNAc-T2 isoform, these support a role in lipid metabolism. The results demonstrate that GalNAc-Ts have different non-redundant glycosylation functions, which may affect distinct cellular processes. The data serves as a comprehensive resource for unique GalNAc-T substrates. Our study provides a new view of the differential regulation of the O-glycoproteome, suggesting that the plurality of GalNAc-Ts arose to regulate distinct protein functions and cellular processes.
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Affiliation(s)
- Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Yun Kong
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Christoffer K Goth
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Sarah Louise King
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
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113
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Olofsson S, Blixt O, Bergström T, Frank M, Wandall HH. Viral O-GalNAc peptide epitopes: a novel potential target in viral envelope glycoproteins. Rev Med Virol 2015; 26:34-48. [PMID: 26524377 DOI: 10.1002/rmv.1859] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 01/01/2023]
Abstract
Viral envelope glycoproteins are major targets for antibodies that bind to and inactivate viral particles. The capacity of a viral vaccine to induce virus-neutralizing antibodies is often used as a marker for vaccine efficacy. Yet the number of known neutralization target epitopes is restricted owing to various viral escape mechanisms. We expand the range of possible viral glycoprotein targets, by presenting a previously unknown type of viral glycoprotein epitope based on a short peptide stretch modified with small O-linked glycans. Besides being immunologically active, these epitopes have a high potential for antigenic variation. Thus, sera from patients infected with EBV develop individual IgG responses addressing the different possible glycopeptide glycoforms of one short peptide backbone that reflect individual variations in the course of virus infection. In contrast, in HSV type 2 meningitis patients, CSF antibodies are focussed to only one single glycoform peptide of a major viral glycoprotein. Thus, dependent on the viral disease, the serological response may be variable or constant with respect to the number of targeted peptide glycoforms. Mapping of these epitopes relies on a novel three-step procedure that identifies any reactive viral O-glycosyl peptide epitope with respect to (i) relevant peptide sequence, (ii) the reactive glycoform out of several possible glycopeptide isomers of that peptide sequence, and (iii) possibly tolerated carbohydrate or peptide structural variations at glycosylation sites. In conclusion, the viral O-glycosyl peptide epitopes may be of relevance for development of subunit vaccines and for improved serodiagnosis of viral diseases. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Sigvard Olofsson
- Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Ola Blixt
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Tomas Bergström
- Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | | | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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114
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Briant K, Koay YH, Otsuka Y, Swanton E. ERAD of proteins containing aberrant transmembrane domains requires ubiquitylation of cytoplasmic lysine residues. J Cell Sci 2015; 128:4112-25. [PMID: 26446255 PMCID: PMC4712780 DOI: 10.1242/jcs.171215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 09/28/2015] [Indexed: 11/29/2022] Open
Abstract
Clearance of misfolded proteins from the endoplasmic reticulum (ER) is mediated by the ubiquitin-proteasome system in a process known as ER-associated degradation (ERAD). The mechanisms through which proteins containing aberrant transmembrane domains are degraded by ERAD are poorly understood. To address this question, we generated model ERAD substrates based on CD8 with either a non-native transmembrane domain but a folded ER luminal domain (CD8TMD*), or the native transmembrane domain but a misfolded luminal domain (CD8LUM*). Although both chimeras were degraded by ERAD, we found that the location of the folding defect determined the initial site of ubiquitylation. Ubiquitylation of cytoplasmic lysine residues was required for the extraction of CD8TMD* from the ER membrane during ERAD, whereas CD8LUM* continued to be degraded in the absence of cytoplasmic lysine residues. Cytoplasmic lysine residues were also required for degradation of an additional ERAD substrate containing an unassembled transmembrane domain and when a non-native transmembrane domain was introduced into CD8LUM*. Our results suggest that proteins with defective transmembrane domains are removed from the ER through a specific ERAD mechanism that depends upon ubiquitylation of cytoplasmic lysine residues. Summary: Proteins containing defective transmembrane domains are removed from the endoplasmic reticulum through a specific mechanism that depends upon the ubiquitylation of cytoplasmic lysine residues.
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Affiliation(s)
- Kit Briant
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Yee-Hui Koay
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Yuka Otsuka
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Eileithyia Swanton
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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Abstract
O-GlcNAcylation is a dynamic protein post-translational modification of serine or threonine residues by an O-linked monosaccharide N-acetylglucosamine (O-GlcNAc). O-GlcNAcylation was discovered three decades ago and its significance has been implicated in several disease states, such as metabolic diseases, cancer and neurological diseases. Yet it remains technically challenging to characterize comprehensively and quantitatively because of its low abundance, low stoichiometry and extremely labile nature under conventional collision-induced dissociation tandem MS conditions. Herein, we review the recent advances addressing these challenges in developing proteomic approaches for site-specific O-GlcNAcylation analysis, including specific enrichment of O-GlcNAc peptides/proteins, unambiguous site-determination of O-GlcNAc modification and quantitative analysis of O-GlcNAcylation.
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116
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Campos D, Freitas D, Gomes J, Magalhães A, Steentoft C, Gomes C, Vester-Christensen MB, Ferreira JA, Afonso LP, Santos LL, Pinto de Sousa J, Mandel U, Clausen H, Vakhrushev SY, Reis CA. Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery. Mol Cell Proteomics 2015; 14:1616-29. [PMID: 25813380 PMCID: PMC4458724 DOI: 10.1074/mcp.m114.046862] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/19/2015] [Indexed: 12/21/2022] Open
Abstract
Circulating O-glycoproteins shed from cancer cells represent important serum biomarkers for diagnostic and prognostic purposes. We have recently shown that selective detection of cancer-associated aberrant glycoforms of circulating O-glycoprotein biomarkers can increase specificity of cancer biomarker assays. However, the current knowledge of secreted and circulating O-glycoproteins is limited. Here, we used the COSMC KO "SimpleCell" (SC) strategy to characterize the O-glycoproteome of two gastric cancer SimpleCell lines (AGS, MKN45) as well as a gastric cell line (KATO III) which naturally expresses at least partially truncated O-glycans. Overall, we identified 499 O-glycoproteins and 1236 O-glycosites in gastric cancer SimpleCells, and a total 47 O-glycoproteins and 73 O-glycosites in the KATO III cell line. We next modified the glycoproteomic strategy to apply it to pools of sera from gastric cancer and healthy individuals to identify circulating O-glycoproteins with the STn glycoform. We identified 37 O-glycoproteins in the pool of cancer sera, and only nine of these were also found in sera from healthy individuals. Two identified candidate O-glycoprotein biomarkers (CD44 and GalNAc-T5) circulating with the STn glycoform were further validated as being expressed in gastric cancer tissue. A proximity ligation assay was used to show that CD44 was expressed with the STn glycoform in gastric cancer tissues. The study provides a discovery strategy for aberrantly glycosylated O-glycoproteins and a set of O-glycoprotein candidates with biomarker potential in gastric cancer.
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Affiliation(s)
- Diana Campos
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Daniela Freitas
- §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Joana Gomes
- §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Ana Magalhães
- §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Catharina Steentoft
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Catarina Gomes
- §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Malene B Vester-Christensen
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - José Alexandre Ferreira
- ¶Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida 4200-072 Porto, Portugal; ‖QOPNA, Department of Chemistry of the University of Aveiro, Campus Universitário de Santiago 3810-193 Aveiro, Portugal
| | - Luis P Afonso
- **Department of Pathology, Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida 4200-072 Porto, Portugal
| | - Lúcio L Santos
- ¶Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida 4200-072 Porto, Portugal
| | - João Pinto de Sousa
- ‡‡Faculty of Medicine of the University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Ulla Mandel
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark;
| | - Celso A Reis
- §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal; ‡‡Faculty of Medicine of the University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; §§Institute of Biomedical Sciences Abel Salazar, ICBAS, Rua de Jorge Viterbo Ferreira n.228, 4050-313 Porto, Portugal
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117
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Hofmann BT, Schlüter L, Lange P, Mercanoglu B, Ewald F, Fölster A, Picksak AS, Harder S, El Gammal AT, Grupp K, Güngör C, Drenckhan A, Schlüter H, Wagener C, Izbicki JR, Jücker M, Bockhorn M, Wolters-Eisfeld G. COSMC knockdown mediated aberrant O-glycosylation promotes oncogenic properties in pancreatic cancer. Mol Cancer 2015; 14:109. [PMID: 26021314 PMCID: PMC4447007 DOI: 10.1186/s12943-015-0386-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 05/12/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Human pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal malignancies in the world and despite great efforts in research types of treatment remain limited. A frequently detected alteration in PDACs is a truncated O-linked N-acetylgalactosamine (GalNAc) glycosylation with expression of the Tn antigen. Changes in O-glycosylation affect posttranslationally modified O-GalNAc proteins resulting in profound cellular alterations. Tn antigen is a tumor associated glycan detected in 75-90 % of PDACs and up to 67 % in its precursor lesions. Since the role of Tn antigen expression in PDAC is insufficiently understood we analyzed the impact of COSMC mediated Tn antigen expression in two human PDAC cell lines on cellular oncogenic properties. METHODS Forced expression of Tn antigen on O-glycosylated proteins in pancreatic cancer cells was induced by lentiviral-mediated knockdown of the COSMC chaperone, which prevented O-glycan elongation beyond the initial GalNAcα1- residue on O-linked glycoproteins. Altered O-GalNAc glycosylation was analyzed in human pancreatic cancer cell lines Panc-1 and L3.6pl using Western and Far-Western blot as well as immunocytochemical techniques. To assess the biological implications of COSMC function on oncogenic properties, cell viability assays, scratch assays combined with live cell imaging, migration and apoptosis assays were performed. Lectin based glycoprotein enrichment with subsequent mass spectrometric analysis identified new cancer O-GalNAc modified proteins. Expression of Tn antigen bearing Nucleolin in patient derived PDAC tumor specimens was evaluated and correlated with clinicopathological data. RESULTS Tn antigen expression was induced on various O-GalNAc glycoproteins in COSMC deficient cell lines compared to the control. Proliferation was reduced (p < 0.001) in COSMC knockdown cells, whereas migration was increased (p < 0.001) and apoptosis was decreased (p = 0.03), highlighting the importance of Tn antigen expression on metastatic and anti-apoptotic behavior of PDAC derived cells. Nucleolin was identified as O-GalNAc modified protein in COSMC deficient PDAC cell lines. Interestingly, immunohistochemical staining and co-localization studies of patient derived PDACs revealed poor survival for patients with strong co-localization of Tn antigen and Nucleolin (p = 0.037). CONCLUSION This study substantiates the influence of altered O-glycan (Tn/STn) expression on oncogenic properties in pancreatic cancer and identifies O-GalNAc modified Nucleolin as novel prognostic marker.
