1
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Torkamannejad S, Chang G, Aroge FA, Sun B. Single Isotopologue for In-Sample Calibration and Absolute Quantitation by LC-MS/MS. J Proteome Res 2024; 23:1351-1359. [PMID: 38445850 DOI: 10.1021/acs.jproteome.3c00848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Targeted mass spectrometry (MS)-based absolute quantitative analysis has been increasingly used in biomarker discovery. The ability to accurately measure the masses by MS enabled the use of isotope-incorporated surrogates having virtually identical physiochemical properties with the target analytes as calibrators. Such a unique capacity allowed for accurate in-sample calibration. Current in-sample calibration uses multiple isotopologues or structural analogues for both the surrogate and the internal standard. Here, we simplified this common practice by using endogenous light peptides as the internal standards and used a mathematical deduction of "heavy matching light, HML" to directly quantify an endogenous analyte. This method provides all necessary assay performance parameters in the authentic matrix, including the lower limit of quantitation (LLOQ) and intercept of the calibration curve, by using only a single isotopologue of the analyte. This method can be applied to the quantitation of proteins, peptides, and small molecules. Using this method, we quantified the efficiency of heart tissue digestion and recovery using sodium deoxycholate as a detergent and two spiked exogenous proteins as mimics of heart proteins. The results demonstrated the robustness of the assay.
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Affiliation(s)
- Soroush Torkamannejad
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Ge Chang
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Fabusuyi A Aroge
- School of Mechatronic Systems Engineering, Simon Fraser University, Surrey, British Columbia V3T0A3, Canada
| | - Bingyun Sun
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
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2
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Binek A, Castans C, Jorge I, Bagwan N, Rodríguez JM, Fernández-Jiménez R, Galán-Arriola C, Oliver E, Gómez M, Clemente-Moragón A, Ibanez B, Camafeita E, Vázquez J. Oxidative Post-translational Protein Modifications upon Ischemia/Reperfusion Injury. Antioxidants (Basel) 2024; 13:106. [PMID: 38247530 PMCID: PMC10812827 DOI: 10.3390/antiox13010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/30/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
While reperfusion, or restoration of coronary blood flow in acute myocardial infarction, is a requisite for myocardial salvage, it can paradoxically induce a specific damage known as ischemia/reperfusion (I/R) injury. Our understanding of the precise pathophysiological molecular alterations leading to I/R remains limited. In this study, we conducted a comprehensive and unbiased time-course analysis of post-translational modifications (PTMs) in the post-reperfused myocardium of two different animal models (pig and mouse) and evaluated the effect of two different cardioprotective therapies (ischemic preconditioning and neutrophil depletion). In pigs, a first wave of irreversible oxidative damage was observed at the earliest reperfusion time (20 min), impacting proteins essential for cardiac contraction. A second wave, characterized by irreversible oxidation on different residues and reversible Cys oxidation, occurred at late stages (6-12 h), affecting mitochondrial, sarcomere, and inflammation-related proteins. Ischemic preconditioning mitigated the I/R damage caused by the late oxidative wave. In the mouse model, the two-phase pattern of oxidative damage was replicated, and neutrophil depletion mitigated the late wave of I/R-related damage by preventing both Cys reversible oxidation and irreversible oxidation. Altogether, these data identify protein PTMs occurring late after reperfusion as an actionable therapeutic target to reduce the impact of I/R injury.
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Grants
- PGC2018-097019-B-I00, PID2021-122348NB-I00, PID2022-140176OB-I00 Spanish Ministry of Science, Innovation and Universities
- Fondo de Investigación Sanitaria grant PRB3 PT17/0019/0003- ISCIII-SGEFI / ERDF, ProteoRed Instituto de Salud Carlos III
- IMMUNO-VAR, P2022/BMD-7333, and RENIM-CM, P2022/BMD-7403 Comunidad de Madrid
- HR17-00247, HR22-00533 and HR22-00253 "la Caixa" Banking Foundation
- ERC Consolidator Grant "MATRIX", 819775 European Commission
- grant PI22/01560 ISCIII-Fondo de Investigación Sanitaria and European Union
- FP7-PEOPLE-2013-ITN-Cardionext European Union's Seventh Framework Programme
- Formacion del Profesorado Universitario (FPU14/05292) Spanish Ministry of Education, Culture and Sports
- PID2021-133167OB-100, RYC2020-028884-I, CEX2020-001041-S MCIN/AEI/10.13039/501100011033
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Affiliation(s)
- Aleksandra Binek
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Celia Castans
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Inmaculada Jorge
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Navratan Bagwan
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - José Manuel Rodríguez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Rodrigo Fernández-Jiménez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
- Department of Cardiology, Hospital Universitario Clínico San Carlos, Profesor Martín Lagos, s/n, 28040 Madrid, Spain
| | - Carlos Galán-Arriola
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Eduardo Oliver
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Mónica Gómez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Agustín Clemente-Moragón
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Borja Ibanez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
- IIS-Fundación Jiménez Díaz Hospital, Avenida Reyes Católicos, 2, 28040 Madrid, Spain
| | - Emilio Camafeita
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
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3
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Park J, Lee SH, Shin D, Kim Y, Kim YS, Seong MY, Lee JJ, Seo HG, Cho WS, Ro YS, Kim Y, Oh BM. Multiplexed Quantitative Proteomics Reveals Proteomic Alterations in Two Rodent Traumatic Brain Injury Models. J Proteome Res 2024; 23:249-263. [PMID: 38064581 DOI: 10.1021/acs.jproteome.3c00544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
In many cases of traumatic brain injury (TBI), conspicuous abnormalities, such as scalp wounds and intracranial hemorrhages, abate over time. However, many unnoticeable symptoms, including cognitive, emotional, and behavioral dysfunction, often last from several weeks to years after trauma, even for mild injuries. Moreover, the cause of such persistence of symptoms has not been examined extensively. Recent studies have implicated the dysregulation of the molecular system in the injured brain, necessitating an in-depth analysis of the proteome and signaling pathways that mediate the consequences of TBI. Thus, in this study, the brain proteomes of two TBI models were examined by quantitative proteomics during the recovery period to determine the molecular mechanisms of TBI. Our results show that the proteomes in both TBI models undergo distinct changes. A bioinformatics analysis demonstrated robust activation and inhibition of signaling pathways and core proteins that mediate biological processes after brain injury. These findings can help determine the molecular mechanisms that underlie the persistent effects of TBI and identify novel targets for drug interventions.
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Affiliation(s)
- Junho Park
- Department of Pharmacology, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Research Institute for Basic Medical Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Seung Hak Lee
- Department of Rehabilitation Medicine, Asan Medical Center, 88 Olympic-Ro 43-Gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Dongyoon Shin
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Yeongshin Kim
- Department of Life Science, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Young Sik Kim
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Min Yong Seong
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Jin Joo Lee
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Han Gil Seo
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Won-Sang Cho
- Department of Neurosurgery, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Young Sun Ro
- Department of Emergency Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Youngsoo Kim
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Department of Life Science, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Byung-Mo Oh
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- Institute of Aging, Seoul National University College of Medicine, 71 Ihwajang-gil, Jongno-gu, Seoul 03080, Republic of Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- National Traffic Injury Rehabilitation Hospital, 260 Jungang-ro, Yangpyeong-gun 12564, Gyeonggi-do, Republic of Korea
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4
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Feng X, Shi Q, Jian Q, Li F, Li Z, Cheng K. Alterations in mitochondrial protein glycosylation in myocardial ischaemia reperfusion injury. Biochem Biophys Rep 2023; 35:101509. [PMID: 37601448 PMCID: PMC10439394 DOI: 10.1016/j.bbrep.2023.101509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/14/2023] [Accepted: 06/29/2023] [Indexed: 08/22/2023] Open
Abstract
The alterations in mitochondrial protein glycosylation in myocardial ischaemia reperfusion (I/R) injury are still unclear. Therefore, based on a lectin microarray and liquid chromatograph-mass spectrometer/mass spectrometer (LC‒MS/MS) technology combined with a bioinformatics analysis, we studied the changes in mitochondrial protein glycosylation during I/R injury. This study revealed significant differences in mitochondrial glycoprotein during I/R injury. Compared with the sham operation group, the model group, which underwent ischaemia for 30 min, showed a high expression of glycan structures recognized by lectins, such as WFA, PTL-I, LTL, GSL-I, SBA and SNA, and a low expression of glycan structures recognized by ConA, VVA and RCA120. The model group, which underwent ischaemia for 45 min, showed a high expression of glycan structures recognized by LTL and SNA and a low expression of glycan structures recognized by ECA. Further analysis showed that the Siaα2-6Gal/N-acetylgalactosamine (GalNAc) structures recognized by SNA were significantly increased. In total, 91 differential proteins were identified by LC‒MS/MS, and 8 hub genes were screened by Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and protein interaction analyses. Compared with the Gene Expression Omnibus (GEO) database genes, two differential genes, Pros1 and Vtn, were obtained. Pros1 is a key regulator of the inflammatory response and vascular injury response. The Vtn gene variant is associated with the risk of myocardial infarction. This study is expected to provide a new method for the treatment of I/R injury and could provide new ideas for the postoperative prognosis of patients.
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Affiliation(s)
- Xinyu Feng
- Department of Cardiac and Pan-Vascular Diseases, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China
| | - Qing Shi
- Xi'an Satellite Control Center, Xi'an, China
| | - Qiang Jian
- Department of Scientific Research, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China
| | - Fan Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Kang Cheng
- Department of Cardiac and Pan-Vascular Diseases, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China
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5
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Révész Á, Hevér H, Steckel A, Schlosser G, Szabó D, Vékey K, Drahos L. Collision energies: Optimization strategies for bottom-up proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1261-1299. [PMID: 34859467 DOI: 10.1002/mas.21763] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 06/07/2023]
Abstract
Mass-spectrometry coupled to liquid chromatography is an indispensable tool in the field of proteomics. In the last decades, more and more complex and diverse biochemical and biomedical questions have arisen. Problems to be solved involve protein identification, quantitative analysis, screening of low abundance modifications, handling matrix effect, and concentrations differing by orders of magnitude. This led the development of more tailored protocols and problem centered proteomics workflows, including advanced choice of experimental parameters. In the most widespread bottom-up approach, the choice of collision energy in tandem mass spectrometric experiments has outstanding role. This review presents the collision energy optimization strategies in the field of proteomics which can help fully exploit the potential of MS based proteomics techniques. A systematic collection of use case studies is then presented to serve as a starting point for related further scientific work. Finally, this article discusses the issue of comparing results from different studies or obtained on different instruments, and it gives some hints on methodology transfer between laboratories based on measurement of reference species.
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Affiliation(s)
- Ágnes Révész
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Helga Hevér
- Chemical Works of Gedeon Richter Plc, Budapest, Hungary
| | - Arnold Steckel
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
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6
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Tian J, Ji M, Liu J, Xia Y, Zhang K, Li H, Gong W, Li Z, Xie W, Wang G, Xie J, Yu E. N-glycosylomic analysis provides new insight into the molecular mechanism of firmness of fish fillet. Food Chem 2023; 424:136417. [PMID: 37244189 DOI: 10.1016/j.foodchem.2023.136417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 05/29/2023]
Abstract
Post-translational protein modification affects muscle physiochemistry. To understand the roles of N-glycosylation in this process, the muscle N-glycoproteomes of crisp grass carp (CGC) and ordinary grass carp (GC) were analyzed and compared. We identified 325 N-glycosylated sites with the NxT motif, classified 177 proteins, and identified 10 upregulated and 19 downregulated differentially glycosylated proteins (DGPs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations revealed that these DGPs participate in myogenesis, extracellular matrix content formation, and muscle function. The DGPs partially accounted for the molecular mechanisms associated with the relatively smaller fiber diameter and higher collagen content observed in CGC. Though the DGPs diverged from the identified differentially phosphorylated proteins and differentially expressed proteins detected in previous study, they all shared similar metabolic and signaling pathways. Thus, they might independently alter fish muscle texture. Overall, the present study provides novel insights into the mechanisms underlying fillet quality.
