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Wu W, Krijgsveld J. Secretome Analysis: Reading Cellular Sign Language to Understand Intercellular Communication. Mol Cell Proteomics 2024; 23:100692. [PMID: 38081362 PMCID: PMC10793180 DOI: 10.1016/j.mcpro.2023.100692] [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: 08/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/06/2024] Open
Abstract
A significant portion of mammalian proteomes is secreted to the extracellular space to fulfill crucial roles in cell-to-cell communication. To best recapitulate the intricate and multi-faceted crosstalk between cells in a live organism, there is an ever-increasing need for methods to study protein secretion in model systems that include multiple cell types. In addition, posttranslational modifications further expand the complexity and versatility of cellular communication. This review aims to summarize recent strategies and model systems that employ cellular coculture, chemical biology tools, protein enrichment, and proteomic methods to characterize the composition and function of cellular secretomes. This is all geared towards gaining better understanding of organismal biology in vivo mediated by secretory signaling.
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Affiliation(s)
- Wei Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore, Singapore.
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty, Heidelberg University, Heidelberg, Germany.
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2
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Jung I, Cho YJ, Park M, Park K, Lee SH, Kim WH, Jeong H, Lee JE, Kim GY. Proteomic analysis reveals activation of platelet- and fibrosis-related pathways in hearts of ApoE -/- mice exposed to diesel exhaust particles. Sci Rep 2023; 13:22636. [PMID: 38114606 PMCID: PMC10730529 DOI: 10.1038/s41598-023-49790-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023] Open
Abstract
Air pollution is an environmental risk factor linked to multiple human diseases including cardiovascular diseases (CVDs). While particulate matter (PM) emitted by diesel exhaust damages multiple organ systems, heart disease is one of the most severe pathologies affected by PM. However, the in vivo effects of diesel exhaust particles (DEP) on the heart and the molecular mechanisms of DEP-induced heart dysfunction have not been investigated. In the current study, we attempted to identify the proteomic signatures of heart fibrosis caused by diesel exhaust particles (DEP) in CVDs-prone apolipoprotein E knockout (ApoE-/-) mice model using tandem mass tag (TMT)-based quantitative proteomic analysis. DEP exposure induced mild heart fibrosis in ApoE-/- mice compared with severe heart fibrosis in ApoE-/- mice that were treated with CVDs-inducing peptide, angiotensin II. TMT-based quantitative proteomic analysis of heart tissues between PBS- and DEP-treated ApoE-/- mice revealed significant upregulation of proteins associated with platelet activation and TGFβ-dependent pathways. Our data suggest that DEP exposure could induce heart fibrosis, potentially via platelet-related pathways and TGFβ induction, causing cardiac fibrosis and dysfunction.
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Affiliation(s)
- Inkyo Jung
- Division of Cardiovascular Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, 187 Osongsaengmyeng2-ro, Osong-eub, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Yoon Jin Cho
- Chemical and Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Chemistry, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul, 04310, Republic of Korea
| | - Minhan Park
- School of Earth Science and Environmental Engineering, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Kihong Park
- School of Earth Science and Environmental Engineering, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Seung Hee Lee
- Division of Cardiovascular Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, 187 Osongsaengmyeng2-ro, Osong-eub, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Won-Ho Kim
- Division of Cardiovascular Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, 187 Osongsaengmyeng2-ro, Osong-eub, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Hyuk Jeong
- Department of Chemistry, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul, 04310, Republic of Korea
| | - Ji Eun Lee
- Chemical and Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea.
| | - Geun-Young Kim
- Division of Cardiovascular Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, 187 Osongsaengmyeng2-ro, Osong-eub, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea.