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Affiliation(s)
- Bianca T Hofmann
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
- Department of Anatomy and Experimental Morphology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Laura Schlüter
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Philip Lange
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Baris Mercanoglu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Florian Ewald
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Aljonna Fölster
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Aeint-Steffen Picksak
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Sönke Harder
- Department of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Alexander T El Gammal
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Katharina Grupp
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Cenap Güngör
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Astrid Drenckhan
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Hartmut Schlüter
- Department of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Christoph Wagener
- Department of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Manfred Jücker
- Institute for Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Maximilian Bockhorn
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Gerrit Wolters-Eisfeld
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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118
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Beatson R, Maurstad G, Picco G, Arulappu A, Coleman J, Wandell HH, Clausen H, Mandel U, Taylor-Papadimitriou J, Sletmoen M, Burchell JM. The Breast Cancer-Associated Glycoforms of MUC1, MUC1-Tn and sialyl-Tn, Are Expressed in COSMC Wild-Type Cells and Bind the C-Type Lectin MGL. PLoS One 2015; 10:e0125994. [PMID: 25951175 PMCID: PMC4423978 DOI: 10.1371/journal.pone.0125994] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/27/2015] [Indexed: 11/19/2022] Open
Abstract
Aberrant glycosylation occurs in the majority of human cancers and changes in mucin-type O-glycosylation are key events that play a role in the induction of invasion and metastases. These changes generate novel cancer-specific glyco-antigens that can interact with cells of the immune system through carbohydrate binding lectins. Two glyco-epitopes that are found expressed by many carcinomas are Tn (GalNAc-Ser/Thr) and STn (NeuAcα2,6GalNAc-Ser/Thr). These glycans can be carried on many mucin-type glycoproteins including MUC1. We show that the majority of breast cancers carry Tn within the same cell and in close proximity to extended glycan T (Galβ1,3GalNAc) the addition of Gal to the GalNAc being catalysed by the T synthase. The presence of active T synthase suggests that loss of the private chaperone for T synthase, COSMC, does not explain the expression of Tn and STn in breast cancer cells. We show that MUC1 carrying both Tn or STn can bind to the C-type lectin MGL and using atomic force microscopy show that they bind to MGL with a similar dead adhesion force. Tumour associated STn is associated with poor prognosis and resistance to chemotherapy in breast carcinomas, inhibition of DC maturation, DC apoptosis and inhibition of NK activity. As engagement of MGL in the absence of TLR triggering may lead to anergy, the binding of MUC1-STn to MGL may be in part responsible for some of the characteristics of STn expressing tumours.
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Affiliation(s)
- Richard Beatson
- Breast Cancer Biology, King’s College London, Guy’s Hospital, London, SE1 9RT, United Kingdom
| | - Gjertrud Maurstad
- Department of Physics, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Gianfranco Picco
- Breast Cancer Biology, King’s College London, Guy’s Hospital, London, SE1 9RT, United Kingdom
| | - Appitha Arulappu
- Breast Cancer Biology, King’s College London, Guy’s Hospital, London, SE1 9RT, United Kingdom
| | - Julia Coleman
- Breast Cancer Biology, King’s College London, Guy’s Hospital, London, SE1 9RT, United Kingdom
| | - Hans H. Wandell
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Ulla Mandel
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | | | - Marit Sletmoen
- Department of Physics, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Joy M. Burchell
- Breast Cancer Biology, King’s College London, Guy’s Hospital, London, SE1 9RT, United Kingdom
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119
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Lira-Navarrete E, de las Rivas M, Compañón I, Pallarés MC, Kong Y, Iglesias-Fernández J, Bernardes GJL, Peregrina JM, Rovira C, Bernadó P, Bruscolini P, Clausen H, Lostao A, Corzana F, Hurtado-Guerrero R. Dynamic interplay between catalytic and lectin domains of GalNAc-transferases modulates protein O-glycosylation. Nat Commun 2015; 6:6937. [PMID: 25939779 PMCID: PMC4432651 DOI: 10.1038/ncomms7937] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/16/2015] [Indexed: 01/07/2023] Open
Abstract
Protein O-glycosylation is controlled by polypeptide GalNAc-transferases (GalNAc-Ts) that uniquely feature both a catalytic and lectin domain. The underlying molecular basis of how the lectin domains of GalNAc-Ts contribute to glycopeptide specificity and catalysis remains unclear. Here we present the first crystal structures of complexes of GalNAc-T2 with glycopeptides that together with enhanced sampling molecular dynamics simulations demonstrate a cooperative mechanism by which the lectin domain enables free acceptor sites binding of glycopeptides into the catalytic domain. Atomic force microscopy and small-angle X-ray scattering experiments further reveal a dynamic conformational landscape of GalNAc-T2 and a prominent role of compact structures that are both required for efficient catalysis. Our model indicates that the activity profile of GalNAc-T2 is dictated by conformational heterogeneity and relies on a flexible linker located between the catalytic and the lectin domains. Our results also shed light on how GalNAc-Ts generate dense decoration of proteins with O-glycans.
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Affiliation(s)
- Erandi Lira-Navarrete
- BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
| | - Matilde de las Rivas
- BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
| | - Ismael Compañón
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | | | - Yun Kong
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Javier Iglesias-Fernández
- Departament de Química Orgànica i IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, 1649-028 Lisboa, Portugal
| | - Jesús M. Peregrina
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | - Carme Rovira
- Departament de Química Orgànica i IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- ICREA, Passeig Lluís Companys 23, 08020 Barcelona, Spain
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université Montpellier 1 and 2, 29 rue de Navacelles, 34090 Montpellier, France
| | - Pierpaolo Bruscolini
- BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
- Departamento de Física Teórica, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Anabel Lostao
- LMA, INA, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Fundación ARAID, 50018 Zaragoza, Spain
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | - Ramon Hurtado-Guerrero
- BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
- Fundación ARAID, 50018 Zaragoza, Spain
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120
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Trnka T, Kozmon S, Tvaroška I, Koča J. Stepwise catalytic mechanism via short-lived intermediate inferred from combined QM/MM MERP and PES calculations on retaining glycosyltransferase ppGalNAcT2. PLoS Comput Biol 2015; 11:e1004061. [PMID: 25849117 PMCID: PMC4388629 DOI: 10.1371/journal.pcbi.1004061] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 11/26/2014] [Indexed: 11/18/2022] Open
Abstract
The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals.