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Affiliation(s)
- Jingjing Tian
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Mengmeng Ji
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jie Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yun Xia
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Kai Zhang
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hongyan Li
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Wangbao Gong
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Zhifei Li
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Wenping Xie
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Guangjun Wang
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jun Xie
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
| | - Ermeng Yu
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
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7
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Xu Z, Liu Y, He S, Sun R, Zhu C, Li S, Hai S, Luo Y, Zhao Y, Dai L. Integrative Proteomics and N-Glycoproteomics Analyses of Rheumatoid Arthritis Synovium Reveal Immune-Associated Glycopeptides. Mol Cell Proteomics 2023; 22:100540. [PMID: 37019382 PMCID: PMC10176071 DOI: 10.1016/j.mcpro.2023.100540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/10/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Rheumatoid arthritis (RA) is a typical autoimmune disease characterized by synovial inflammation, synovial tissue hyperplasia, and destruction of bone and cartilage. Protein glycosylation plays key roles in the pathogenesis of RA but in-depth glycoproteomics analysis of synovial tissues is still lacking. Here, by using a strategy to quantify intact N-glycopeptides, we identified 1260 intact N-glycopeptides from 481 N-glycosites on 334 glycoproteins in RA synovium. Bioinformatics analysis revealed that the hyper-glycosylated proteins in RA were closely linked to immune responses. By using DNASTAR software, we identified 20 N-glycopeptides whose prototype peptides were highly immunogenic. We next calculated the enrichment scores of nine types of immune cells using specific gene sets from public single-cell transcriptomics data of RA and revealed that the N-glycosylation levels at some sites, such as IGSF10_N2147, MOXD2P_N404, and PTCH2_N812, were significantly correlated with the enrichment scores of certain immune cell types. Furthermore, we showed that aberrant N-glycosylation in the RA synovium was related to increased expression of glycosylation enzymes. Collectively, this work presents, for the first time, the N-glycoproteome of RA synovium and describes immune-associated glycosylation, providing novel insights into RA pathogenesis.
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Affiliation(s)
- Zhiqiang Xu
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yi Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Siyu He
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Rui Sun
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Chenxi Zhu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Shuangqing Li
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shan Hai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yubin Luo
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhao
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China.
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China.
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8
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Reproducing extracellular matrix adverse remodelling of non-ST myocardial infarction in a large animal model. Nat Commun 2023; 14:995. [PMID: 36813782 PMCID: PMC9945840 DOI: 10.1038/s41467-023-36350-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 01/23/2023] [Indexed: 02/24/2023] Open
Abstract
The rising incidence of non-ST-segment elevation myocardial infarction (NSTEMI) and associated long-term high mortality constitutes an urgent clinical issue. Unfortunately, the study of possible interventions to treat this pathology lacks a reproducible pre-clinical model. Indeed, currently adopted small and large animal models of MI mimic only full-thickness, ST-segment-elevation (STEMI) infarcts, and hence cater only for an investigation into therapeutics and interventions directed at this subset of MI. Thus, we develop an ovine model of NSTEMI by ligating the myocardial muscle at precise intervals parallel to the left anterior descending coronary artery. Upon histological and functional investigation to validate the proposed model and comparison with STEMI full ligation model, RNA-seq and proteomics show the distinctive features of post-NSTEMI tissue remodelling. Transcriptome and proteome-derived pathway analyses at acute (7 days) and late (28 days) post-NSTEMI pinpoint specific alterations in cardiac post-ischaemic extracellular matrix. Together with the rise of well-known markers of inflammation and fibrosis, NSTEMI ischaemic regions show distinctive patterns of complex galactosylated and sialylated N-glycans in cellular membranes and extracellular matrix. Identifying such changes in molecular moieties accessible to infusible and intra-myocardial injectable drugs sheds light on developing targeted pharmacological solutions to contrast adverse fibrotic remodelling.
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9
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Barallobre-Barreiro J, Radovits T, Fava M, Mayr U, Lin WY, Ermolaeva E, Martínez-López D, Lindberg EL, Duregotti E, Daróczi L, Hasman M, Schmidt LE, Singh B, Lu R, Baig F, Siedlar AM, Cuello F, Catibog N, Theofilatos K, Shah AM, Crespo-Leiro MG, Doménech N, Hübner N, Merkely B, Mayr M. Extracellular Matrix in Heart Failure: Role of ADAMTS5 in Proteoglycan Remodeling. Circulation 2021; 144:2021-2034. [PMID: 34806902 PMCID: PMC8687617 DOI: 10.1161/circulationaha.121.055732] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/20/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Remodeling of the extracellular matrix (ECM) is a hallmark of heart failure (HF). Our previous analysis of the secretome of murine cardiac fibroblasts returned ADAMTS5 (a disintegrin and metalloproteinase with thrombospondin motifs 5) as one of the most abundant proteases. ADAMTS5 cleaves chondroitin sulfate proteoglycans such as versican. The contribution of ADAMTS5 and its substrate versican to HF is unknown. METHODS Versican remodeling was assessed in mice lacking the catalytic domain of ADAMTS5 (Adamts5ΔCat). Proteomics was applied to study ECM remodeling in left ventricular samples from patients with HF, with a particular focus on the effects of common medications used for the treatment of HF. RESULTS Versican and versikine, an ADAMTS-specific versican cleavage product, accumulated in patients with ischemic HF. Versikine was also elevated in a porcine model of cardiac ischemia/reperfusion injury and in murine hearts after angiotensin II infusion. In Adamts5ΔCat mice, angiotensin II infusion resulted in an aggravated versican build-up and hyaluronic acid disarrangement, accompanied by reduced levels of integrin β1, filamin A, and connexin 43. Echocardiographic assessment of Adamts5ΔCat mice revealed a reduced ejection fraction and an impaired global longitudinal strain on angiotensin II infusion. Cardiac hypertrophy and collagen deposition were similar to littermate controls. In a proteomics analysis of a larger cohort of cardiac explants from patients with ischemic HF (n=65), the use of β-blockers was associated with a reduction in ECM deposition, with versican being among the most pronounced changes. Subsequent experiments in cardiac fibroblasts confirmed that β1-adrenergic receptor stimulation increased versican expression. Despite similar clinical characteristics, patients with HF treated with β-blockers had a distinct cardiac ECM profile. CONCLUSIONS Our results in animal models and patients suggest that ADAMTS proteases are critical for versican degradation in the heart and that versican accumulation is associated with impaired cardiac function. A comprehensive characterization of the cardiac ECM in patients with ischemic HF revealed that β-blockers may have a previously unrecognized beneficial effect on cardiac chondroitin sulfate proteoglycan content.
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Affiliation(s)
- Javier Barallobre-Barreiro
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Tamás Radovits
- Heart and Vascular Center, Department of Cardiology, Semmelweis University, Budapest, Hungary (T.R., L.D., B.M.)
| | - Marika Fava
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Ursula Mayr
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Wen-Yu Lin
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
- Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan (W.-Y.L.)
| | - Elizaveta Ermolaeva
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Diego Martínez-López
- IIS-Fundación Jiménez Díaz–Universidad Autónoma and CIBERCV, Madrid, Spain (D.M.-L.)
| | - Eric L. Lindberg
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (E.L.L., N.H.)
| | - Elisa Duregotti
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - László Daróczi
- Heart and Vascular Center, Department of Cardiology, Semmelweis University, Budapest, Hungary (T.R., L.D., B.M.)
| | - Maria Hasman
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Lukas E. Schmidt
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Bhawana Singh
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Ruifang Lu
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Ferheen Baig
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Aleksandra Malgorzata Siedlar
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Friederike Cuello
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, German Center for Heart Research (DZHK), Hamburg, Germany (F.C.)
| | - Norman Catibog
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Konstantinos Theofilatos
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Ajay M. Shah
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
| | - Maria G. Crespo-Leiro
- Instituto de Investigación Biomédica de A Coruña (INIBIC)–CIBERCV, Complexo Hospitalario Universitario de A Coruña (CHUAC), Universidade da Coruña, Spain (M.G.C.-L., N.D.)
| | - Nieves Doménech
- Instituto de Investigación Biomédica de A Coruña (INIBIC)–CIBERCV, Complexo Hospitalario Universitario de A Coruña (CHUAC), Universidade da Coruña, Spain (M.G.C.-L., N.D.)
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (E.L.L., N.H.)
- Charité-Universitätsmedizin, Berlin, Germany (N.H.)
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany (N.H.)
| | - Béla Merkely
- Heart and Vascular Center, Department of Cardiology, Semmelweis University, Budapest, Hungary (T.R., L.D., B.M.)
| | - Manuel Mayr
- King’s BHF Centre of Research Excellence, London, UK (J.B.-B., M.F., U.M., W.-Y.L., E.E., E.D., M.H., L.E.S., B.S., R.L., F.B., A.M.S., N.C., K.T., A.M.S., M.M.)
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10
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Plasma membrane N-glycoproteome analysis of wheat seedling leaves under drought stress. Int J Biol Macromol 2021; 193:1541-1550. [PMID: 34740685 DOI: 10.1016/j.ijbiomac.2021.10.217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/29/2021] [Indexed: 01/23/2023]
Abstract
Protein glycosylation is one of the ubiquitous post-translational modifications in eukaryotic cells, which play important roles in plant growth and adverse response. In this study, we performed the first comprehensive wheat plasma membrane N-glycoproteome analysis under drought stress via glycopeptide HILIC enrichment and LC-MS/MS identification. In total, 414 glycosylated sites corresponding to 407 glycopeptides and 312 unique glycoproteins were identified, of which 173 plasma membrane glycoproteins with 215 N-glycosylation sites were significantly regulated by drought stress. Functional enrichment analysis reveals that the significantly regulated N-glycosylation proteins were particularly related to protein kinase activity involved in the reception and transduction of extracellular signal and plant cell wall remolding. The motifs and sequence structures analysis showed that the significantly regulated N-glycosylation sites were concentrated within [NxT] motif, and 79.5% of them were located on the random coil that is always on the protein surface and flexible regions, which could facilitate protein glycosylated modification and enhance protein structural stability via reducing protein flexibility. PNGase F enzyme digestion and glycosylation site mutation further indicated that N-glycosylated modification could increase protein stability. Therefore, N-glycosylated modification is involved in plant adaptation to drought stress by improving the stability of cell wall remodeling related plasma membrane proteins.
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11
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Mule SN, Rosa-Fernandes L, Coutinho JVP, Gomes VDM, Macedo-da-Silva J, Santiago VF, Quina D, de Oliveira GS, Thaysen-Andersen M, Larsen MR, Labriola L, Palmisano G. Systems-wide analysis of glycoprotein conformational changes by limited deglycosylation assay. J Proteomics 2021; 248:104355. [PMID: 34450331 DOI: 10.1016/j.jprot.2021.104355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/08/2021] [Accepted: 08/14/2021] [Indexed: 10/20/2022]
Abstract
A new method to probe the conformational changes of glycoproteins on a systems-wide scale, termed limited deglycosylation assay (LDA), is described. The method measures the differential rate of deglycosylation of N-glycans on natively folded proteins by the common peptide:N-glycosidase F (PNGase F) enzyme which in turn informs on their spatial presentation and solvent exposure on the protein surface hence ultimately the glycoprotein conformation. LDA involves 1) protein-level N-deglycosylation under native conditions, 2) trypsin digestion, 3) glycopeptide enrichment, 4) peptide-level N-deglycosylation and 5) quantitative MS-based analysis of formerly N-glycosylated peptides (FNGPs). LDA was initially developed and the experimental conditions optimized using bovine RNase B and fetuin. The method was then applied to glycoprotein extracts from LLC-MK2 epithelial cells upon treatment with dithiothreitol to induce endoplasmic reticulum stress and promote protein misfolding. Data from the LDA and 3D structure analysis showed that glycoproteins predominantly undergo structural changes in loops/turns upon ER stress as exemplified with detailed analysis of ephrin-A5, GALNT10, PVR and BCAM. These results show that LDA accurately reports on systems-wide conformational changes of glycoproteins induced under controlled treatment regimes. Thus, LDA opens avenues to study glycoprotein structural changes in a range of other physiological and pathophysiological conditions relevant to acute and chronic diseases. SIGNIFICANCE: We describe a novel method termed limited deglycosylation assay (LDA), to probe conformational changes of glycoproteins on a systems-wide scale. This method improves the current toolbox of structural proteomics by combining site and conformational-specific PNGase F enzymatic activity with large scale quantitative proteomics. X-ray crystallography, nuclear magnetic resonance spectroscopy and cryoEM techniques are the major techniques applied to elucidate macromolecule structures. However, the size and heterogeneity of the oligosaccharide chains poses several challenges to the applications of these techniques to glycoproteins. The LDA method presented here, can be applied to a range of pathophysiological conditions and expanded to investigate PTMs-mediated structural changes in complex proteomes.