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3
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Atashi M, Reyes CDG, Sandilya V, Purba W, Ahmadi P, Hakim MA, Kobeissy F, Plazzi G, Moresco M, Lanuzza B, Ferri R, Mechref Y. LC-MS/MS Quantitation of HILIC-Enriched N-glycopeptides Derived from Low-Abundance Serum Glycoproteins in Patients with Narcolepsy Type 1. Biomolecules 2023; 13:1589. [PMID: 38002271 PMCID: PMC10669497 DOI: 10.3390/biom13111589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Glycoproteomic analysis is always challenging because of low abundance and complex site-specific heterogeneity. Glycoproteins are involved in various biological processes such as cell signaling, adhesion, and cell-cell communication and may serve as potential biomarkers when analyzing different diseases. Here, we investigate glycoproteins in narcolepsy type 1 (NT1) disease, a form of narcolepsy characterized by cataplexy-the sudden onset of muscle paralysis that is typically triggered by intense emotions. In this study, 27 human blood serum samples were analyzed, 16 from NT1 patients and 11 from healthy individuals serving as controls. We quantified hydrophilic interaction liquid chromatography (HILIC)-enriched glycopeptides from low-abundance serum samples of controls and NT1 patients via LC-MS/MS. Twenty-eight unique N-glycopeptides showed significant changes between the two studied groups. The sialylated N-glycopeptide structures LPTQNITFQTESSVAEQEAEFQSPK HexNAc6, Hex3, Neu5Ac2 (derived from the ITIH4 protein) and the structure IVLDPSGSMNIYLVLDGSDSIGASNFTGAK HexNAc5, Hex4, Fuc1 (derived from the CFB protein), with p values of 0.008 and 0.01, respectively, were elevated in NT1 samples compared with controls. In addition, the N-glycopeptide protein sources Ceruloplasmin, Complement factor B, and ITH4 were observed to play an important role in the complement activation and acute-phase response signaling pathways. This may explain the possible association between the biomarkers and pathophysiological effects.
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Affiliation(s)
- Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Cristian D. Gutierrez Reyes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Vishal Sandilya
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Waziha Purba
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Md. Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Firas Kobeissy
- Department of biochemistry and molecular genetics, Faculty of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 11072020, Lebanon;
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), Neuroscience Institute, Morehouse School of Medicine, Atlanta, GE 30310, USA
| | - Giuseppe Plazzi
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40124 Bologna, Italy; (G.P.); (M.M.)
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Monica Moresco
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40124 Bologna, Italy; (G.P.); (M.M.)
| | - Bartolo Lanuzza
- Sleep Research Center, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Tronia, Italy; (B.L.); (R.F.)
| | - Raffaele Ferri
- Sleep Research Center, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Tronia, Italy; (B.L.); (R.F.)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
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Yang D, Han F, Cai J, Sun H, Wang F, Jiang M, Zhang M, Yuan M, Zhou W, Li H, Yang L, Bai Y, Xiao L, Dong H, Cheng Q, Mao H, Zhou L, Wang R, Li Y, Nie H. N-glycosylation by N-acetylglucosaminyltransferase IVa enhances the interaction of integrin β1 with vimentin and promotes hepatocellular carcinoma cell motility. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119513. [PMID: 37295747 DOI: 10.1016/j.bbamcr.2023.119513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
N-glycosylation has been revealed to be tightly associated with cancer metastasis. As a key transferase that catalyzes the formation of β1,4 N-acetylglucosamine (β1,4GlcNAc) branches on the mannose core of N-glycans, N-acetylglucosaminyltransferase IVa (GnT-IVa) has been reported to be involved in hepatocellular carcinoma (HCC) metastasis by forming N-glycans; however, the underlying mechanisms are largely unknown. In the current study, we found that GnT-IVa was upregulated in HCC tissues and positively correlated with worse outcomes in HCC patients. We found that GnT-IVa could promote tumor growth in mice; notably, this effect was attenuated after mutating the enzymatic site (D445A) of GnT-IVa, suggesting that GnT-IVa regulated HCC progression by forming β1,4GlcNAc branches. To mechanistically investigate the role of GnT-IVa in HCC, we conducted GSEA and GO functional analysis as well as in vitro experiments. The results showed that GnT-IVa could enhance HCC cell migration, invasion and adhesion ability and increase β1,4GlcNAc branch glycans on integrin β1 (ITGB1), a tumor-associated glycoprotein that is closely involved in cell motility by interacting with vimentin. Interruption of β1,4GlcNAc branch glycan modification on ITGB1 could suppress the interaction of ITGB1 with vimentin and inhibit cell motility. These results revealed that GnT-IVa could promote HCC cell motility by affecting the biological functions of ITGB1 through N-glycosylation. In summary, our results revealed that GnT-IVa is highly expressed in HCC and can form β1,4GlcNAc branches on ITGB1, which are essential for interactions with vimentin to promote HCC cell motility. These findings not only proposed a novel mechanism for GnT-IVa in HCC progression but also revealed the significance of N-glycosylation on ITGB1 during the process, which may provide a novel target for future HCC therapy.