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Affiliation(s)
- Tomáš Trnka
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Faculty of Science—National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Stanislav Kozmon
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Faculty of Science—National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- On leave from the Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Igor Tvaroška
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Jaroslav Koča
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Faculty of Science—National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
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121
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Yen-Nicolaÿ S, Boursier C, Rio M, Lefeber DJ, Pilon A, Seta N, Bruneel A. MALDI-TOF MS applied to apoC-III glycoforms of patients with congenital disorders affecting O-glycosylation. Comparison with two-dimensional electrophoresis. Proteomics Clin Appl 2015; 9:787-93. [PMID: 25641685 DOI: 10.1002/prca.201400187] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/07/2015] [Indexed: 11/06/2022]
Abstract
PURPOSE The O-glycan abnormalities accompanying some congenital disorders of glycosylation, namely conserved oligomeric Golgi-congenital disorders of glycosylation (COG-CDGs) and ATP6V0A2-CDGs, are mainly detected using electrophoresis methods applied to circulating apolipoprotein C-III. The objective of this study was to evaluate the reliability of MALDI-TOF MS of apoC-III for the detection and characterization of CDG-associated O-glycan defects. EXPERIMENTAL DESIGN plasmas from CDG-negative, COG-CDG, and ATP6V0A2-CDG patients were analyzed and results were compared to those obtained using 2DE followed by Western blot. RESULTS MALDI-TOF of apoC-III allowed to detect various significant O-glycan abnormalities in CDG-patients with emphasis to COG-CDG. Furthermore, in CDG samples, comparison study between 2DE and MALDI-TOF showed a particular behavior of monosialylated apoC-III in the mass spectrometer that could be related to an abnormal O-glycan structure. CONCLUSIONS AND CLINICAL RELEVANCE MALDI-TOF MS appears as a powerful technique for the analysis of apoC-III glycoforms for potential routine screening of COG- and ATP6V0A2-CDGs.
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Affiliation(s)
| | - Céline Boursier
- Trans-Prot, Proteomic facility, Université Paris-Sud, Châtenay-Malabry, France
| | - Marlène Rio
- Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Dirk J Lefeber
- Laboratory of Genetics, Endocrine and Metabolic Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Antoine Pilon
- EA4530, Dynamique des microtubules en physiopathologie, Faculté de Pharmacie, Université Paris-Sud, Châtenay-Malabry, France.,APHP, Unité d'Hormonologie et Immunoanalyse, Pôle de Biologie Médicale et Pathologie, Hôpitaux Universitaires Est Parisien, Paris, France
| | - Nathalie Seta
- AP-HP, Biochimie métabolique et cellulaire, hôpital Bichat, Paris, France
| | - Arnaud Bruneel
- EA4530, Dynamique des microtubules en physiopathologie, Faculté de Pharmacie, Université Paris-Sud, Châtenay-Malabry, France.,AP-HP, Biochimie métabolique et cellulaire, hôpital Bichat, Paris, France
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122
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Ju T, Aryal RP, Kudelka MR, Wang Y, Cummings RD. The Cosmc connection to the Tn antigen in cancer. Cancer Biomark 2015; 14:63-81. [PMID: 24643043 DOI: 10.3233/cbm-130375] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The Tn antigen is a tumor-associated carbohydrate antigen that is not normally expressed in peripheral tissues or blood cells. Expression of this antigen, which is found in a majority of human carcinomas of all types, arises from a blockage in the normal O-glycosylation pathway in which glycans are extended from the common precursor GalNAcα1-O-Ser/Thr (Tn antigen). This precursor is generated in the Golgi apparatus on newly synthesized glycoproteins by a family of polypeptide α-N-acetylgalactosaminyltransferases (ppGalNAcTs) and then extended to the common core 1 O-glycan Galβ1-3GalNAcα1-O-Ser/Thr (T antigen) by a single enzyme termed the T-synthase (core 1 β3-galactosyltransferase or C1GalT). Formation of the active form of the T-synthase requires a unique molecular chaperone termed Cosmc, encoded by Cosmc on the X-chromosome (Xq24 in humans, Xc3 in mice). Cosmc resides in the endoplasmic reticulum (ER) and prevents misfolding, aggregation, and proteasome-dependent degradation of newly synthesized T-synthase. Loss of expression of active T-synthase or Cosmc can lead to expression of the Tn antigen, along with its sialylated version Sialyl Tn antigen as observed in several cancers. Both genetic and epigenetic pathways, in addition to potential metabolic regulation, can result in abnormal expression of the Tn antigen. Engineered expression of the Tn antigen by disruption of either C1GalT (T-syn) or Cosmc in mice is associated with a tremendous range of pathologies and engineered expression of the Tn antigen in mouse embryos leads to embryonic death. Studies indicate that many membrane glycoproteins expressing the Tn antigen and/or truncated O-glycans may be dysfunctional, due to degradation and/or misfolding. Thus, expression of normal O-glycans is associated with health and homeostasis whereas truncation of O-glycans, e.g. the Tn and/or Sialyl Tn antigens is associated with cancer and other pathologies.
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Affiliation(s)
- Tongzhong Ju
- Department of Biochemistry and the Emory Glycomics Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Rajindra P Aryal
- Department of Biochemistry and the Emory Glycomics Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Matthew R Kudelka
- Department of Biochemistry and the Emory Glycomics Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Yingchun Wang
- Department of Biochemistry and the Emory Glycomics Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard D Cummings
- Department of Biochemistry and the Emory Glycomics Center, Emory University School of Medicine, Atlanta, GA, USA
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123
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Nordén R, Halim A, Nyström K, Bennett EP, Mandel U, Olofsson S, Nilsson J, Larson G. O-linked glycosylation of the mucin domain of the herpes simplex virus type 1-specific glycoprotein gC-1 is temporally regulated in a seed-and-spread manner. J Biol Chem 2014; 290:5078-5091. [PMID: 25548287 DOI: 10.1074/jbc.m114.616409] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The herpes simplex virus type 1 (HSV-1) glycoprotein gC-1, participating in viral receptor interactions and immunity interference, harbors a mucin-like domain with multiple clustered O-linked glycans. Using HSV-1-infected diploid human fibroblasts, an authentic target for HSV-1 infection, and a protein immunoaffinity procedure, we enriched fully glycosylated gC-1 and a series of its biosynthetic intermediates. This fraction was subjected to trypsin digestion and a LC-MS/MS glycoproteomics approach. In parallel, we characterized the expression patterns of the 20 isoforms of human GalNAc transferases responsible for initiation of O-linked glycosylation. The gC-1 O-glycosylation was regulated in an orderly manner initiated by synchronous addition of one GalNAc unit each to Thr-87 and Thr-91 and one GalNAc unit to either Thr-99 or Thr-101, forming a core glycopeptide for subsequent additions of in all 11 GalNAc residues to selected Ser and Thr residues of the Thr-76-Lys-107 stretch of the mucin domain. The expression patterns of GalNAc transferases in the infected cells suggested that initial additions of GalNAc were carried out by initiating GalNAc transferases, in particular GalNAc-T2, whereas subsequent GalNAc additions were carried out by followup transferases, in particular GalNAc-T10. Essentially all of the susceptible Ser or Thr residues had to acquire their GalNAc units before any elongation to longer O-linked glycans of the gC-1-associated GalNAc units was permitted. Because the GalNAc occupancy pattern is of relevance for receptor binding of gC-1, the data provide a model to delineate biosynthetic steps of O-linked glycosylation of the gC-1 mucin domain in HSV-1-infected target cells.
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Affiliation(s)
- Rickard Nordén
- From the Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, DK-2200 Copenhagen, Denmark, and; Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Kristina Nyström
- From the Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, DK-2200 Copenhagen, Denmark, and
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, University of Copenhagen, DK-2200 Copenhagen, Denmark, and
| | - Sigvard Olofsson
- From the Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden.
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124
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Pan M, Li S, Li X, Shao F, Liu L, Hu HG. Synthesis of and Specific Antibody Generation for Glycopeptides with ArginineN-GlcNAcylation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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125
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Pan M, Li S, Li X, Shao F, Liu L, Hu HG. Synthesis of and Specific Antibody Generation for Glycopeptides with ArginineN-GlcNAcylation. Angew Chem Int Ed Engl 2014; 53:14517-21. [DOI: 10.1002/anie.201407824] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/13/2014] [Indexed: 12/23/2022]
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126
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Ricardo S, Marcos-Silva L, Pereira D, Pinto R, Almeida R, Söderberg O, Mandel U, Clausen H, Felix A, Lunet N, David L. Detection of glyco-mucin profiles improves specificity of MUC16 and MUC1 biomarkers in ovarian serous tumours. Mol Oncol 2014; 9:503-12. [PMID: 25454345 DOI: 10.1016/j.molonc.2014.10.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/11/2014] [Accepted: 10/17/2014] [Indexed: 11/15/2022] Open
Abstract
The CA125 assay detects circulating MUC16 and is one of the most widely used cancer biomarkers for the follow-up of ovarian cancer. We previously demonstrated that detection of aberrant cancer-associated glycoforms of MUC16 as well as MUC1 in circulation could improve the yield of these serum assays. Our aim was to refine ovarian cancer biomarkers by detection of aberrant glycoforms (Tn, STn, and T) of MUC16 and MUC1 in ovarian cancer tissue using Proximity Ligation Assays (PLA). We studied two series of serous ovarian tumours, a pilot series of 66 ovarian tumours (27 cystadenomas, 16 borderline tumours and 23 adenocarcinomas) from Centro Hospitalar S. João, Porto and a validation series of 89 ovarian tumours (17 cystadenomas, 25 borderline tumours and 47 adenocarcinomas) from the Portuguese Institute of Oncology Francisco Gentil, Lisbon. PLA reactions for MUC16/Tn, MUC16/STn, MUC1/Tn and MUC1/STn were negative in benign lesions but often positive in borderline and malignant lesions, in both series. An even better yield was obtained based on positivity for any of the four glyco-mucin profiles, further increasing sensitivity to 72% and 83% in the two series, respectively, with 100% specificity. The strategy is designated glyco-mucin profiling and provides strong support for development of PLA-based serum assays for early diagnosis.