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Affiliation(s)
- Simon Ngao Mule
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - João V P Coutinho
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Vinícius De Morais Gomes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil; Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Janaina Macedo-da-Silva
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Verônica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Daniel Quina
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Gilberto Santos de Oliveira
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, DK, Denmark
| | - Letícia Labriola
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil.
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12
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Upregulation of Long Noncoding RNA FGD5-AS1 Ameliorates Myocardial Ischemia/Reperfusion Injury via MicroRNA-106a-5p and MicroRNA-106b-5p. J Cardiovasc Pharmacol 2021; 78:e45-e54. [PMID: 34173804 DOI: 10.1097/fjc.0000000000001036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 03/16/2021] [Indexed: 01/20/2023]
Abstract
ABSTRACT Long noncoding RNAs have been known to play key roles in myocardial ischemia/reperfusion injury. This study was conducted to investigate whether upregulation of FGD5-AS1 can improve hypoxia/reoxygenation (H/R) injury of cardiomyocytes and its underlying mechanisms. Pc-FGD5-AS1 was used to overexpress FGD5-AS1 in cardiomyocytes. Cholecystokinin octapeptide and flow cytometry assays were performed to detect the effect of FGD5-AS1 on myocardial cell H/R injury. Quantitative real-time polymerase chain reaction and luciferase reporter assay were performed to assess the relationship between FGD5-AS1 and microRNA-106a-5p (miR-106a-5p) or miR-106b-5p. In patients with acute myocardial infarction and in H/R cardiomyocytes and ischemia/reperfusion myocardium, the expression levels of FGD5-AS1 were reduced, whereas the expression levels of miR-106a-5p and miR-106b-5p were increased. Overexpression of FGD5-AS1 increased the viability of H/R-treated cardiomyocytes and reduced the levels of apoptosis and creatine kinase-MB. In addition, FGD5-AS1 could bind to miR-106a-5p or miR-106b-5p and showed a mutual inhibitory effect between them. Furthermore, overexpression of miR-106a-5p or miR-106b-5p inhibited the expression of SMAD5. FGD5-AS1 upregulated the expression of SMAD5. In conclusion, FGD5-AS1 may be a potential therapeutic target for myocardial H/R injury, and its cardioprotective effect may be realized by reducing inflammatory response and cell apoptosis.
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13
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Therapies to prevent post-infarction remodelling: From repair to regeneration. Biomaterials 2021; 275:120906. [PMID: 34139506 DOI: 10.1016/j.biomaterials.2021.120906] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 05/02/2021] [Accepted: 05/20/2021] [Indexed: 12/15/2022]
Abstract
Myocardial infarction is the first cause of worldwide mortality, with an increasing incidence also reported in developing countries. Over the past decades, preclinical research and clinical trials continually tested the efficacy of cellular and acellular-based treatments. However, none of them resulted in a drug or device currently used in combination with either percutaneous coronary intervention or coronary artery bypass graft. Inflammatory, proliferation and remodelling phases follow the ischaemic event in the myocardial tissue. Only recently, single-cell sequencing analyses provided insights into the specific cell populations which determine the final fibrotic deposition in the affected region. In this review, ischaemia, inflammation, fibrosis, angiogenesis, cellular stress and fundamental cellular and molecular components are evaluated as therapeutic targets. Given the emerging evidence of biomaterial-based systems, the increasing use of injectable hydrogels/scaffolds and epicardial patches is reported both as acellular and cellularised/functionalised treatments. Since several variables influence the outcome of any experimented treatment, we return to the pathological basis with an unbiased view towards any specific process or cellular component. Thus, by evaluating the benefits and limitations of the approaches based on these targets, the reader can weigh the rationale of each of the strategies that reached the clinical trials stage. As recent studies focused on the relevance of the extracellular matrix in modulating ischaemic remodelling and enhancing myocardial regeneration, we aim to portray current trends in the field with this review. Finally, approaches towards feasible translational studies that are as yet unexplored are also suggested.
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14
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Bagwan N, El Ali HH, Lundby A. Proteome-wide profiling and mapping of post translational modifications in human hearts. Sci Rep 2021; 11:2184. [PMID: 33500497 PMCID: PMC7838296 DOI: 10.1038/s41598-021-81986-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/14/2021] [Indexed: 11/21/2022] Open
Abstract
Post translational modifications (PTMs) are covalent modifications of proteins that can range from small chemical modifications to addition of entire proteins. PTMs contribute to regulation of protein function and thereby greatly increase the functional diversity of the proteome. In the heart, a few well-studied PTMs, such as phosphorylation and glycosylation, are known to play essential roles for cardiac function. Yet, only a fraction of the ~ 300 known PTMs have been studied in a cardiac context. Here we investigated the proteome-wide map of PTMs present in human hearts by utilizing high-resolution mass spectrometry measurements and a suite of PTM identification algorithms. Our approach led to identification of more than 150 different PTMs across three of the chambers in human hearts. This finding underscores that decoration of cardiac proteins by PTMs is much more diverse than hitherto appreciated and provides insights in cardiac protein PTMs not yet studied. The results presented serve as a catalogue of which PTMs are present in human hearts and outlines the particular protein and the specific amino acid modified, and thereby provides a detail-rich resource for exploring protein modifications in human hearts beyond the most studied PTMs.
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Affiliation(s)
- Navratan Bagwan
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Henrik H El Ali
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Alicia Lundby
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark. .,The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenahagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark.
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15
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Marsico G, Jin C, Abbah SA, Brauchle EM, Thomas D, Rebelo AL, Orbanić D, Chantepie S, Contessotto P, Papy-Garcia D, Rodriguez-Cabello C, Kilcoyne M, Schenke-Layland K, Karlsson NG, McCullagh KJA, Pandit A. Elastin-like hydrogel stimulates angiogenesis in a severe model of critical limb ischemia (CLI): An insight into the glyco-host response. Biomaterials 2021; 269:120641. [PMID: 33493768 DOI: 10.1016/j.biomaterials.2020.120641] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022]
Abstract
Critical limb ischemia (CLI) is characterized by the impairment of microcirculation, necrosis and inflammation of the muscular tissue. Although the role of glycans in mediating inflammation has been reported, changes in the glycosylation following muscle ischemia remains poorly understood. Here, a murine CLI model was used to show the increase of high mannose, α-(2, 6)-sialic acid and the decrease of hybrid and bisected N-glycans as glycosylation associated with the ischemic environment. Using this model, the efficacy of an elastin-like recombinamers (ELR) hydrogel was assessed. The hydrogel modulates key angiogenic signaling pathways, resulting in capillary formation, and ECM remodeling. Arterioles formation, reduction of fibrosis and anti-inflammatory macrophage polarization wa also induced by the hydrogel administration. Modulation of glycosylation was observed, suggesting, in particular, a role for mannosylation and sialylation in the mediation of tissue repair. Our study elucidates the angiogenic potential of the ELR hydrogel for CLI applications and identifies glycosylation alterations as potential new therapeutic targets.
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Affiliation(s)
- Grazia Marsico
- CÚRAM SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway H92 W2TY, Ireland
| | - Chunseng Jin
- Department of Medical Biochemistry and Cell Biology at Institute of Biomedicine, Sahlgrenska Academy, The University of Gothenburg, Sweden
| | - Sunny A Abbah
- CÚRAM SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway H92 W2TY, Ireland
| | - Eva M Brauchle
- Department of Women's Health, Research Institute for Women's Health, The Eberhard-Karls-University Tuebingen, Germany; The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
| | - Dilip Thomas
- CÚRAM SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway H92 W2TY, Ireland
| | - Ana Lúcia Rebelo
- CÚRAM SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway H92 W2TY, Ireland
| | | | - Sandrine Chantepie
- Cell Growth, Tissue Repair and Regeneration (CRRET), UPEC EA 4397/ERL CNRS 9215, Université Paris Est Créteil, Université Paris Est, Créteil, France
| | - Paolo Contessotto
- CÚRAM SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway H92 W2TY, Ireland
| | - Dulce Papy-Garcia
- Cell Growth, Tissue Repair and Regeneration (CRRET), UPEC EA 4397/ERL CNRS 9215, Université Paris Est Créteil, Université Paris Est, Créteil, France
| | | | - Michelle Kilcoyne
- CÚRAM SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway H92 W2TY, Ireland; Carbohydrate Signalling Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway H92 W2TY, Ireland
| | - K Schenke-Layland
- Department of Women's Health, Research Institute for Women's Health, The Eberhard-Karls-University Tuebingen, Germany; The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
| | - N G Karlsson
- Department of Medical Biochemistry and Cell Biology at Institute of Biomedicine, Sahlgrenska Academy, The University of Gothenburg, Sweden
| | - Karl J A McCullagh
- Physiology Department, National University of Ireland Galway, Galway H92 W2TY, Ireland
| | - Abhay Pandit
- CÚRAM SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway H92 W2TY, Ireland.
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16
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Rookyard AW, Paulech J, Thyssen S, Liddy KA, Puckeridge M, Li DK, White MY, Cordwell SJ. A Global Profile of Reversible and Irreversible Cysteine Redox Post-Translational Modifications During Myocardial Ischemia/Reperfusion Injury and Antioxidant Intervention. Antioxid Redox Signal 2021; 34:11-31. [PMID: 32729339 DOI: 10.1089/ars.2019.7765] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aims: Cysteine (Cys) is a major target for redox post-translational modifications (PTMs) that occur in response to changes in the cellular redox environment. We describe multiplexed, peptide-based enrichment and quantitative mass spectrometry (MS) applied to globally profile reversible redox Cys PTM in rat hearts during ischemia/reperfusion (I/R) in the presence or absence of an aminothiol antioxidant, N-2-mercaptopropionylglycine (MPG). Parallel fractionation also allowed identification of irreversibly oxidized Cys peptides (Cys-SO2H/SO3H). Results: We identified 4505 reversibly oxidized Cys peptides of which 1372 were significantly regulated by ischemia and/or I/R. An additional 219 peptides (247 sites) contained Cys-SO2H/Cys-SO3H modifications, and these were predominantly identified from hearts subjected to I/R (n = 168 peptides). Parallel reaction monitoring MS (PRM-MS) enabled relative quantitation of 34 irreversibly oxidized Cys peptides. MPG attenuated a large cluster of I/R-associated reversibly oxidized Cys peptides and irreversible Cys oxidation to less than nonischemic controls (n = 24 and 34 peptides, respectively). PRM-MS showed that Cys sites oxidized during ischemia and/or I/R and "protected" by MPG were largely mitochondrial, and were associated with antioxidant functions (peroxiredoxins 5 and 6) and metabolic processes, including glycolysis. Metabolomics revealed I/R induced changes in glycolytic intermediates that were reversed in the presence of MPG, which were consistent with irreversible PTM of triose phosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), altered GAPDH enzyme activity, and reduced I/R glycolytic payoff as evidenced by adenosine triphosphate and NADH levels. Innovation: Novel enrichment and PRM-MS approaches developed here enabled large-scale relative quantitation of Cys redox sites modified by reversible and irreversible PTM during I/R and antioxidant remediation. Conclusions: Cys sites identified here are targets of reactive oxygen species that can contribute to protein dysfunction and the pathogenesis of I/R.