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Affiliation(s)
- Depeng Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Fang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Jialing Cai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Handi Sun
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Fengyou Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Meiyi Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Mengmeng Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Mengfan Yuan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Huaxin Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Lijun Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Yan Bai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Lixing Xiao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Haiyang Dong
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Qixiang Cheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Haoyu Mao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Lu Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Ruonan Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
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5
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Chien YC, Wang YS, Sridharan D, Kuo CW, Chien CT, Uchihashi T, Kato K, Angata T, Meng TC, Hsu STD, Khoo KH. High Density of N- and O-Glycosylation Shields and Defines the Structural Dynamics of the Intrinsically Disordered Ectodomain of Receptor-type Protein Tyrosine Phosphatase Alpha. JACS AU 2023; 3:1864-1875. [PMID: 37502146 PMCID: PMC10369406 DOI: 10.1021/jacsau.3c00124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/29/2023]
Abstract
The intracellular phosphatase domain of the receptor-type protein tyrosine phosphatase alpha (PTPRA) is known to regulate various signaling pathways related to cell adhesion through c-Src kinase activation. In contrast, the functional significance of its relatively short, intrinsically disordered, and heavily glycosylated ectodomain remains unclear. Through detailed mass spectrometry analyses of a combination of protease and glycosidase digests, we now provide the first experimental evidence for its site-specific glycosylation pattern. This includes the occurrence of O-glycan at the N-glycosylation sequon among the more than 30 O-glycosylation sites confidently identified beside the 7 N-glycosylation sites. The closely spaced N- and O-glycans appear to have mutually limited the extent of further galactosylation and sialylation. An immature smaller form of full-length PTPRA was found to be deficient in O-glycosylation, most likely due to failure to transit the Golgi. N-glycosylation, on the other hand, is dispensable for cell surface expression and contributes less than the extensive O-glycosylation to the overall solution structure of the ectodomain. The glycosylation information is combined with the overall structural features of the ectodomain derived from small-angle X-ray scattering and high-speed atomic force microscopy monitoring to establish a dynamic structural model of the densely glycosylated PTPRA ectodomain. The observed high structural flexibility, as manifested by continuous transitioning from fully to partially extended and fold-back conformations, suggests that the receptor-type phosphatase is anchored to the membrane and kept mostly at a monomeric state through an ectodomain shaped and fully shielded by glycosylation.