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Affiliation(s)
- Sara Ricardo
- IPATIMUP, Institute of Molecular Pathology and Immunology of The University of Porto, Portugal
| | - Lara Marcos-Silva
- IPATIMUP, Institute of Molecular Pathology and Immunology of The University of Porto, Portugal; Faculty of Medicine of The University of Porto, Porto, Portugal; Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniela Pereira
- IPATIMUP, Institute of Molecular Pathology and Immunology of The University of Porto, Portugal
| | - Rita Pinto
- IPATIMUP, Institute of Molecular Pathology and Immunology of The University of Porto, Portugal
| | - Raquel Almeida
- IPATIMUP, Institute of Molecular Pathology and Immunology of The University of Porto, Portugal; Faculty of Medicine of The University of Porto, Porto, Portugal; Department of Biology, Faculty of Sciences of The University of Porto, Porto, Portugal
| | - Ola Söderberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ana Felix
- Instituto Português de Oncologia de Lisboa, Lisboa, Portugal; Faculdade de Ciências Médicas - CEDOC, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Nuno Lunet
- Department of Clinical Epidemiology, Predictive Medicine and Public Health, Faculty of Medicine, University of Porto, Porto, Portugal; Institute of Public Health, University of Porto (ISPUP), Porto, Portugal
| | - Leonor David
- IPATIMUP, Institute of Molecular Pathology and Immunology of The University of Porto, Portugal; Faculty of Medicine of The University of Porto, Porto, Portugal.
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Levery SB, Steentoft C, Halim A, Narimatsu Y, Clausen H, Vakhrushev SY. Advances in mass spectrometry driven O-glycoproteomics. Biochim Biophys Acta Gen Subj 2014; 1850:33-42. [PMID: 25284204 DOI: 10.1016/j.bbagen.2014.09.026] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Global analyses of proteins and their modifications by mass spectrometry are essential tools in cell biology and biomedical research. Analyses of glycoproteins represent particular challenges and we are only at the beginnings of the glycoproteomic era. Some of the challenges have been overcome with N-glycoproteins and proteome-wide analysis of N-glycosylation sites is accomplishable today but only by sacrificing information of structures at individual glycosites. More recently advances in analysis of O-glycoproteins have been made and proteome-wide analysis of O-glycosylation sites is becoming available as well. SCOPE OF REVIEW Here we discuss the challenges of analysis of O-glycans and new O-glycoproteomics strategies focusing on O-GalNAc and O-Man glycoproteomes. MAJOR CONCLUSIONS A variety of strategies are now available for proteome-wide analysis of O-glycosylation sites enabling functional studies. However, further developments are still needed for complete analysis of glycan structures at individual sites for both N- and O-glycoproteomics strategies. GENERAL SIGNIFICANCE The advances in O-glycoproteomics have led to identification of new biological functions of O-glycosylation and a new understanding of the importance of where O-glycans are positioned on proteins.
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Affiliation(s)
- Steven B Levery
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Catharina Steentoft
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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128
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Pan Y, Karagiannis K, Zhang H, Dingerdissen H, Shamsaddini A, Wan Q, Simonyan V, Mazumder R. Human germline and pan-cancer variomes and their distinct functional profiles. Nucleic Acids Res 2014; 42:11570-88. [PMID: 25232094 PMCID: PMC4191387 DOI: 10.1093/nar/gku772] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Identification of non-synonymous single nucleotide variations (nsSNVs) has exponentially increased due to advances in Next-Generation Sequencing technologies. The functional impacts of these variations have been difficult to ascertain because the corresponding knowledge about sequence functional sites is quite fragmented. It is clear that mapping of variations to sequence functional features can help us better understand the pathophysiological role of variations. In this study, we investigated the effect of nsSNVs on more than 17 common types of post-translational modification (PTM) sites, active sites and binding sites. Out of 1 705 285 distinct nsSNVs on 259 216 functional sites we identified 38 549 variations that significantly affect 10 major functional sites. Furthermore, we found distinct patterns of site disruptions due to germline and somatic nsSNVs. Pan-cancer analysis across 12 different cancer types led to the identification of 51 genes with 106 nsSNV affected functional sites found in 3 or more cancer types. 13 of the 51 genes overlap with previously identified Significantly Mutated Genes (Nature. 2013 Oct 17;502(7471)). 62 mutations in these 13 genes affecting functional sites such as DNA, ATP binding and various PTM sites occur across several cancers and can be prioritized for additional validation and investigations.
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Affiliation(s)
- Yang Pan
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Konstantinos Karagiannis
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Haichen Zhang
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Hayley Dingerdissen
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Amirhossein Shamsaddini
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Quan Wan
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Vahan Simonyan
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Raja Mazumder
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA
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129
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Song L, 宋 丽, Bachert C, Schjoldager KT, Clausen H, Linstedt AD. Development of isoform-specific sensors of polypeptide GalNAc-transferase activity. J Biol Chem 2014; 289:30556-30566. [PMID: 25225288 DOI: 10.1074/jbc.m114.599563] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Humans express up to 20 isoforms of GalNAc-transferase (herein T1-T20) that localize to the Golgi apparatus and initiate O-glycosylation. Regulation of this enzyme family affects a vast array of proteins transiting the secretory pathway and diseases arise upon misregulation of specific isoforms. Surprisingly, molecular probes to monitor GalNAc-transferase activity are lacking and there exist no effective global or isoform-specific inhibitors. Here we describe the development of T2- and T3-isoform specific fluorescence sensors that traffic in the secretory pathway. Each sensor yielded little signal when glycosylated but was strongly activated in the absence of its glycosylation. Specificity of each sensor was assessed in HEK cells with either the T2 or T3 enzymes deleted. Although the sensors are based on specific substrates of the T2 and T3 enzymes, elements in or near the enzyme recognition sequence influenced their activity and required modification, which we carried out based on previous in vitro work. Significantly, the modified T2 and T3 sensors were activated only in cells lacking their corresponding isozymes. Thus, we have developed T2- and T3-specific sensors that will be valuable in both the study of GalNAc-transferase regulation and in high-throughput screening for potential therapeutic regulators of specific GalNAc-transferases.
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Affiliation(s)
- Lina Song
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 and
| | - 丽娜 宋
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 and
| | - Collin Bachert
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 and
| | - Katrine T Schjoldager
- Departments of Cellular and Molecular Medicine and School of Dentistry, Copenhagen Center for Glycomics, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Henrik Clausen
- Departments of Cellular and Molecular Medicine and School of Dentistry, Copenhagen Center for Glycomics, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Adam D Linstedt
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 and.
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130
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Lehoux S, Mi R, Aryal RP, Wang Y, Schjoldager KTBG, Clausen H, van Die I, Han Y, Chapman AB, Cummings RD, Ju T. Identification of distinct glycoforms of IgA1 in plasma from patients with immunoglobulin A (IgA) nephropathy and healthy individuals. Mol Cell Proteomics 2014; 13:3097-113. [PMID: 25071157 DOI: 10.1074/mcp.m114.039693] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Immunoglobulin A nephropathy (IgAN) is the most common form of glomerulonephritis worldwide and is histologically characterized by the deposition of IgA1 and consequent inflammation in the glomerular mesangium. Prior studies suggested that serum IgA1 from IgAN patients contains aberrant, undergalactosylated O-glycans, for example, Tn antigen and its sialylated version, SialylTn (STn), but the mechanisms underlying aberrant O-glycosylation are not well understood. Here we have used serial lectin separation technologies, Western blot, enzymatic modifications, and mass spectrometry to explore whether there are different glycoforms of IgA1 in plasma from patients with IgAN and healthy individuals. Although total plasma IgA in IgAN patients was elevated ∼ 1.6-fold compared with that in healthy donors, IgA1 in all samples was unexpectedly separable into two distinct glycoforms: one with core 1 based O-glycans, and the other exclusively containing Tn/STn structures. Importantly, Tn antigen present on IgA1 from IgAN patients and controls was convertible into the core 1 structure in vitro by recombinant T-synthase. Our results demonstrate that undergalactosylation of O-glycans in IgA1 is not restricted to IgAN and suggest that in vivo inefficiency of T-synthase toward IgA1 in a subpopulation of B or plasma cells, as well as overall elevation of IgA, may contribute to IgAN pathogenesis.