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Affiliation(s)
- Alexander W Rookyard
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Jana Paulech
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Stine Thyssen
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Kiersten A Liddy
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Max Puckeridge
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Desmond K Li
- Charles Perkins Centre, The University of Sydney, Sydney, Australia.,Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Melanie Y White
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia.,Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Stuart J Cordwell
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia.,Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, Australia.,Sydney Mass Spectrometry, The University of Sydney, Sydney, Australia
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17
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Zhao Y, Raidas S, Mao Y, Li N. Glycine additive facilitates site-specific glycosylation profiling of biopharmaceuticals by ion-pairing hydrophilic interaction chromatography mass spectrometry. Anal Bioanal Chem 2020; 413:1267-1277. [PMID: 33244686 DOI: 10.1007/s00216-020-03089-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 11/28/2022]
Abstract
Many biotherapeutics such as monoclonal antibodies (mAb) and Fc-domain fusion proteins contain heterogeneous glycan contents at one or multiple glycosylation site(s). Site-specific glycan profile characterization is critical for monitoring the quality of these molecules during different stages of drug development. Hydrophilic interaction chromatography (HILIC) as an orthogonal separation method to reversed-phase liquid chromatography (RPLC) can achieve better glycopeptide identification due to the effective separation between individual glycoforms as well as the separation of glycopeptides from high-abundance non-glycosylated peptides, which can be further improved by modifying the mobile phases with ion-pairing agents (IP-HILIC). However, an online IP-HILIC coupled to mass spectrometry (MS) detection may suffer from the suppression of mass spectrometry signal during electrospray ionization due to the trifluoroacetic acid (TFA), commonly used as an ion-pairing agent. Here, we reported an optimized experimental condition for IP-HILIC-MS where glycine is added in the TFA-containing mobile phases to enhance the MS detection sensitivity for glycopeptides up to ~ 50-fold by eliminating the ion-suppression effect of an ion-pairing agent while still retaining excellent separation capacity. We demonstrated that with enhanced detection sensitivity, IP-HILIC-MS can confidently identify an increased number of site-specific N-linked glycans for IgG1, and IgG4 mAbs as well as an Fc-domain fusion protein (containing five N-glycosylation sites) through MS/MS-based search in the data-dependent acquisition mode, meanwhile, achieve comparable quantitative results compared with the traditional methods. We also demonstrated that IP-HILIC-MS can be used to identify low-level O-glycosylation and non-consensus N-glycosylation on mAbs without any enrichment prior to LC-MS analysis. Graphical abstract.
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Affiliation(s)
- Yunlong Zhao
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Shivkumar Raidas
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Yuan Mao
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA.
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
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18
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Glycoproteomics Technologies in Glycobiotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 175:413-434. [PMID: 33205259 DOI: 10.1007/10_2020_144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Glycosylation is a key factor determining the pharmacological properties of biotherapeutics, including their stability, solubility, bioavailability, pharmacokinetics, and immunogenicity. As such, comprehensive information about glycosylation of biotherapeutics is critical to demonstrate similarity. Regulatory agencies also require extensive documentation of the comprehensive analyses of glycosylation-related critical quality attributes (CQAs) during the development, manufacturing, and release of biosimilars. Mass spectrometry has catalysed tremendous advancements in the characterisation of glycosylation CQAs of biotherapeutics. Here we provide a perspective overview on the MS-based technologies relevant for biotherapeutic product characterisation with an emphasis on the recent developments that allow determination of glycosylation features such as site of glycosylation, sialic acid linkage, glycan structure, and content.
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19
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Drucker A, Yoo BH, Khan IA, Choi D, Montermini L, Liu X, Jovanovic S, Younis T, Rosen KV. Trastuzumab-induced upregulation of a protein set in extracellular vesicles emitted by ErbB2-positive breast cancer cells correlates with their trastuzumab sensitivity. Breast Cancer Res 2020; 22:105. [PMID: 33023655 PMCID: PMC7541295 DOI: 10.1186/s13058-020-01342-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/16/2020] [Indexed: 12/27/2022] Open
Abstract
Background ErbB2/HER2 oncoprotein often drives breast cancers (BCs) which are treated with the anti-ErbB2 antibody trastuzumab. The efficacy of trastuzumab-based metastatic BC therapies is routinely assessed by imaging studies. Trastuzumab typically becomes ineffective in the case of this disease and is then replaced by other drugs. Biomarkers of BC trastuzumab response could allow imaging studies and the switch to other drugs to occur earlier than is now possible. Moreover, bone-only BC metastases can be hard to measure, and biomarkers of their trastuzumab response could facilitate further treatment decisions. Such biomarkers are presently unavailable. In this study, we searched for proteins whose levels in BC cell-emitted extracellular vesicles (EVs) potentially correlate with BC trastuzumab sensitivity. Methods We isolated EVs from cultured trastuzumab-sensitive and trastuzumab-resistant human BC cells before and after trastuzumab treatment and characterized these EVs by nanoparticle tracking analysis and electron microscopy. We found previously that ErbB2 drives BC by downregulating a pro-apoptotic protein PERP. We now tested whether trastuzumab-induced PERP upregulation in EVs emitted by cultured human BC cells correlates with their trastuzumab sensitivity. We also used mass spectrometry to search for additional proteins whose levels in such EVs reflect BC cell trastuzumab sensitivity. Once we identified proteins whose EV levels correlate with this sensitivity in culture, we explored the feasibility of testing whether their levels in the blood EVs of trastuzumab-treated metastatic BC patients correlate with patients’ response to trastuzumab-based treatments. Results We found that neither trastuzumab nor acquisition of trastuzumab resistance by BC cells affects the size or morphology of EVs emitted by cultured BC cells. We established that EV levels of proteins PERP, GNAS2, GNA13, ITB1, and RAB10 correlate with BC cell trastuzumab response. Moreover, these proteins were upregulated during trastuzumab-based therapies in the blood EVs of a pilot cohort of metastatic BC patients that benefited from these therapies but not in those derived from patients that failed such treatments. Conclusions Upregulation of a protein set in EVs derived from cultured breast tumor cells correlates with tumor cell trastuzumab sensitivity. It is feasible to further evaluate these proteins as biomarkers of metastatic BC trastuzumab response.
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Affiliation(s)
- Arik Drucker
- Department of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Byong Hoon Yoo
- Departments of Pediatrics & Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Iman Aftab Khan
- Departments of Pediatrics & Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Dongsic Choi
- Research Institute of the McGill University Health Centre, Glen Site, McGill University, Montreal, QC, Canada
| | - Laura Montermini
- Research Institute of the McGill University Health Centre, Glen Site, McGill University, Montreal, QC, Canada
| | - Xiaoyang Liu
- Departments of Pediatrics & Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Sanja Jovanovic
- Department of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Tallal Younis
- Department of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Kirill V Rosen
- Departments of Pediatrics & Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada. .,Atlantic Research Centre, Rm C-304, CRC, 5849 University Avenue, PO Box 15000, Halifax, NS, B3H 4R2, Canada.
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20
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Contessotto P, Ellis BW, Jin C, Karlsson NG, Zorlutuna P, Kilcoyne M, Pandit A. Distinct glycosylation in membrane proteins within neonatal versus adult myocardial tissue. Matrix Biol 2019; 85-86:173-188. [PMID: 31108197 DOI: 10.1016/j.matbio.2019.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/18/2019] [Accepted: 05/14/2019] [Indexed: 12/16/2022]
Abstract
Mammalian hearts have regenerative potential restricted to early neonatal stage and lost within seven days after birth. Carbohydrates exclusive to cardiac neonatal tissue may be key regulators of regenerative potential. Although cell surface and extracellular matrix glycosylation are known modulators of tissue and cellular function and development, variation in cardiac glycosylation from neonatal tissue to maturation has not been fully examined. In this study, glycosylation of the adult rat cardiac ventricle showed no variability between the two strains analysed, nor were there any differences between the glycosylation of the right or left ventricle using lectin histochemistry and microarray profiling. However, in the Sprague-Dawley strain, neonatal cardiac glycosylation in the left ventricle differed from adult tissues using mass spectrometric analysis, showing a higher expression of high mannose structures and lower expression of complex N-linked glycans in the three-day-old neonatal tissue. Man6GlcNAc2 was identified as the main high mannose N-linked structure that was decreased in adult while higher expression of sialylated N-linked glycans and lower core fucosylation for complex structures were associated with ageing. The occurrence of mucin core type 2 O-linked glycans was reduced in adult and one sulfated core type 2 O-linked structure was identified in neonatal tissue. Interestingly, O-linked glycans from mature tissue contained both N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc), while all sialylated N-linked glycans detected contained only Neu5Ac. As glycans are associated with intracellular communication, the specific neonatal structures found may indicate a role for glycosylation in the neonatal associated regenerative capacity of the mammalian heart. New strategies targeting tissue glycosylation could be a key contributor to achieve an effective regeneration of the mammalian heart in pathological scenarios such as myocardial infarction.
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Affiliation(s)
- Paolo Contessotto
- CÚRAM Centre for Research in Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Bradley W Ellis
- Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN, USA
| | - Chunsheng Jin
- Department of Medical Biochemistry, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Pinar Zorlutuna
- Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN, USA; Aerospace and Mechanical Engineering Department, University of Notre Dame, Notre Dame, IN, USA
| | - Michelle Kilcoyne
- CÚRAM Centre for Research in Medical Devices, National University of Ireland Galway, Galway, Ireland; Carbohydrate Signalling Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Abhay Pandit
- CÚRAM Centre for Research in Medical Devices, National University of Ireland Galway, Galway, Ireland.
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21
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Li J, Yang H, Lu Q, Chen D, Zhou M, Kuang Y, Ying S, Song J. Proteomics and N‐glycoproteomics analysis of an extracellular matrix‐based scaffold‐human treated dentin matrix. J Tissue Eng Regen Med 2019; 13:1164-1177. [DOI: 10.1002/term.2866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/07/2018] [Accepted: 02/13/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Jie Li
- College of StomatologyChongqing Medical University Chongqing China
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesChongqing Medical University Chongqing China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationChongqing Medical University Chongqing China
| | - Hefeng Yang
- Department of Dental ResearchThe Affiliated Stomatological Hospital of Kunming Medical University Kunming China
| | - Qi Lu
- College of StomatologyChongqing Medical University Chongqing China
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesChongqing Medical University Chongqing China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationChongqing Medical University Chongqing China
| | - Duanjing Chen
- College of StomatologyChongqing Medical University Chongqing China
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesChongqing Medical University Chongqing China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationChongqing Medical University Chongqing China
| | - Mengjiao Zhou
- College of StomatologyChongqing Medical University Chongqing China
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesChongqing Medical University Chongqing China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationChongqing Medical University Chongqing China
| | - Yunchun Kuang
- College of StomatologyChongqing Medical University Chongqing China
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesChongqing Medical University Chongqing China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationChongqing Medical University Chongqing China
| | - Siqi Ying
- College of StomatologyChongqing Medical University Chongqing China
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesChongqing Medical University Chongqing China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationChongqing Medical University Chongqing China
| | - Jinlin Song
- College of StomatologyChongqing Medical University Chongqing China
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesChongqing Medical University Chongqing China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationChongqing Medical University Chongqing China
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22
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Mnatsakanyan R, Shema G, Basik M, Batist G, Borchers CH, Sickmann A, Zahedi RP. Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry. Expert Rev Proteomics 2019; 15:515-535. [PMID: 29893147 DOI: 10.1080/14789450.2018.1483340] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Numerous diseases are caused by changes in post-translational modifications (PTMs). Therefore, the number of clinical proteomics studies that include the analysis of PTMs is increasing. Combining complementary information-for example changes in protein abundance, PTM levels, with the genome and transcriptome (proteogenomics)-holds great promise for discovering important drivers and markers of disease, as variations in copy number, expression levels, or mutations without spatial/functional/isoform information is often insufficient or even misleading. Areas covered: We discuss general considerations, requirements, pitfalls, and future perspectives in applying PTM-centric proteomics to clinical samples. This includes samples obtained from a human subject, for instance (i) bodily fluids such as plasma, urine, or cerebrospinal fluid, (ii) primary cells such as reproductive cells, blood cells, and (iii) tissue samples/biopsies. Expert commentary: PTM-centric discovery proteomics can substantially contribute to the understanding of disease mechanisms by identifying signatures with potential diagnostic or even therapeutic relevance but may require coordinated efforts of interdisciplinary and eventually multi-national consortia, such as initiated in the cancer moonshot program. Additionally, robust and standardized mass spectrometry (MS) assays-particularly targeted MS, MALDI imaging, and immuno-MALDI-may be transferred to the clinic to improve patient stratification for precision medicine, and guide therapies.