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Affiliation(s)
| | | | | | | | - Katrine T-B G Schjoldager
- §Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, Copenhagen, Denmark
| | - Henrik Clausen
- §Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, Copenhagen, Denmark
| | - Irma van Die
- ¶Department of Molecular Cell Biology & Immunology, VU University Medical Center, Amsterdam, The Netherlands
| | - Yoosun Han
- ‖Medicine, Emory University School of Medicine, Atlanta, GA 30322
| | - Arlene B Chapman
- ‖Medicine, Emory University School of Medicine, Atlanta, GA 30322
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Van Breedam W, Pöhlmann S, Favoreel HW, de Groot RJ, Nauwynck HJ. Bitter-sweet symphony: glycan-lectin interactions in virus biology. FEMS Microbiol Rev 2014; 38:598-632. [PMID: 24188132 PMCID: PMC7190080 DOI: 10.1111/1574-6976.12052] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 09/27/2013] [Accepted: 10/14/2013] [Indexed: 01/01/2023] Open
Abstract
Glycans are carbohydrate modifications typically found on proteins or lipids, and can act as ligands for glycan-binding proteins called lectins. Glycans and lectins play crucial roles in the function of cells and organs, and in the immune system of animals and humans. Viral pathogens use glycans and lectins that are encoded by their own or the host genome for their replication and spread. Recent advances in glycobiological research indicate that glycans and lectins mediate key interactions at the virus-host interface, controlling viral spread and/or activation of the immune system. This review reflects on glycan-lectin interactions in the context of viral infection and antiviral immunity. A short introduction illustrates the nature of glycans and lectins, and conveys the basic principles of their interactions. Subsequently, examples are discussed highlighting specific glycan-lectin interactions and how they affect the progress of viral infections, either benefiting the host or the virus. Moreover, glycan and lectin variability and their potential biological consequences are discussed. Finally, the review outlines how recent advances in the glycan-lectin field might be transformed into promising new approaches to antiviral therapy.
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Affiliation(s)
- Wander Van Breedam
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Herman W. Favoreel
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Raoul J. de Groot
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Hans J. Nauwynck
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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132
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Ong YS, Tran THT, Gounko NV, Hong W. TMEM115 is an integral membrane protein of the Golgi complex involved in retrograde transport. J Cell Sci 2014; 127:2825-39. [PMID: 24806965 PMCID: PMC4077589 DOI: 10.1242/jcs.136754] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Searching and evaluating the Human Protein Atlas for transmembrane proteins enabled us to identify an integral membrane protein, TMEM115, that is enriched in the Golgi complex. Biochemical and cell biological analysis suggested that TMEM115 has four candidate transmembrane domains located in the N-terminal region. Both the N- and C-terminal domains are oriented towards the cytoplasm. Immunofluorescence analysis supports that TMEM115 is enriched in the Golgi cisternae. Functionally, TMEM115 knockdown or overexpression delays Brefeldin-A-induced Golgi-to-ER retrograde transport, phenocopying cells with mutations or silencing of the conserved oligomeric Golgi (COG) complex. Co-immunoprecipitation and in vitro binding experiments reveals that TMEM115 interacts with the COG complex, and might self-interact to form dimers or oligomers. A short region (residues 206–229) immediately to the C-terminal side of the fourth transmembrane domain is both necessary and sufficient for Golgi targeting. Knockdown of TMEM115 also reduces the binding of the lectins peanut agglutinin (PNA) and Helix pomatia agglutinin (HPA), suggesting an altered O-linked glycosylation profile. These results establish that TMEM115 is an integral membrane protein of the Golgi stack regulating Golgi-to-ER retrograde transport and is likely to be part of the machinery of the COG complex.
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Affiliation(s)
- Yan Shan Ong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Ton Hoai Thi Tran
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Natalia V Gounko
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore IMB-IMCB Joint Electron Microscopy Suite, 20 Biopolis Street, Singapore 138671, Singapore
| | - Wanjin Hong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore Department of Biochemistry, National University of Singapore, Singapore 117599, Singapore
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133
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Pedersen NB, Wang S, Narimatsu Y, Yang Z, Halim A, Schjoldager KTBG, Madsen TD, Seidah NG, Bennett EP, Levery SB, Clausen H. Low density lipoprotein receptor class A repeats are O-glycosylated in linker regions. J Biol Chem 2014; 289:17312-24. [PMID: 24798328 DOI: 10.1074/jbc.m113.545053] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The low density lipoprotein receptor (LDLR) is crucial for cholesterol homeostasis and deficiency in LDLR functions cause hypercholesterolemia. LDLR is a type I transmembrane protein that requires O-glycosylation for stable expression at the cell surface. It has previously been suggested that LDLR O-glycosylation is found N-terminal to the juxtamembrane region. Recently we identified O-glycosylation sites in the linker regions between the characteristic LDLR class A repeats in several LDLR-related receptors using the "SimpleCell" O-glycoproteome shotgun strategy. Herein, we have systematically characterized O-glycosylation sites on recombinant LDLR shed from HEK293 SimpleCells and CHO wild-type cells. We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position -1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. The glycosites in linker regions of LDLR class A repeats are conserved in LDLR from man to Xenopus and found in other homologous receptors. O-Glycosylation is controlled by a large family of polypeptide GalNAc transferases. Probing into which isoform(s) contributed to glycosylation of the linker regions of the LDLR class A repeats by in vitro enzyme assays suggested a major role of GalNAc-T11. This was supported by expression of LDLR in HEK293 cells, where knock-out of the GalNAc-T11 isoform resulted in the loss of glycosylation of three of four linker regions.
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Affiliation(s)
- Nis Borbye Pedersen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Shengjun Wang
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Yoshiki Narimatsu
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Zhang Yang
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Adnan Halim
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Katrine Ter-Borch Gram Schjoldager
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Thomas Daugbjerg Madsen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Nabil G Seidah
- the Clinical Research Institute of Montreal, University of Montreal, Montreal, Quebec H2W 1R7, Canada
| | - Eric Paul Bennett
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Steven B Levery
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Henrik Clausen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
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134
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He H, Shen Z, Zhang H, Wang X, Tang Z, Xu J, Sun Y. Clinical significance of polypeptide N-acetylgalactosaminyl transferase-5 (GalNAc-T5) expression in patients with gastric cancer. Br J Cancer 2014; 110:2021-9. [PMID: 24619076 PMCID: PMC3992513 DOI: 10.1038/bjc.2014.93] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/30/2013] [Accepted: 01/23/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The family of polypeptide N-acetylgalactosaminyl transferases is responsible for the altered O-linked glycosylation occurring during the development of various cancers and their progression via altering O-glycan biosynthesis. Our studies were designed to investigate the expression and prognostic values of GalNAc-T5 and improve the risk stratification in patients with gastric cancer. METHODS Tissue samples from a training set and a validation set of patients with gastric adenocarcinoma from China were used for analyses. GalNAc-T5 expression was retrospectively analysed by immunohistochemistry. Results were assessed for association with clinicopathological parameters and overall survival by using Kaplan-Meier analysis. Prognostic values of GalNAc-T5 expression and clinical outcomes were evaluated by Cox regression analysis. A molecular prognostic stratification scheme incorporating GalNAc-T5 expression was determined by using receiver operating characteristic analysis. RESULTS GalNAc-T5 expression was markedly reduced in gastric cancer tissues compared with non-malignant gastric mucosa. Low intratumoral GalNAc-T5 density, which was associated with tumour cell differentiation, T classification, N classification, and TNM stage in the two independent sets, was an independent prognosticator for poor prognosis of gastric cancer patients. Applying the prognostic value of intratumoral GalNAc-T5 density to the conventional clinicopathologic TNM stage system showed a better prognostic value in patients with gastric cancer. CONCLUSIONS Intratumoral GalNAc-T5 expression was recognised as an independent prognostic marker for the overall survival of gastric cancer patients. Detection of GalNAc-T5 expression in gastric cancer tissues might add some prognostic information for patients with this disease and lead to a more accurate classification under the TNM stage system.