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Affiliation(s)
- Ruzanna Mnatsakanyan
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Gerta Shema
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Mark Basik
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Gerald Batist
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Christoph H Borchers
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,c University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria , Victoria , British Columbia V8Z 7X8 , Canada.,d Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , V8P 5C2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
| | - Albert Sickmann
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,f Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum , 44801 Bochum , Germany.,g Department of Chemistry , College of Physical Sciences, University of Aberdeen , Aberdeen AB24 3FX , Scotland , United Kingdom
| | - René P Zahedi
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
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23
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Liu S, Yu F, Hu Q, Wang T, Yu L, Du S, Yu W, Li N. Development of in Planta Chemical Cross-Linking-Based Quantitative Interactomics in Arabidopsis. J Proteome Res 2018; 17:3195-3213. [DOI: 10.1021/acs.jproteome.8b00320] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Shichang Liu
- Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fengchao Yu
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Qin Hu
- Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Tingliang Wang
- Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lujia Yu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Shengwang Du
- Department of Physics, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Weichuan Yu
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ning Li
- Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen Guangdong 518057, China
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24
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Jylhä A, Nättinen J, Aapola U, Mikhailova A, Nykter M, Zhou L, Beuerman R, Uusitalo H. Comparison of iTRAQ and SWATH in a clinical study with multiple time points. Clin Proteomics 2018; 15:24. [PMID: 30069167 PMCID: PMC6065059 DOI: 10.1186/s12014-018-9201-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/23/2018] [Indexed: 12/21/2022] Open
Abstract
Background Advances in mass spectrometry have accelerated biomarker discovery in many areas of medicine. The purpose of this study was to compare two mass spectrometry (MS) methods, isobaric tags for relative and absolute quantitation (iTRAQ) and sequential window acquisition of all theoretical fragment ion spectra (SWATH), for analytical efficiency in biomarker discovery when there are multiple methodological constraints such as limited sample size and several time points for each patient to be analyzed. Methods A total of 140 tear samples were collected from 28 glaucoma patients at 5 time points in a glaucoma drug switch study. Samples were analyzed with iTRAQ and SWATH methods using NanoLC-MSTOF mass spectrometry. Results We discovered that even though iTRAQ is faster than SWATH with respect to analysis time per sample, it loses in sensitivity, reliability and robustness. While SWATH analysis yielded complete data of 456 proteins in all samples, with iTRAQ we were able to quantify 477 proteins in total but on average only 125 proteins were quantified in a sample. 283 proteins were common in the datasets produced by the two methods. Repeatability of the methods was assessed by calculating percent relative standard deviation (% RSD) between replicate MS analyses: SWATH was more repeatable (56% of proteins < 20% RSD), compared to iTRAQ (43% of proteins < 20% RSD). Despite the overall benefits of SWATH, both methods showed less than 1 log fold change difference in the expression of 74% common proteins. In addition, comparison to MS/MS peptide results using 8 isotopically labeled peptide standards, SWATH and iTRAQ showed similar results in terms of accuracy. Moreover, both methods detected similar trends in a longitudinal analysis of protein expression of two known tear biomarkers. Conclusions Overall, we conclude that SWATH should be preferred for biomarker discovery studies when analyzing limited volumes of clinical samples collected at multiple time points. Trial Registeration The study was approved by the Ethics Committee at Tampere University Hospital and was registered in EU clinical trials register (EudraCT Number: 2010-021039-14).
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Affiliation(s)
- Antti Jylhä
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Janika Nättinen
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Ulla Aapola
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Alexandra Mikhailova
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Matti Nykter
- 2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Lei Zhou
- 3Singapore Eye Research Institute, Singapore, Singapore.,4Duke-NUS SRP NBD, Singapore, Singapore.,5Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,6Ophthalmology and Visual Sciences Academic Clinical Research Program, Duke-NUS Medical School, Singapore, Singapore
| | - Roger Beuerman
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,3Singapore Eye Research Institute, Singapore, Singapore.,4Duke-NUS SRP NBD, Singapore, Singapore
| | - Hannu Uusitalo
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,7Tays Eye Center, Tampere University Hospital, Tampere, Finland
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25
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Haverland NA, Waas M, Ntai I, Keppel T, Gundry RL, Kelleher NL. Cell Surface Proteomics of N-Linked Glycoproteins for Typing of Human Lymphocytes. Proteomics 2018; 17. [PMID: 28834292 DOI: 10.1002/pmic.201700156] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/27/2017] [Indexed: 11/12/2022]
Abstract
Lymphocytes are immune cells that are critical for the maintenance of adaptive immunity. Differentiation of lymphoid progenitors yields B-, T-, and NK-cell subtypes that individually correlate with specific forms of leukemia or lymphoma. Therefore, it is imperative a precise method of cell categorization is utilized to detect differences in distinct disease states present in patients. One viable means of classification involves evaluation of the cell surface proteome of lymphoid malignancies. Specifically, this manuscript details the use of an antibody independent approach known as Cell Surface Capture Technology, to assess the N-glycoproteome of four human lymphocyte cell lines. Altogether, 404 cell surface N-glycoproteins were identified as markers for specific cell types involved in lymphocytic malignancies, including 82 N-glycoproteins that had not been previously been described for B or T cells within the Cell Surface Protein Atlas. Comparative analysis, hierarchical clustering techniques, and label-free quantitation were used to reveal proteins most informative for each cell type. Undoubtedly, the characterization of the cell surface proteome of lymphoid malignancies is a first step toward improving personalized diagnosis and treatment of leukemia and lymphoma.
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Affiliation(s)
- Nicole A Haverland
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ioanna Ntai
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Theodore Keppel
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
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Liu S, Yu F, Yang Z, Wang T, Xiong H, Chang C, Yu W, Li N. Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis. Mol Cell Proteomics 2018; 17:1010-1027. [PMID: 29440448 DOI: 10.1074/mcp.ra117.000530] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/18/2018] [Indexed: 12/19/2022] Open
Abstract
Protein acetylation, one of many types of post-translational modifications (PTMs), is involved in a variety of biological and cellular processes. In the present study, we applied both CsCl density gradient (CDG) centrifugation-based protein fractionation and a dimethyl-labeling-based 4C quantitative PTM proteomics workflow in the study of dynamic acetylproteomic changes in Arabidopsis. This workflow integrates the dimethyl chemical labeling with chromatography-based acetylpeptide separation and enrichment followed by mass spectrometry (MS) analysis, the extracted ion chromatogram (XIC) quantitation-based computational analysis of mass spectrometry data to measure dynamic changes of acetylpeptide level using an in-house software program, named Stable isotope-based Quantitation-Dimethyl labeling (SQUA-D), and finally the confirmation of ethylene hormone-regulated acetylation using immunoblot analysis. Eventually, using this proteomic approach, 7456 unambiguous acetylation sites were found from 2638 different acetylproteins, and 5250 acetylation sites, including 5233 sites on lysine side chain and 17 sites on protein N termini, were identified repetitively. Out of these repetitively discovered acetylation sites, 4228 sites on lysine side chain (i.e. 80.5%) are novel. These acetylproteins are exemplified by the histone superfamily, ribosomal and heat shock proteins, and proteins related to stress/stimulus responses and energy metabolism. The novel acetylproteins enriched by the CDG centrifugation fractionation contain many cellular trafficking proteins, membrane-bound receptors, and receptor-like kinases, which are mostly involved in brassinosteroid, light, gravity, and development signaling. In addition, we identified 12 highly conserved acetylation site motifs within histones, P-glycoproteins, actin depolymerizing factors, ATPases, transcription factors, and receptor-like kinases. Using SQUA-D software, we have quantified 33 ethylene hormone-enhanced and 31 hormone-suppressed acetylpeptide groups or called unique PTM peptide arrays (UPAs) that share the identical unique PTM site pattern (UPSP). This CDG centrifugation protein fractionation in combination with dimethyl labeling-based quantitative PTM proteomics, and SQUA-D may be applied in the quantitation of any PTM proteins in any model eukaryotes and agricultural crops as well as tissue samples of animals and human beings.
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Affiliation(s)
- Shichang Liu
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fengchao Yu
- §Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,¶Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Zhu Yang
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,‖The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
| | - Tingliang Wang
- **Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hairong Xiong
- ‡‡College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Caren Chang
- §§Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland 20742-5815
| | - Weichuan Yu
- §Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China; .,¶Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ning Li
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China; .,‖The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
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Thygesen C, Boll I, Finsen B, Modzel M, Larsen MR. Characterizing disease-associated changes in post-translational modifications by mass spectrometry. Expert Rev Proteomics 2018; 15:245-258. [DOI: 10.1080/14789450.2018.1433036] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Camilla Thygesen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Inga Boll
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bente Finsen
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Maciej Modzel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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28
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Fang P, Wang XJ, Xue Y, Liu MQ, Zeng WF, Zhang Y, Zhang L, Gao X, Yan GQ, Yao J, Shen HL, Yang PY. In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins. Oncotarget 2018; 7:38796-38809. [PMID: 27259237 PMCID: PMC5122430 DOI: 10.18632/oncotarget.9737] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/26/2016] [Indexed: 01/16/2023] Open
Abstract
N-glycosylation is one of the most prominent and abundant posttranslational modifications of proteins. It is estimated that over 50% of mammalian proteins undergo glycosylation. However, the analysis of N-glycoproteins has been limited by the available analytical technology. In this study, we comprehensively mapped the N-glycosylation sites in the mouse brain proteome by combining complementary methods, which included seven protease treatments, four enrichment techniques and two fractionation strategies. Altogether, 13492 N-glycopeptides containing 8386 N-glycosylation sites on 3982 proteins were identified. After evaluating the performance of the above methods, we proposed a simple and efficient workflow for large-scale N-glycosylation site mapping. The optimized workflow yielded 80% of the initially identified N-glycosylation sites with considerably less effort. Analysis of the identified N-glycoproteins revealed that many of the mouse brain proteins are N-glycosylated, including those proteins in critical pathways for nervous system development and neurological disease. Additionally, several important biomarkers of various diseases were found to be N-glycosylated. These data confirm that N-glycosylation is important in both physiological and pathological processes in the brain, and provide useful details about numerous N-glycosylation sites in brain proteins.
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Affiliation(s)
- Pan Fang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xin-Jian Wang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Yu Xue
- Department of Chemistry, Fudan University, Shanghai, China
| | - Ming-Qi Liu
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Wen-Feng Zeng
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Yang Zhang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lei Zhang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xing Gao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guo-Quan Yan
- Department of Chemistry, Fudan University, Shanghai, China
| | - Jun Yao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hua-Li Shen
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Peng-Yuan Yang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China.,Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai, China
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29
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Genome-wide association and pathway analysis of left ventricular function after anthracycline exposure in adults. Pharmacogenet Genomics 2018; 27:247-254. [PMID: 28542097 DOI: 10.1097/fpc.0000000000000284] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Anthracyclines are important chemotherapeutic agents, but their use is limited by cardiotoxicity. Candidate gene and genome-wide studies have identified putative risk loci for overt cardiotoxicity and heart failure, but there has been no comprehensive assessment of genomic variation influencing the intermediate phenotype of anthracycline-related changes in left ventricular (LV) function. The purpose of this study was to identify genetic factors influencing changes in LV function after anthracycline chemotherapy. METHODS We conducted a genome-wide association study (GWAS) of change in LV function after anthracycline exposure in 385 patients identified from BioVU, a resource linking DNA samples to de-identified electronic medical record data. Variants with P values less than 1×10 were independently tested for replication in a cohort of 181 anthracycline-exposed patients from a prospective clinical trial. Pathway analysis was performed to assess combined effects of multiple genetic variants. RESULTS Both cohorts were middle-aged adults of predominantly European descent. Among 11 candidate loci identified in discovery GWAS, one single nucleotide polymorphism near PR domain containing 2, with ZNF domain (PRDM2), rs7542939, had a combined P value of 6.5×10 in meta-analysis. Eighteen Kyoto Encyclopedia of Gene and Genomes pathways showed strong enrichment for variants associated with the primary outcome. Identified pathways related to DNA repair, cellular metabolism, and cardiac remodeling. CONCLUSION Using genome-wide association we identified a novel candidate susceptibility locus near PRDM2. Variation in genes belonging to pathways related to DNA repair, metabolism, and cardiac remodeling may influence changes in LV function after anthracycline exposure.