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Affiliation(s)
- H He
- Department of General Surgery, Zhongshan Hospital, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Z Shen
- Department of General Surgery, Zhongshan Hospital, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - H Zhang
- Department of General Surgery, Zhongshan Hospital, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - X Wang
- Department of General Surgery, Zhongshan Hospital, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Z Tang
- Department of General Surgery, Zhongshan Hospital, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - J Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
- Key Laboratory of Glycoconjugate Research, MOH, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
- Key Laboratory of Medical Molecular Virology, MOE & MOH, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Y Sun
- Department of General Surgery, Zhongshan Hospital, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
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135
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Tagliabracci VS, Engel JL, Wiley SE, Xiao J, Gonzalez DJ, Nidumanda Appaiah H, Koller A, Nizet V, White KE, Dixon JE. Dynamic regulation of FGF23 by Fam20C phosphorylation, GalNAc-T3 glycosylation, and furin proteolysis. Proc Natl Acad Sci U S A 2014; 111:5520-5. [PMID: 24706917 PMCID: PMC3992636 DOI: 10.1073/pnas.1402218111] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The family with sequence similarity 20, member C (Fam20C) has recently been identified as the Golgi casein kinase. Fam20C phosphorylates secreted proteins on Ser-x-Glu/pSer motifs and loss-of-function mutations in the kinase cause Raine syndrome, an often-fatal osteosclerotic bone dysplasia. Fam20C is potentially an upstream regulator of the phosphate-regulating hormone fibroblast growth factor 23 (FGF23), because humans with FAM20C mutations and Fam20C KO mice develop hypophosphatemia due to an increase in full-length, biologically active FGF23. However, the mechanism by which Fam20C regulates FGF23 is unknown. Here we show that Fam20C directly phosphorylates FGF23 on Ser(180), within the FGF23 R(176)XXR(179)/S(180)AE subtilisin-like proprotein convertase motif. This phosphorylation event inhibits O-glycosylation of FGF23 by polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3), and promotes FGF23 cleavage and inactivation by the subtilisin-like proprotein convertase furin. Collectively, our results provide a molecular mechanism by which FGF23 is dynamically regulated by phosphorylation, glycosylation, and proteolysis. Furthermore, our findings suggest that cross-talk between phosphorylation and O-glycosylation of proteins in the secretory pathway may be an important mechanism by which secreted proteins are regulated.
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Affiliation(s)
| | | | | | | | | | - Hitesh Nidumanda Appaiah
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202; and
| | - Antonius Koller
- Stony Brook University Proteomics Center, School of Medicine, Stony Brook University, Stony Brook, NY 11794
| | - Victor Nizet
- Pediatrics
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Kenneth E. White
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202; and
| | - Jack E. Dixon
- Departments of Pharmacology
- Cellular and Molecular Medicine, and
- Chemistry and Biochemistry and
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136
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Kober OI, Ahl D, Pin C, Holm L, Carding SR, Juge N. γδ T-cell-deficient mice show alterations in mucin expression, glycosylation, and goblet cells but maintain an intact mucus layer. Am J Physiol Gastrointest Liver Physiol 2014; 306:G582-93. [PMID: 24503767 PMCID: PMC3962592 DOI: 10.1152/ajpgi.00218.2013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Intestinal homeostasis is maintained by a hierarchy of immune defenses acting in concert to minimize contact between luminal microorganisms and the intestinal epithelial cell surface. The intestinal mucus layer, covering the gastrointestinal tract epithelial cells, contributes to mucosal homeostasis by limiting bacterial invasion. In this study, we used γδ T-cell-deficient (TCRδ(-/-)) mice to examine whether and how γδ T-cells modulate the properties of the intestinal mucus layer. Increased susceptibility of TCRδ(-/-) mice to dextran sodium sulfate (DSS)-induced colitis is associated with a reduced number of goblet cells. Alterations in the number of goblet cells and crypt lengths were observed in the small intestine and colon of TCRδ(-/-) mice compared with C57BL/6 wild-type (WT) mice. Addition of keratinocyte growth factor to small intestinal organoid cultures from TCRδ(-/-) mice showed a marked increase in crypt growth and in both goblet cell number and redistribution along the crypts. There was no apparent difference in the thickness or organization of the mucus layer between TCRδ(-/-) and WT mice, as measured in vivo. However, γδ T-cell deficiency led to reduced sialylated mucins in association with increased gene expression of gel-secreting Muc2 and membrane-bound mucins, including Muc13 and Muc17. Collectively, these data provide evidence that γδ T cells play an important role in the maintenance of mucosal homeostasis by regulating mucin expression and promoting goblet cell function in the small intestine.
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Affiliation(s)
- Olivia I. Kober
- 1Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich, United Kingdom;
| | - David Ahl
- 2Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden; and
| | - Carmen Pin
- 1Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich, United Kingdom;
| | - Lena Holm
- 2Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden; and
| | - Simon R. Carding
- 1Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich, United Kingdom; ,3Faculty of Medical and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Nathalie Juge
- 1Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich, United Kingdom;
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137
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Freire-de-Lima L. Sweet and sour: the impact of differential glycosylation in cancer cells undergoing epithelial-mesenchymal transition. Front Oncol 2014; 4:59. [PMID: 24724053 PMCID: PMC3971198 DOI: 10.3389/fonc.2014.00059] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/11/2014] [Indexed: 01/11/2023] Open
Abstract
Glycosylation changes are a feature of disease states. One clear example is cancer cells, which commonly express glycans at atypical levels or with different structural attributes than those found in normal cells. Epithelial–mesenchymal transition (EMT) was initially recognized as an important step for morphogenesis during embryonic development, and is now shown to be one of the key steps promoting tumor metastasis. Cancer cells undergoing EMT are characterized by significant changes in glycosylation of the extracellular matrix (ECM) components and cell-surface glycoconjugates. Current scientific methodology enables all hallmarks of EMT to be monitored in vitro and this experimental model has been extensively used in oncology research during the last 10 years. Several studies have shown that cell-surface carbohydrates attached to proteins through the amino acids, serine, or threonine (O-glycans), are involved in tumor progression and metastasis, however, the impact of O-glycans on EMT is poorly understood. Recent studies have demonstrated that transforming growth factor-beta (TGF-β), a known EMT inducer, has the ability to promote the up-regulation of a site-specific O-glycosylation in the IIICS domain of human oncofetal fibronectin, a major ECM component expressed by cancer cells and embryonic tissues. Armed with the knowledge that cell-surface glycoconjugates play a major role in the maintenance of cell homeostasis and that EMT is closely associated with glycosylation changes, we may benefit from understanding how unusual glycans can govern the molecular pathways associated with cancer progression. This review initially focuses on some well-known changes found in O-glycans expressed by cancer cells, and then discusses how these alterations may modulate the EMT process.
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Affiliation(s)
- Leonardo Freire-de-Lima
- Laboratório de Glicobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ, Brazil
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138
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Finer G, Price HE, Shore RM, White KE, Langman CB. Hyperphosphatemic familial tumoral calcinosis: response to acetazolamide and postulated mechanisms. Am J Med Genet A 2014; 164A:1545-9. [PMID: 24668887 DOI: 10.1002/ajmg.a.36476] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 01/02/2014] [Indexed: 01/17/2023]
Abstract
Hyperphosphatemic familial tumoral calcinosis (HFTC) is characterized by enhanced renal phosphate absorption, hyperphosphatemia, and tumor-like extraosseous calcifications due to inactivating mutations in FGF23 or associated proteins. Surgical excision is needed when low phosphate diet and phosphate binders are ineffective. Sporadic reports have supported acetazolamide use. We report on a 7-year-old African American boy who presented with severe HFTC requiring numerous surgical excisions. Tumors continued to appear and others reoccurred despite phosphate restriction and sevelamer carbonate. At the age of 9.5 years, acetazolamide (40 mg/kg/day) was added and resulted in mild metabolic acidosis (bicarbonate 25.3 mEq/L vs. 21.4 mEq/L, P < 0.001; serum pH 7.38 vs. 7.31, P = 0.013, pre- and post-acetazolamide, respectively) but no change in tubular reabsorption of phosphate (TRP) (96.9% vs. 95.9%, P = 0.34) or serum phosphate (6.6 mg/dl vs. 6.9 mg/dl, P = 0.52 pre- and post-acetazolamide, respectively). Following the initiation of acetazolamide therapy, the patient experienced significant improvement in disease course as indicated by resolution of localized bone pain, cessation of tumor formation, and no tumor recurrence. Despite mild metabolic acidosis, our patient had improved linear growth and did not develop any other side effects related to therapy. Intact FGF23 remained abnormally low throughout disease course, while C-terminal FGF23 increased with acetazolamide. We conclude that acetazolamide can control severe HFTC by inducing mild metabolic acidosis despite no change in serum phosphate or TRP. This effect may be exerted though improved calcium-phosphate complex solubility and increased FGF23 locally.
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Affiliation(s)
- Gal Finer
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, and Kidney Diseases, The Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois
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139
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Addicted to secrete - novel concepts and targets in cancer therapy. Trends Mol Med 2014; 20:242-50. [PMID: 24456621 DOI: 10.1016/j.molmed.2013.12.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 12/17/2013] [Accepted: 12/19/2013] [Indexed: 12/15/2022]
Abstract
The unfolded protein response (UPR) mediates the adaptation of the secretory pathway (SP) to fluctuations in cellular protein demand or to environmental variations. Recently, drug screenings have confirmed the therapeutic potential of targeting the UPR in cancer models. However, the UPR may not be the only druggable target of the SP. Moreover, recent studies have revealed other contributions of the SP to cancer development. This article does not intend to describe the well-established implication of UPR signaling pathways in cancer cell life and cell decision, but rather aims at defining the concept of 'tumor cell secretory addiction', from molecular, cellular, and therapeutic perspectives. Furthermore, the implication of UPR modulations in this context will be discussed.