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30
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Cao L, Qu Y, Zhang Z, Wang Z, Prytkova I, Wu S. Intact glycopeptide characterization using mass spectrometry. Expert Rev Proteomics 2017; 13:513-22. [PMID: 27140194 DOI: 10.1586/14789450.2016.1172965] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Glycosylation is one of the most prominent and extensively studied protein post-translational modifications. However, traditional proteomic studies at the peptide level (bottom-up) rarely characterize intact glycopeptides (glycosylated peptides without removing glycans), so no glycoprotein heterogeneity information is retained. Intact glycopeptide characterization, on the other hand, provides opportunities to simultaneously elucidate the glycan structure and the glycosylation site needed to reveal the actual biological function of protein glycosylation. Recently, significant improvements have been made in the characterization of intact glycopeptides, ranging from enrichment and separation, mass spectroscopy (MS) detection, to bioinformatics analysis. In this review, we recapitulated currently available intact glycopeptide characterization methods with respect to their advantages and limitations as well as their potential applications.
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Affiliation(s)
- Li Cao
- a Pharma Research and Development , R&D Platform Technology & Science, GSK , King of Prussia , PA , USA
| | - Yi Qu
- b ChemEco Division , Evans Analytical Group , Hercules , CA , USA
| | - Zhaorui Zhang
- c Process Research & Development , AbbVie , North Chicago , IL , USA
| | - Zhe Wang
- d Department of Chemistry and Biochemistry , University of Oklahoma , Norman , OK , USA
| | - Iya Prytkova
- d Department of Chemistry and Biochemistry , University of Oklahoma , Norman , OK , USA
| | - Si Wu
- d Department of Chemistry and Biochemistry , University of Oklahoma , Norman , OK , USA
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31
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Barallobre-Barreiro J, Baig F, Fava M, Yin X, Mayr M. Glycoproteomics of the Extracellular Matrix: A Method for Intact Glycopeptide Analysis Using Mass Spectrometry. J Vis Exp 2017:55674. [PMID: 28518125 PMCID: PMC5565024 DOI: 10.3791/55674] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Fibrosis is a hallmark of many cardiovascular diseases and is associated with the exacerbated secretion and deposition of the extracellular matrix (ECM). Using proteomics, we have previously identified more than 150 ECM and ECM-associated proteins in cardiovascular tissues. Notably, many ECM proteins are glycosylated. This post-translational modification affects protein folding, solubility, binding, and degradation. We have developed a sequential extraction and enrichment method for ECM proteins that is compatible with the subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of intact glycopeptides. The strategy is based on sequential incubations with NaCl, SDS for tissue decellularization, and guanidine hydrochloride for the solubilization of ECM proteins. Recent advances in LC-MS/MS include fragmentation methods, such as combinations of higher-energy collision dissociation (HCD) and electron transfer dissociation (ETD), which allow for the direct compositional analysis of glycopeptides of ECM proteins. In the present paper, we describe a method to prepare the ECM from tissue samples. The method not only allows for protein profiling but also the assessment and characterization of glycosylation by MS analysis.
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Affiliation(s)
| | - Ferheen Baig
- King's British Heart Foundation Centre, King's College London
| | - Marika Fava
- King's British Heart Foundation Centre, King's College London
| | - Xiaoke Yin
- King's British Heart Foundation Centre, King's College London
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London;
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32
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Mallanna SK, Waas M, Duncan SA, Gundry RL. N-glycoprotein surfaceome of human induced pluripotent stem cell derived hepatic endoderm. Proteomics 2017; 17. [PMID: 27966262 DOI: 10.1002/pmic.201600397] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/20/2022]
Abstract
Using cell surface capture technology, the cell surface N-glycoproteome of human-induced pluripotent stem cell derived hepatic endoderm cells was assessed. Altogether, 395 cell surface N-glycoproteins were identified, represented by 1273 N-glycopeptides. This study identified N-glycoproteins that are not predicted to be localized to the cell surface and provides experimental data that assist in resolving ambiguous or incorrectly annotated transmembrane topology annotations. In a proof-of-concept analysis, combining these data with other cell surface proteome datasets is useful for identifying potentially cell type and lineage restricted markers and drug targets to advance the use of stem cell technologies for mechanistic developmental studies, disease modeling, drug discovery, and regenerative medicine.
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Affiliation(s)
- Sunil K Mallanna
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA.,Present address: National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Stephen A Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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33
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Lam MPY, Ping P, Murphy E. Proteomics Research in Cardiovascular Medicine and Biomarker Discovery. J Am Coll Cardiol 2016; 68:2819-2830. [PMID: 28007144 PMCID: PMC5189682 DOI: 10.1016/j.jacc.2016.10.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 11/21/2022]
Abstract
Proteomics is a systems physiology discipline to address the large-scale characterization of protein species within a biological system, be it a cell, a tissue, a body biofluid, an organism, or a cohort population. Building on advances from chemical analytical platforms (e.g., mass spectrometry and other technologies), proteomics approaches have contributed powerful applications in cardiovascular biomedicine, most notably in: 1) the discovery of circulating protein biomarkers of heart diseases from plasma samples; and 2) the identification of disease mechanisms and potential therapeutic targets in cardiovascular tissues, in both preclinical models and translational studies. Contemporary proteomics investigations offer powerful means to simultaneously examine tens of thousands of proteins in various samples, and understand their molecular phenotypes in health and disease. This concise review introduces study design considerations, example applications and use cases, as well as interpretation and analysis of proteomics data in cardiovascular biomedicine.
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Affiliation(s)
- Maggie P Y Lam
- NIH BD2K Center of Excellence and Department of Physiology, Medicine and Bioinformatics, University of California, Los Angeles, California.
| | - Peipei Ping
- NIH BD2K Center of Excellence and Department of Physiology, Medicine and Bioinformatics, University of California, Los Angeles, California
| | - Elizabeth Murphy
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
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34
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Hsu JL, Chen SH. Stable isotope dimethyl labelling for quantitative proteomics and beyond. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0364. [PMID: 27644970 PMCID: PMC5031631 DOI: 10.1098/rsta.2015.0364] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 05/21/2023]
Abstract
Stable-isotope reductive dimethylation, a cost-effective, simple, robust, reliable and easy-to- multiplex labelling method, is widely applied to quantitative proteomics using liquid chromatography-mass spectrometry. This review focuses on biological applications of stable-isotope dimethyl labelling for a large-scale comparative analysis of protein expression and post-translational modifications based on its unique properties of the labelling chemistry. Some other applications of the labelling method for sample preparation and mass spectrometry-based protein identification and characterization are also summarized.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Jue-Liang Hsu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan, Republic of China
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan City, Taiwan, Republic of China
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35
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Srikanth J, Agalyadevi R, Babu P. Targeted, Site-specific quantitation of N- and O-glycopeptides using 18O-labeling and product ion based mass spectrometry. Glycoconj J 2016; 34:95-105. [PMID: 27714477 DOI: 10.1007/s10719-016-9733-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/17/2016] [Accepted: 09/21/2016] [Indexed: 10/20/2022]
Abstract
The site-specific quantitation of N- and O-glycosylation is vital to understanding the function(s) of different glycans expressed at a given site of a protein under physiological and disease conditions. Most commonly used precursor ion intensity based quantification method is less accurate and other labeled methods are expensive and require enrichment of glycopeptides. Here, we used glycopeptide product (y and Y0) ions and 18O-labeling of C-terminal carboxyl group as a strategy to obtain quantitative information about fold-change and relative abundance of most of the glycoforms attached to the glycopeptides. As a proof of concept, the accuracy and robustness of this targeted, relative quantification LC-MS method was demonstrated using Rituximab. Furthermore, the N-glycopeptide quantification results were compared with a biosimilar of Rituximab and validated with quantitative data obtained from 2-AB-UHPLC-FL method. We further demonstrated the intensity fold-change and relative abundance of 46 unique N- and O-glycopeptides and aglycopeptides from innovator and biosimilar samples of Etanercept using both the normal-MS and product ion based quantitation. The results showed a very similar site-specific expression of N- and O-glycopeptides between the samples but with subtle differences. Interestingly, we have also been able to quantify macro-heterogeneity of all N- and O-glycopetides of Etanercept. In addition to applications in biotherapeutics, the developed method can also be used for site-specific quantitation of N- and O-glycopeptides and aglycopeptides of glycoproteins with known glycosylation pattern.
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Affiliation(s)
- Jandhyam Srikanth
- Glycomics and Glycoproteomics & Biologics Characterization Facility, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences (NCBS) - TIFR, GKVK Post, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Rathinasamy Agalyadevi
- Glycomics and Glycoproteomics & Biologics Characterization Facility, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences (NCBS) - TIFR, GKVK Post, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Ponnusamy Babu
- Glycomics and Glycoproteomics & Biologics Characterization Facility, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences (NCBS) - TIFR, GKVK Post, Bellary Road, Bangalore, Karnataka, 560065, India.
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36
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Abstract
The vasculature is essential for proper organ function. Many pathologies are directly and indirectly related to vascular dysfunction, which causes significant morbidity and mortality. A common pathophysiological feature of diseased vessels is extracellular matrix (ECM) remodelling. Analysing the protein composition of the ECM by conventional antibody-based techniques is challenging; alternative splicing or post-translational modifications, such as glycosylation, can mask epitopes required for antibody recognition. By contrast, proteomic analysis by mass spectrometry enables the study of proteins without the constraints of antibodies. Recent advances in proteomic techniques make it feasible to characterize the composition of the vascular ECM and its remodelling in disease. These developments may lead to the discovery of novel prognostic and diagnostic markers. Thus, proteomics holds potential for identifying ECM signatures to monitor vascular disease processes. Furthermore, a better understanding of the ECM remodelling processes in the vasculature might make ECM-associated proteins more attractive targets for drug discovery efforts. In this review, we will summarize the role of the ECM in the vasculature. Then, we will describe the challenges associated with studying the intricate network of ECM proteins and the current proteomic strategies to analyse the vascular ECM in metabolic and cardiovascular diseases.
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Affiliation(s)
- M Lynch
- King's British Heart Foundation Centre, King's College London, London, UK
| | | | | | - M Mayr
- King's British Heart Foundation Centre, King's College London, London, UK.
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37
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Barallobre-Barreiro J, Lynch M, Yin X, Mayr M. Systems biology-opportunities and challenges: the application of proteomics to study the cardiovascular extracellular matrix. Cardiovasc Res 2016; 112:626-636. [PMID: 27635058 PMCID: PMC5157133 DOI: 10.1093/cvr/cvw206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 08/31/2016] [Accepted: 09/09/2016] [Indexed: 12/29/2022] Open
Abstract
Systems biology approaches including proteomics are becoming more widely used in cardiovascular research. In this review article, we focus on the application of proteomics to the cardiac extracellular matrix (ECM). ECM remodelling is a hallmark of many cardiovascular diseases. Proteomic techniques using mass spectrometry (MS) provide a platform for the comprehensive analysis of ECM proteins without a priori assumptions. Proteomics overcomes various constraints inherent to conventional antibody detection. On the other hand, studies that use whole tissue lysates for proteomic analysis mask the identification of the less abundant ECM constituents. In this review, we first discuss decellularization-based methods that enrich for ECM proteins in cardiac tissue, and how targeted MS allows for accurate protein quantification. The second part of the review will focus on post-translational modifications including hydroxylation and glycosylation and on the release of matrix fragments with biological activity (matrikines), all of which can be interrogated by proteomic techniques.