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140
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Generation of monoclonal antibodies to native active human glycosyltransferases. Methods Mol Biol 2014; 1022:403-20. [PMID: 23765678 DOI: 10.1007/978-1-62703-465-4_30] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Complex carbohydrates serve a wide range of biological functions in cells and tissues. Their biosynthesis involves more than 200 distinct glycosyltransferases in human cells, and the expression, properties, and topology of these enzymes regulate the glycosylation patterns of proteins and lipids. Glycosyltransferases are ER-Golgi resident enzymes with slow turnover, which makes monitoring of protein expression a method more directly linked to enzyme function, than monitoring gene expression. In situ monitoring of expression and subcellular topology of glycosyltransferase proteins by immunological techniques using monoclonal antibodies therefore provides an excellent strategy to analyze the glycosylation process in cells. A major drawback has been difficulties in generating antibodies to glycosyltransferases and validating their specificities. Here we describe a simple strategy for generating and characterizing monoclonal antibodies to human glycosyltransferases. This strategy includes a process for recombinant production and purification of enzymes for immunization, a simple selection strategy for isolation of antibodies with optimal properties for in situ detection of enzyme expression, and a comprehensive strategy for characterizing the fine specificity of such antibodies.
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141
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Rao R, Xu D, Thelen JJ, Miernyk JA. Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation. BMC Bioinformatics 2013; 14 Suppl 14:S14. [PMID: 24267725 PMCID: PMC3851202 DOI: 10.1186/1471-2105-14-s14-s14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Reversible posttranslational protein modifications such as phosphorylation of Ser/Thr/Tyr and Met oxidation are critical for both metabolic regulation and cellular signalling. Although these modifications are typically studied individually, herein we describe the potential for cross-talk and hierarchical regulation. RESULTS The proximity of Met to Ser/Thr/Tyr within the proteome has not previously been addressed. In order to consider the possibility of a generalized interaction, we performed a trans-kingdom sequence analysis of known phosphorylation sites in proteins from bacteria, fungi, plants, and animals. The proportion of phosphorylation sites that include a Met within a 13-residue window centered upon Ser/Thr/Tyr is significantly less than the occurrence of Met in proximity to all Ser/Thr/Tyr residues. Met residues are present at all positions (-6 to +6, inclusive) within the 13-residue window that we have considered. Detailed analysis of sequences from eight disparate plant taxa revealed that many conserved phosphorylation sites have a Met residue in the proximity. Results from GO enrichment analysis indicated that the potential for phosphorylation and Met oxidation crosstalk is most prevalent in kinases and proteins involved in signalling. CONCLUSION The large proportion of known phosphorylation sites with Met in the proximity fulfils the necessary condition for cross-talk. Kinases/signalling proteins are enriched for Met around phosphorylation sites. These proteins/sites are likely candidates for cross-talk between oxidative signalling and reversible phosphorylation.
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142
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Mining the O-mannose glycoproteome reveals cadherins as major O-mannosylated glycoproteins. Proc Natl Acad Sci U S A 2013; 110:21018-23. [PMID: 24101494 DOI: 10.1073/pnas.1313446110] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The metazoan O-mannose (O-Man) glycoproteome is largely unknown. It has been shown that up to 30% of brain O-glycans are of the O-Man type, but essentially only alpha-dystroglycan (α-DG) of the dystrophin-glycoprotein complex is well characterized as an O-Man glycoprotein. Defects in O-Man glycosylation underlie congenital muscular dystrophies and considerable efforts have been devoted to explore this O-glycoproteome without much success. Here, we used our SimpleCell strategy using nuclease-mediated gene editing of a human cell line (MDA-MB-231) to reduce the structural heterogeneity of O-Man glycans and to probe the O-Man glycoproteome. In this breast cancer cell line we found that O-Man glycosylation is primarily found on cadherins and plexins on β-strands in extracellular cadherin and Ig-like, plexin and transcription factor domains. The positions and evolutionary conservation of O-Man glycans in cadherins suggest that they play important functional roles for this large group of cell adhesion glycoproteins, which can now be addressed. The developed O-Man SimpleCell strategy is applicable to most types of cell lines and enables proteome-wide discovery of O-Man protein glycosylation.
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143
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Morgan GW, Kail M, Hollinshead M, Vaux DJ. Combined biochemical and cytological analysis of membrane trafficking using lectins. Anal Biochem 2013; 441:21-31. [PMID: 23756734 DOI: 10.1016/j.ab.2013.05.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 05/30/2013] [Accepted: 05/31/2013] [Indexed: 02/03/2023]
Abstract
We have tested the application of high-mannose-binding lectins as analytical reagents to identify N-glycans in the early secretory pathway of HeLa cells during subcellular fractionation and cytochemistry. Post-endoplasmic reticulum (ER) pre-Golgi intermediates were separated from the ER on Nycodenz-sucrose gradients, and the glycan composition of each gradient fraction was profiled using lectin blotting. The fractions containing the post-ER pre-Golgi intermediates are found to contain a subset of N-linked α-mannose glycans that bind the lectins Galanthus nivalis agglutinin (GNA), Pisum sativum agglutinin (PSA), and Lens culinaris agglutinin (LCA) but not lectins binding Golgi-modified glycans. Cytochemical analysis demonstrates that high-mannose-containing glycoproteins are predominantly localized to the ER and the early secretory pathway. Indirect immunofluorescence microscopy revealed that GNA colocalizes with the ER marker protein disulfide isomerase (PDI) and the COPI coat protein β-COP. In situ competition with concanavalin A (ConA), another high-mannose specific lectin, and subsequent GNA lectin histochemistry refined the localization of N-glyans containing nonreducing mannosyl groups, accentuating the GNA vesicular staining. Using GNA and treatments that perturb ER-Golgi transport, we demonstrate that lectins can be used to detect changes in membrane trafficking pathways histochemically. Overall, we find that conjugated plant lectins are effective tools for combinatory biochemical and cytological analysis of membrane trafficking of glycoproteins.
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Affiliation(s)
- Gareth W Morgan
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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144
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Agarwal K, Kaul R, Garg M, Shajahan A, Jha SK, Sampathkumar SG. Inhibition of mucin-type O-glycosylation through metabolic processing and incorporation of N-thioglycolyl-D-galactosamine peracetate (Ac5GalNTGc). J Am Chem Soc 2013; 135:14189-97. [PMID: 23987472 DOI: 10.1021/ja405189k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mucin-type O-glycans form one of the most abundant and complex post-translational modifications (PTM) on cell surface proteins that govern adhesion, migration, and trafficking of hematopoietic cells. Development of targeted approaches to probe functions of O-glycans is at an early stage. Among several approaches, small molecules with unique chemical functional groups that could modulate glycan biosynthesis form a critical tool. Herein, we show that metabolism of peracetyl N-acyl-D-galactosamine derivatives carrying an N-thioglycolyl (Ac5GalNTGc, 1) moiety-but not N-glycolyl (Ac5GalNGc, 2) and N-acetyl (Ac4GalNAc, 3)-through the N-acetyl-D-galactosamine (GalNAc) salvage pathway induced abrogation of MAL-II and PNA epitopes in Jurkat cells. Mass spectrometry of permethylated O-glycans from Jurkat cells confirmed the presence of significant amounts of elaborated O-glycans (sialyl-T and disialyl-T) which were inhibited upon treatment with 1. O-Glycosylation of CD43, a cell surface antigen rich in O-glycans, was drastically reduced by 1 in a thiol-dependent manner. By contrast, only mild effects were observed for CD45 glycoforms. Direct metabolic incorporation of 1 was confirmed by thiol-selective Michael addition reaction of immunoprecipitated CD43-myc/FLAG. Mechanistically, CD43 glycoforms were unperturbed by peracetylated N-(3-acetylthiopropanoyl) (4), N-(4-acetylthiobutanoyl) (5), and N-methylthioacetyl (6) galactosamine derivatives, N-thioglycolyl-D-glucosamine (7, C-4 epimer of 1), and α-O-benzyl 2-acetamido-2-deoxy-D-galactopyranoside (8), confirming the critical requirement of both free sulfhydryl and galactosamine moieties for inhibition of mucin-type O-glycans. Similar, yet differential, effects of 1 were observed for CD43 glycoforms in multiple hematopoietic cells. Development of small molecules that could alter glycan patterns in an antigen-selective and cell-type selective manner might provide avenues for understanding biological functions of glycans.
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Affiliation(s)
- Kavita Agarwal
- Laboratory of Chemical Glycobiology (CGB), National Institute of Immunology (NII) , Aruna Asaf Ali Marg, New Delhi 110067, India
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145
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Gerken TA, Revoredo L, Thome JJC, Tabak LA, Vester-Christensen MB, Clausen H, Gahlay GK, Jarvis DL, Johnson RW, Moniz HA, Moremen K. The lectin domain of the polypeptide GalNAc transferase family of glycosyltransferases (ppGalNAc Ts) acts as a switch directing glycopeptide substrate glycosylation in an N- or C-terminal direction, further controlling mucin type O-glycosylation. J Biol Chem 2013; 288:19900-14. [PMID: 23689369 PMCID: PMC3707691 DOI: 10.1074/jbc.m113.477877] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/17/2013] [Indexed: 01/22/2023] Open
Abstract
Mucin type O-glycosylation is initiated by a large family of polypeptide GalNAc transferases (ppGalNAc Ts) that add α-GalNAc to the Ser and Thr residues of peptides. Of the 20 human isoforms, all but one are composed of two globular domains linked by a short flexible linker: a catalytic domain and a ricin-like lectin carbohydrate binding domain. Presently, the roles of the catalytic and lectin domains in peptide and glycopeptide recognition and specificity remain unclear. To systematically study the role of the lectin domain in ppGalNAc T glycopeptide substrate utilization, we have developed a series of novel random glycopeptide substrates containing a single GalNAc-O-Thr residue placed near either the N or C terminus of the glycopeptide substrate. Our results reveal that the presence and N- or C-terminal placement of the GalNAc-O-Thr can be important determinants of overall catalytic activity and specificity that differ between transferase isoforms. For example, ppGalNAc T1, T2, and T14 prefer C-terminally placed GalNAc-O-Thr, whereas ppGalNAc T3 and T6 prefer N-terminally placed GalNAc-O-Thr. Several transferase isoforms, ppGalNAc T5, T13, and T16, display equally enhanced N- or C-terminal activities relative to the nonglycosylated control peptides. This N- and/or C-terminal selectivity is presumably due to weak glycopeptide binding to the lectin domain, whose orientation relative to the catalytic domain is dynamic and isoform-dependent. Such N- or C-terminal glycopeptide selectivity provides an additional level of control or fidelity for the O-glycosylation of biologically significant sites and suggests that O-glycosylation may in some instances be exquisitely controlled.
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Affiliation(s)
- Thomas A. Gerken
- From the Departments of Pediatrics (W. A. Bernbaum Center for Cystic Fibrosis Research)
- Biochemistry, and
- Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Leslie Revoredo
- Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Joseph J. C. Thome
- From the Departments of Pediatrics (W. A. Bernbaum Center for Cystic Fibrosis Research)
| | - Lawrence A. Tabak
- the Section on Biological Chemistry, NIDCR, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892
| | - Malene Bech Vester-Christensen
- the Copenhagen Center for Glycomics (CCG), Departments of Cellular and Molecular Medicine and Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- the Copenhagen Center for Glycomics (CCG), Departments of Cellular and Molecular Medicine and Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Gagandeep K. Gahlay
- the Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, and
| | - Donald L. Jarvis
- the Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, and
| | - Roy W. Johnson
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Heather A. Moniz
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Kelley Moremen
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
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Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KTBG, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Paul Bennett E, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H. Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J 2013; 32:1478-88. [PMID: 23584533 PMCID: PMC3655468 DOI: 10.1038/emboj.2013.79] [Citation(s) in RCA: 1014] [Impact Index Per Article: 92.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/18/2013] [Indexed: 12/12/2022] Open
Abstract
Glycosylation is the most abundant and diverse posttranslational modification of proteins. While several types of glycosylation can be predicted by the protein sequence context, and substantial knowledge of these glycoproteomes is available, our knowledge of the GalNAc-type O-glycosylation is highly limited. This type of glycosylation is unique in being regulated by 20 polypeptide GalNAc-transferases attaching the initiating GalNAc monosaccharides to Ser and Thr (and likely some Tyr) residues. We have developed a genetic engineering approach using human cell lines to simplify O-glycosylation (SimpleCells) that enables proteome-wide discovery of O-glycan sites using 'bottom-up' ETD-based mass spectrometric analysis. We implemented this on 12 human cell lines from different organs, and present a first map of the human O-glycoproteome with almost 3000 glycosites in over 600 O-glycoproteins as well as an improved NetOGlyc4.0 model for prediction of O-glycosylation. The finding of unique subsets of O-glycoproteins in each cell line provides evidence that the O-glycoproteome is differentially regulated and dynamic. The greatly expanded view of the O-glycoproteome should facilitate the exploration of how site-specific O-glycosylation regulates protein function.
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Affiliation(s)
- Catharina Steentoft
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
- Center for Biological Sequence Analysis, Department of Systems Biology Technical University of Denmark, Lyngby, Denmark
| | - Yun Kong
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Malene B Vester-Christensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Katrine T-B G Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Kirstine Lavrsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Sally Dabelsteen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Nis B Pedersen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Lara Marcos-Silva
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Ramneek Gupta
- Center for Biological Sequence Analysis, Department of Systems Biology Technical University of Denmark, Lyngby, Denmark
| | - Eric Paul Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Steven B Levery
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
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147
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RNAi screening reveals a large signaling network controlling the Golgi apparatus in human cells. Mol Syst Biol 2013; 8:629. [PMID: 23212246 PMCID: PMC3542528 DOI: 10.1038/msb.2012.59] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 10/11/2012] [Indexed: 12/11/2022] Open
Abstract
RNAi screening and automated image analysis reveal 180 kinases and phosphatases regulating the organization of the Golgi apparatus. Most of these genes also control the expression of specific glycans, pointing to a web of interactions between signaling cascades and glycosylation at the Golgi. ![]()
Golgi organization was probed with three markers of different Golgi compartments and quantitative morphological analysis. Knockdowns of ∼20% of all known kinases and phosphatases affected the Golgi globally or in a compartment-specific manner, and were comparable in degree to the depletion of known membrane traffic regulators such as SNAREs. Several cell surface receptors, their cognate ligands and downstream effectors regulate Golgi organization, suggesting a large regulatory network. Most signaling genes affected both Golgi morphology and the expression of specific glycans.
The Golgi apparatus has many important physiological functions, including sorting of secretory cargo and biosynthesis of complex glycans. These functions depend on the intricate and compartmentalized organization of the Golgi apparatus. To investigate the mechanisms that regulate Golgi architecture, we developed a quantitative morphological assay using three different Golgi compartment markers and quantitative image analysis, and performed a kinome- and phosphatome-wide RNAi screen in HeLa cells. Depletion of 159 signaling genes, nearly 20% of genes assayed, induced strong and varied perturbations in Golgi morphology. Using bioinformatics data, a large regulatory network could be constructed. Specific subnetworks are involved in phosphoinositides regulation, acto-myosin dynamics and mitogen activated protein kinase signaling. Most gene depletion also affected Golgi functions, in particular glycan biosynthesis, suggesting that signaling cascades can control glycosylation directly at the Golgi level. Our results provide a genetic overview of the signaling pathways that control the Golgi apparatus in human cells.
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148
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Chandler K, Goldman R. Glycoprotein disease markers and single protein-omics. Mol Cell Proteomics 2013; 12:836-45. [PMID: 23399550 PMCID: PMC3617330 DOI: 10.1074/mcp.r112.026930] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/07/2013] [Indexed: 12/14/2022] Open
Abstract
Glycoproteins are well represented among biomarkers for inflammatory and cancer diseases. Secreted and membrane-associated glycoproteins make excellent targets for noninvasive detection. In this review, we discuss clinically applicable markers of cancer diseases and methods for their analysis. High throughput discovery continues to supply marker candidates with unusual glycan structures, altered glycoprotein abundance, or distribution of site-specific glycoforms. Improved analytical methods are needed to unlock the potential of these discoveries in validated clinical assays. A new generation of targeted quantitative assays is expected to advance the use of glycoproteins in early detection of diseases, molecular disease classification, and monitoring of therapeutic interventions.
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Affiliation(s)
- Kevin Chandler
- From the Departments of ‡Biochemistry and Molecular and Cellular Biology and
| | - Radoslav Goldman
- From the Departments of ‡Biochemistry and Molecular and Cellular Biology and
- ¶Oncology, Georgetown University, Washington, D.C. 20057
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149
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Deciphering O-glycomics for the development and production of biopharmaceuticals. ACTA ACUST UNITED AC 2013. [DOI: 10.4155/pbp.13.7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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150
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Duan X, Cai L, Lee LA, Chen H, Wang Q. Incorporation of azide sugar analogue decreases tumorigenic potential of breast cancer cells by reducing cancer stem cell population. Sci China Chem 2013. [DOI: 10.1007/s11426-012-4806-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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