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Affiliation(s)
| | - Marc Lynch
- King's British Heart Foundation Centre, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Xiaoke Yin
- King's British Heart Foundation Centre, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
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38
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Barallobre-Barreiro J, Gupta SK, Zoccarato A, Kitazume-Taneike R, Fava M, Yin X, Werner T, Hirt MN, Zampetaki A, Viviano A, Chong M, Bern M, Kourliouros A, Domenech N, Willeit P, Shah AM, Jahangiri M, Schaefer L, Fischer JW, Iozzo RV, Viner R, Thum T, Heineke J, Kichler A, Otsu K, Mayr M. Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human Atrial Fibrillation. Circulation 2016; 134:817-32. [PMID: 27559042 DOI: 10.1161/circulationaha.115.016423] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 06/27/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND Myocardial fibrosis is a feature of many cardiac diseases. We used proteomics to profile glycoproteins in the human cardiac extracellular matrix (ECM). METHODS Atrial specimens were analyzed by mass spectrometry after extraction of ECM proteins and enrichment for glycoproteins or glycopeptides. RESULTS ECM-related glycoproteins were identified in left and right atrial appendages from the same patients. Several known glycosylation sites were confirmed. In addition, putative and novel glycosylation sites were detected. On enrichment for glycoproteins, peptides of the small leucine-rich proteoglycan decorin were identified consistently in the flowthrough. Of all ECM proteins identified, decorin was found to be the most fragmented. Within its protein core, 18 different cleavage sites were identified. In contrast, less cleavage was observed for biglycan, the most closely related proteoglycan. Decorin processing differed between human ventricles and atria and was altered in disease. The C-terminus of decorin, important for the interaction with connective tissue growth factor, was detected predominantly in ventricles in comparison with atria. In contrast, atrial appendages from patients in persistent atrial fibrillation had greater levels of full-length decorin but also harbored a cleavage site that was not found in atrial appendages from patients in sinus rhythm. This cleavage site preceded the N-terminal domain of decorin that controls muscle growth by altering the binding capacity for myostatin. Myostatin expression was decreased in atrial appendages of patients with persistent atrial fibrillation and hearts of decorin null mice. A synthetic peptide corresponding to this decorin region dose-dependently inhibited the response to myostatin in cardiomyocytes and in perfused mouse hearts. CONCLUSIONS This proteomics study is the first to analyze the human cardiac ECM. Novel processed forms of decorin protein core, uncovered in human atrial appendages, can regulate the local bioavailability of antihypertrophic and profibrotic growth factors.
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Affiliation(s)
- Javier Barallobre-Barreiro
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Shashi K Gupta
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Anna Zoccarato
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Rika Kitazume-Taneike
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Marika Fava
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Xiaoke Yin
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Tessa Werner
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Marc N Hirt
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Anna Zampetaki
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Alessandro Viviano
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Mei Chong
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Marshall Bern
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Antonios Kourliouros
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Nieves Domenech
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Peter Willeit
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Ajay M Shah
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Marjan Jahangiri
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Liliana Schaefer
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Jens W Fischer
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Renato V Iozzo
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Rosa Viner
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Thomas Thum
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Joerg Heineke
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Antoine Kichler
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Kinya Otsu
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.)
| | - Manuel Mayr
- From King's British Heart Foundation Centre, King's College London, United Kingdom (J.B.-B., A. Zoccarato, R.K.-T., M.F., X.Y., A. Zampetaki, M.C., P.W., A.M.S., K.O., M.M.); Institute for Molecular and Translational Therapeutic Strategies, MH-Hannover, Germany (S.K.G., T.T.); St George's Hospital, NHS Trust, London, United Kingdom (M.F., A.V., A.K., M.J.); University Medical Center Hamburg-Eppendorf, Germany (T.W., M.N.H.); Protein Metrics, San Carlos, CA (M.B.); Biobanco A Coruña, INIBIC-Complexo Hospitalario Universitario de A Coruña, Spain (N.D.); Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt, Frankfurt am Main, Germany (L.S.); Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany (J.W.F.); Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (R.V.I.); Thermo Fisher Scientific, San Jose, CA (R.V.); Experimental Cardiology, Department of Cardiology and Angiology, MH-Hannover, Germany (J.H.); and Laboratoire Vecteurs: Synthèse et Applications Thérapeutiques, UMR 7199 CNRS Université de Strasbourg, Illkirch, France (A.K.).
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39
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Zhang C, Ye Z, Xue P, Shu Q, Zhou Y, Ji Y, Fu Y, Wang J, Yang F. Evaluation of Different N-Glycopeptide Enrichment Methods for N-Glycosylation Sites Mapping in Mouse Brain. J Proteome Res 2016; 15:2960-8. [PMID: 27480293 DOI: 10.1021/acs.jproteome.6b00098] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-Glycosylation of proteins plays a critical role in many biological pathways. Because highly heterogeneous N-glycopeptides are present in biological sources, the enrichment procedure is a crucial step for mass spectrometry analysis. Five enrichment methods, including IP-ZIC-HILIC, hydrazide chemistry, lectin affinity, ZIC-HILIC-FA, and TiO2 affinity were evaluated and compared in the study of mapping N-glycosylation sites in mouse brain. On the basis of our results, the identified N-glycosylation sites were 1891, 1241, 891, 869, and 710 and the FDR values were 3.29, 5.62, 9.54, 9.54, and 20.02%, respectively. Therefore, IP-ZIC-HILIC enrichment method displayed the highest sensitivity and specificity. In this work, we identified a total of 3446 unique glycosylation sites conforming to the N-glycosylation consensus motif (N-X-T/S/C; X ≠ P) with (18)O labeling in 1597 N-glycoproteins. N-glycosylation site information was used to confirm or correct the transmembrane topology of the 57 novel transmembrane N-glycoproteins.
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Affiliation(s)
- Chengqian Zhang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Zilu Ye
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Peng Xue
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
| | - Qingbo Shu
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Yue Zhou
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Yanlong Ji
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Ying Fu
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Jifeng Wang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
| | - Fuquan Yang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
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40
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Chandler KB, Costello CE. Glycomics and glycoproteomics of membrane proteins and cell-surface receptors: Present trends and future opportunities. Electrophoresis 2016; 37:1407-19. [PMID: 26872045 PMCID: PMC4889498 DOI: 10.1002/elps.201500552] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/02/2016] [Accepted: 02/02/2016] [Indexed: 12/16/2022]
Abstract
Membrane proteins mediate cell-cell interactions and adhesion, the transfer of ions and metabolites, and the transmission of signals from the extracellular environment to the cell interior. The extracellular domains of most cell membrane proteins are glycosylated, often at multiple sites. There is a growing awareness that glycosylation impacts the structure, interaction, and function of membrane proteins. The application of glycoproteomics and glycomics methods to membrane proteins has great potential. However, challenges also arise from the unique physical properties of membrane proteins. Successful analytical workflows must be developed and disseminated to advance functional glycoproteomics and glycomics studies of membrane proteins. This review explores the opportunities and challenges related to glycomic and glycoproteomic analysis of membrane proteins, including discussion of sample preparation, enrichment, and MS/MS analyses, with a focus on recent successful workflows for analysis of N- and O-linked glycosylation of mammalian membrane proteins.
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Affiliation(s)
- Kevin Brown Chandler
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
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41
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Hinneburg H, Stavenhagen K, Schweiger-Hufnagel U, Pengelley S, Jabs W, Seeberger PH, Silva DV, Wuhrer M, Kolarich D. The Art of Destruction: Optimizing Collision Energies in Quadrupole-Time of Flight (Q-TOF) Instruments for Glycopeptide-Based Glycoproteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:507-19. [PMID: 26729457 PMCID: PMC4756043 DOI: 10.1007/s13361-015-1308-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 05/12/2023]
Abstract
In-depth site-specific investigations of protein glycosylation are the basis for understanding the biological function of glycoproteins. Mass spectrometry-based N- and O-glycopeptide analyses enable determination of the glycosylation site, site occupancy, as well as glycan varieties present on a particular site. However, the depth of information is highly dependent on the applied analytical tools, including glycopeptide fragmentation regimes and automated data analysis. Here, we used a small set of synthetic disialylated, biantennary N-glycopeptides to systematically tune Q-TOF instrument parameters towards optimal energy stepping collision induced dissociation (CID) of glycopeptides. A linear dependency of m/z-ratio and optimal fragmentation energy was found, showing that with increasing m/z-ratio, more energy is required for glycopeptide fragmentation. Based on these optimized fragmentation parameters, a method combining lower- and higher-energy CID was developed, allowing the online acquisition of glycan and peptide-specific fragments within a single tandem MS experiment. We validated this method analyzing a set of human immunoglobulins (IgA1+2, sIgA, IgG1+2, IgE, IgD, IgM) as well as bovine fetuin. These optimized fragmentation parameters also enabled software-assisted glycopeptide assignment of both N- and O-glycopeptides including information about the most abundant glycan compositions, peptide sequence and putative structures. Twenty-six out of 30 N-glycopeptides and four out of five O-glycopeptides carrying >110 different glycoforms could be identified by this optimized LC-ESI tandem MS method with minimal user input. The Q-TOF based glycopeptide analysis platform presented here opens the way to a range of different applications in glycoproteomics research as well as biopharmaceutical development and quality control.
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Affiliation(s)
- Hannes Hinneburg
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Kathrin Stavenhagen
- Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Daniel Varón Silva
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
| | - Manfred Wuhrer
- Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany.
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Kim EH, Galchev VI, Kim JY, Misek SA, Stevenson TK, Campbell MD, Pagani FD, Day SM, Johnson TC, Washburn JG, Vikstrom KL, Michele DE, Misek DE, Westfall MV. Differential protein expression and basal lamina remodeling in human heart failure. Proteomics Clin Appl 2016; 10:585-96. [PMID: 26756417 DOI: 10.1002/prca.201500099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/27/2015] [Accepted: 01/05/2016] [Indexed: 12/17/2022]
Abstract
PURPOSE A goal of this study was to identify and investigate previously unrecognized components of the remodeling process in the progression to heart failure by comparing protein expression in ischemic failing (F) and nonfailing (NF) human hearts. EXPERIMENTAL DESIGN Protein expression differences were investigated using multidimensional protein identification and validated by Western analysis. This approach detected basal lamina (BL) remodeling, and further studies analyzed samples for evidence of structural BL remodeling. A rat model of pressure overload (PO) was studied to determine whether nonischemic stressors also produce BL remodeling and impact cellular adhesion. RESULTS Differential protein expression of collagen IV, laminin α2, and nidogen-1 indicated BL remodeling develops in F versus NF hearts Periodic disruption of cardiac myocyte BL accompanied this process in F, but not NF heart. The rat PO myocardium also developed BL remodeling and compromised myocyte adhesion compared to sham controls. CONCLUSIONS AND CLINICAL RELEVANCE Differential protein expression and evidence of structural and functional BL alterations develop during heart failure. The compromised adhesion associated with this remodeling indicates a high potential for dysfunctional cellular integrity and tethering in failing myocytes. Therapeutically targeting BL remodeling could slow or prevent the progression of heart disease.
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Affiliation(s)
- Evelyn H Kim
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Sean A Misek
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Tamara K Stevenson
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Matthew D Campbell
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Francis D Pagani
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Sharlene M Day
- Cardiovascular Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - T Craig Johnson
- DNA Sequencing and Microarray Facility, University of Michigan, Ann Arbor, MI, USA
| | - Joseph G Washburn
- DNA Sequencing and Microarray Facility, University of Michigan, Ann Arbor, MI, USA
| | - Karen L Vikstrom
- Cardiovascular Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Daniel E Michele
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.,Cardiovascular Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - David E Misek
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Margaret V Westfall
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
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43
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Lindoso RS, Sandim V, Collino F, Carvalho AB, Dias J, da Costa MR, Zingali RB, Vieyra A. Proteomics of cell-cell interactions in health and disease. Proteomics 2015; 16:328-44. [PMID: 26552723 DOI: 10.1002/pmic.201500341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/29/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022]
Abstract
The mechanisms of cell-cell communications are now under intense study by proteomic approaches. Proteomics has unraveled changes in protein profiling as the result of cell interactions mediated by ligand/receptor, hormones, soluble factors, and the content of extracellular vesicles. Besides being a brief overview of the main and profitable methodologies now available (evaluating theory behind the methods, their usefulness, and pitfalls), this review focuses on-from a proteome perspective-some signaling pathways and post-translational modifications (PTMs), which are essential for understanding ischemic lesions and their recovery in two vital organs in mammals, the heart, and the kidney. Knowledge of misdirection of the proteome during tissue recovery, such as represented by the convergence between fibrosis and cancer, emerges as an important tool in prognosis. Proteomics of cell-cell interaction is also especially useful for understanding how stem cells interact in injured tissues, anticipating clues for rational therapeutic interventions. In the effervescent field of induced pluripotency and cell reprogramming, proteomic studies have shown what proteins from specialized cells contribute to the recovery of infarcted tissues. Overall, we conclude that proteomics is at the forefront in helping us to understand the mechanisms that underpin prevalent pathological processes.
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Affiliation(s)
- Rafael S Lindoso
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil
| | - Vanessa Sandim
- National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Federica Collino
- Department of Medical Sciences and Molecular Biotechnology Center, University of Turin, Turin, Italy.,Translational Center of Regenerative Medicine, University of Turin/Fresenius Medical Care, Turin, Italy
| | - Adriana B Carvalho
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil
| | - Juliana Dias
- National Institute of Cancer, Rio de Janeiro, RJ, Brazil
| | - Milene R da Costa
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Russolina B Zingali
- National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Proteomic Network of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Adalberto Vieyra
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Translational Biomedicine Graduate Program, Grand Rio University, Duque de Caxias, RJ, Brazil
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44
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Pabst M, Benešová I, Fagerer SR, Jacobsen M, Eyer K, Schmidt G, Steinhoff R, Krismer J, Wahl F, Preisler J, Zenobi R. Differential Isotope Labeling of Glycopeptides for Accurate Determination of Differences in Site-Specific Glycosylation. J Proteome Res 2015; 15:326-31. [DOI: 10.1021/acs.jproteome.5b00899] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Pabst
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Iva Benešová
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
- Department
of Chemistry, Masaryk University, 625 00 Brno, Czech Republic
| | - Stephan R. Fagerer
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Mathias Jacobsen
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Klaus Eyer
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Gregor Schmidt
- Department
of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland
| | - Robert Steinhoff
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Jasmin Krismer
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Fabian Wahl
- Sigma-Aldrich Chemie GmbH, 9470 Buchs, Switzerland
| | - Jan Preisler
- Department
of Chemistry, Masaryk University, 625 00 Brno, Czech Republic
- Central
European Institute of Technology (CEITEC), Masaryk University, 625
00 Brno, Czech Republic
| | - Renato Zenobi
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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45
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Applying Proteomics to Investigate Extracellular Matrix in Health and Disease. CURRENT TOPICS IN MEMBRANES 2015; 76:171-96. [PMID: 26610914 DOI: 10.1016/bs.ctm.2015.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The molecular composition of basement membranes (BMs) has traditionally been investigated by candidate-based approaches leading to the identification of key structural components as described in previous chapters. Laminins, collagen IV, nidogens, perlecan, and type XV/XVIII collagen are integral to BMs with isoforms showing tissue specificity. More recently the application of mass spectrometry (MS)-based proteomics has led to the discovery of many more structural and regulatory components of BMs and more broadly, extracellular matrix (ECM). These investigations have revealed tissue-specific signatures of between 100 and 150 ECM components, demonstrating the complexity of the extracellular niche. In addition to providing a structural scaffold for cells, ECM is a dynamic extracellular environment capable of regulating the physical properties of tissues. Global investigations of ECM with proteomics in turn enable systems level analyses and when applied to health and disease states these investigations provide insights into pathways regulating matrix dysregulation. This chapter focuses on the methods used to extract ECM and on the analysis of its composition using MS-based proteomics, and it provides examples of how these approaches have been used to investigate health and disease states.
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46
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Kropp EM, Bhattacharya S, Waas M, Chuppa SL, Hadjantonakis AK, Boheler KR, Gundry RL. N-glycoprotein surfaceomes of four developmentally distinct mouse cell types. Proteomics Clin Appl 2015; 8:603-9. [PMID: 24920426 DOI: 10.1002/prca.201400021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/06/2014] [Accepted: 06/06/2014] [Indexed: 11/12/2022]
Abstract
PURPOSE Detailed knowledge of cell surface proteins present during early embryonic development remains limited for most cell lineages. Due to the relevance of cell surface proteins in their functional roles controlling cell signaling and their utility as accessible, nongenetic markers for cell identification and sorting, the goal of this study was to provide new information regarding the cell surface proteins present during early mouse embryonic development. EXPERIMENTAL DESIGN Using the cell surface capture technology, the cell surface N-glycoproteomes of three cell lines and one in vitro differentiated cell type representing distinct cell fates and stages in mouse embryogenesis were assessed. RESULTS Altogether, more than 600 cell surface N-glycoproteins were identified represented by >5500 N-glycopeptides. CONCLUSIONS AND CLINICAL RELEVANCE The development of new, informative cell surface markers for the reliable identification and isolation of functionally defined subsets of cells from early developmental stages will advance the use of stem cell technologies for mechanistic developmental studies, including disease modeling and drug discovery.
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Affiliation(s)
- Erin M Kropp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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Goyallon A, Cholet S, Chapelle M, Junot C, Fenaille F. Evaluation of a combined glycomics and glycoproteomics approach for studying the major glycoproteins present in biofluids: Application to cerebrospinal fluid. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:461-473. [PMID: 26160412 DOI: 10.1002/rcm.7125] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/08/2014] [Accepted: 12/14/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE Glycosylation is one of the most complex types of post-translational modifications of proteins. The alteration of glycans bound to proteins from cerebrospinal fluid (CSF) in relation to disorders of the central nervous system is a highly relevant subject, but only few studies have focused on the glycosylation of CSF proteins. METHODS Reproducible profiles of CSF N-glycans were first obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry after permethylation. Tryptic glycopeptides from CSF proteins were also enriched by hydrophilic interaction, and the resulting extracts divided into two equal aliquots. A first aliquot was enzymatically deglycosylated and analyzed by nano-liquid chromatography/tandem mass spectrometry while the second one, containing intact enriched glycopeptides, was directly analyzed. Site-specific data were obtained by combining the data from these three experiments. RESULTS We describe the development of a versatile approach for obtaining site-specific information on the N-glycosylation of CSF glycoproteins. Under these conditions, 124 N-glycopeptides representing 55 N-glycosites from 36 glycoproteins were tentatively identified. Special emphasis was placed on the analysis of glycoproteins/glycopeptides bearing 'brain-type' N-glycans, representing potential biologically relevant structures in the field of neurodegenerative disorders. Using our workflow, only a few proteins were shown to carry such particular glycan motifs. CONCLUSIONS We developed an approach combining N-glycomics and N-glycoproteomics and underline its usefulness to study the site-specific glycosylation of major human CSF proteins. The final rather long-term objective is to combine these data with those from other omics approaches to delve deeper into the understanding of particular neurological disorders.
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Affiliation(s)
- Arnaud Goyallon
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | - Sophie Cholet
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | | | - Christophe Junot
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | - François Fenaille
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
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Pabst M, Küster SK, Wahl F, Krismer J, Dittrich PS, Zenobi R. A Microarray-Matrix-assisted Laser Desorption/Ionization-Mass Spectrometry Approach for Site-specific Protein N-glycosylation Analysis, as Demonstrated for Human Serum Immunoglobulin M (IgM). Mol Cell Proteomics 2015; 14:1645-56. [PMID: 25802287 DOI: 10.1074/mcp.o114.046748] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 12/31/2022] Open
Abstract
We demonstrate a new approach for the site-specific identification and characterization of protein N-glycosylation. It is based on a nano-liquid chromatography microarray-matrix assisted laser desorption/ionization-MS platform, which employs droplet microfluidics for on-plate nanoliter reactions. A chromatographic separation of a proteolytic digest is deposited at a high frequency on the microarray. In this way, a short separation run is archived into thousands of nanoliter reaction cavities, and chromatographic peaks are spread over multiple array spots. After fractionation, each other spot is treated with PNGaseF to generate two correlated traces within one run, one with treated spots where glycans are enzymatically released from the peptides, and one containing the intact glycopeptides. Mining for distinct glycosites is performed by searching for the predicted deglycosylated peptides in the treated trace. An identified peptide then leads directly to the position of the "intact" glycopeptide clusters, which are located in the adjacent spots. Furthermore, the deglycosylated peptide can be sequenced efficiently in a simple collision-induced dissociation-MS experiment. We applied the microarray approach to a detailed site-specific glycosylation analysis of human serum IgM. By scanning the treated spots with low-resolution matrix assisted laser desorption/ionization-time-of-flight-MS, we observed all five deglycosylated peptides, including the one originating from the secretory chain. A detailed glycopeptide characterization was then accomplished on the adjacent, untreated spots with high mass resolution and high mass accuracy using a matrix assisted laser desorption ionization-Fourier transform-MS. We present the first detailed and comprehensive mass spectrometric analysis on the glycopeptide level for human polyclonal IgM with high mass accuracy. Besides complex type glycans on Asn 395, 332, 171, and on the J chain, we observed oligomannosidic glycans on Asn 563, Asn 402 and minor amounts of oligomannosidic glycans on the glycosite Asn 171. Furthermore, hybrid type glycans were found on Asn 402, Asn 171 and in traces Asn 332.
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Affiliation(s)
- Martin Pabst
- From the ‡Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Simon Karl Küster
- From the ‡Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Fabian Wahl
- §Sigma-Aldrich Chemie GmbH, Industriestrasse 25, 9471 Buchs (SG), Switzerland
| | - Jasmin Krismer
- From the ‡Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Petra S Dittrich
- From the ‡Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Renato Zenobi
- From the ‡Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland;
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49
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Ahn YH, Kim JY, Yoo JS. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods. MASS SPECTROMETRY REVIEWS 2015; 34:148-65. [PMID: 24889823 PMCID: PMC4340049 DOI: 10.1002/mas.21428] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/20/2013] [Indexed: 05/12/2023]
Abstract
Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies.
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Affiliation(s)
- Yeong Hee Ahn
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
| | - Jin Young Kim
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
| | - Jong Shin Yoo
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
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50
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Dubayle J, Vialle S, Schneider D, Pontvianne J, Mantel N, Adam O, Guy B, Talaga P. Site-specific characterization of envelope protein N-glycosylation on Sanofi Pasteur's tetravalent CYD dengue vaccine. Vaccine 2015; 33:1360-8. [PMID: 25660649 DOI: 10.1016/j.vaccine.2015.01.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 01/16/2023]
Abstract
Recently, several virus studies have shown that protein glycosylation play a fundamental role in the virus-host cell interaction. Glycosylation characterization of the envelope proteins in both insect and mammalian cell-derived dengue virus (DENV) has established that two potential glycosylation residues, the asparagine 67 and 153 can potentially be glycosylated. Moreover, it appears that the glycosylation of these two residues can influence dramatically the virus production and the infection spreading in either mosquito or mammalian cells. The Sanofi Pasteur tetravalent dengue vaccine (CYD) consists of four chimeric viruses produced in mammalian vero cells. As DENV, the CYDs are able to infect human monocyte-derived dendritic cells in vitro via C-type lectins cell-surface molecules. Despite the importance of this interaction, the specific glycosylation pattern of the DENV has not been clearly documented so far. In this paper, we investigated the structure of the N-linked glycans in the four CYD serotypes. Using MALDI-TOF analysis, the N-linked glycans of CYDs were found to be a mix of high-mannose, hybrid and complex glycans. Site-specific N-glycosylation analysis of CYDs using nanoLC-ESI-MS/MS demonstrates that both asparagine residues 67 and 153 are glycosylated. Predominant glycoforms at asparagine 67 are high mannose-type structures while mainly complex- and hybrid-type structures are detected at asparagine 153. In vitro studies have shown that the immunological consequences of infection by the CYD dengue viruses 1-4 versus the wild type parents are comparable in human monocyte-derived dendritic cells. Our E-protein glycan characterizations of CYD are consistent with those observations from the wild type parents and thus support in vitro studies. In addition, these data provide new insights for the role of glycans in the dengue virus-host cell interactions.
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Affiliation(s)
- Jean Dubayle
- Research and Development Department, Sanofi Pasteur, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy L'Etoile, France.
| | - Sandrine Vialle
- Research and Development Department, Sanofi Pasteur, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy L'Etoile, France
| | - Diane Schneider
- Research and Development Department, Sanofi Pasteur, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy L'Etoile, France
| | - Jérémy Pontvianne
- Research and Development Department, Sanofi Pasteur, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy L'Etoile, France
| | - Nathalie Mantel
- Research and Development Department, Sanofi Pasteur, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy L'Etoile, France
| | - Olivier Adam
- Research and Development Department, Sanofi Pasteur, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy L'Etoile, France
| | - Bruno Guy
- Research and Development Department, Sanofi Pasteur, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy L'Etoile, France
| | - Philippe Talaga
- Research and Development Department, Sanofi Pasteur, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy L'Etoile, France
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