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Affiliation(s)
- Yu-Chun Chien
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Yong-Sheng Wang
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Deepa Sridharan
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chu-Wei Kuo
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Ta Chien
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Takayuki Uchihashi
- Department
of Physics, Nagoya University, Nagoya 464-8602, Japan
- Exploratory
Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Koichi Kato
- Exploratory
Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Institute
for Molecular Science, National Institutes
of Natural Sciences, Okazaki 444-8787, Japan
- Graduate
School of Pharmaceutical Sciences, Nagoya
City University, Nagoya 467-8603, Japan
| | - Takashi Angata
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Tzu-Ching Meng
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Shang-Te Danny Hsu
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
- International
Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashihiroshima 739-8527, Japan
| | - Kay-Hooi Khoo
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
- Exploratory
Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
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Conway JRW, Dinç DD, Follain G, Paavolainen O, Kaivola J, Boström P, Hartiala P, Peuhu E, Ivaska J. IGFBP2 secretion by mammary adipocytes limits breast cancer invasion. SCIENCE ADVANCES 2023; 9:eadg1840. [PMID: 37436978 DOI: 10.1126/sciadv.adg1840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
The progression of noninvasive ductal carcinoma in situ to invasive ductal carcinoma for patients with breast cancer results in a significantly poorer prognosis and is the precursor to metastatic disease. In this work, we have identified insulin-like growth factor-binding protein 2 (IGFBP2) as a potent adipocrine factor secreted by healthy breast adipocytes that acts as a barrier against invasive progression. In line with this role, adipocytes differentiated from patient-derived stromal cells were found to secrete IGFBP2, which significantly inhibited breast cancer invasion. This occurred through binding and sequestration of cancer-derived IGF-II. Moreover, depletion of IGF-II in invading cancer cells using small interfering RNAs or an IGF-II-neutralizing antibody ablated breast cancer invasion, highlighting the importance of IGF-II autocrine signaling for breast cancer invasive progression. Given the abundance of adipocytes in the healthy breast, this work exposes the important role they play in suppressing cancer progression and may help expound upon the link between increased mammary density and poorer prognosis.
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Affiliation(s)
- James R W Conway
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Defne D Dinç
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Institute of Biomedicine, and Cancer Research Laboratory FICAN West, University of Turku, FI-20520 Turku, Finland
- Western Finnish Cancer Center (FICAN West), University of Turku and Turku University Hospital, FI-20520 Turku, Finland
| | - Gautier Follain
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Oona Paavolainen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Institute of Biomedicine, and Cancer Research Laboratory FICAN West, University of Turku, FI-20520 Turku, Finland
- Western Finnish Cancer Center (FICAN West), University of Turku and Turku University Hospital, FI-20520 Turku, Finland
| | - Jasmin Kaivola
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Pia Boström
- Department of Pathology, Turku University Hospital, 20520 Turku, Finland; University of Turku, 20520 Turku, Finland
| | - Pauliina Hartiala
- Department of Plastic and General Surgery, Turku University Hospital, 20520 Turku, Finland
- Medicity Research Laboratory, InFLAMES Research Flagship, University of Turku, Turku, Finland
| | - Emilia Peuhu
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Institute of Biomedicine, and Cancer Research Laboratory FICAN West, University of Turku, FI-20520 Turku, Finland
- Western Finnish Cancer Center (FICAN West), University of Turku and Turku University Hospital, FI-20520 Turku, Finland
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Western Finnish Cancer Center (FICAN West), University of Turku and Turku University Hospital, FI-20520 Turku, Finland
- Department of Life Technologies, University of Turku, FI-20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, FI-00014 Helsinki, Finland
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7
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Xu M, Yang A, Xia J, Jiang J, Liu CF, Ye Z, Ma J, Yang S. Protein glycosylation in urine as a biomarker of diseases. Transl Res 2023; 253:95-107. [PMID: 35952983 DOI: 10.1016/j.trsl.2022.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023]
Abstract
Human body fluids have become an indispensable resource for clinical research, diagnosis and prognosis. Urine is widely used to discover disease-specific glycoprotein biomarkers because of its recurrently non-invasive collection and disease-indicating properties. While urine is an unstable fluid in that its composition changes with ingested nutrients and further as it is excreted through micturition, urinary proteins are more stable and their abnormal glycosylation is associated with diseases. It is known that aberrant glycosylation can define tumor malignancy and indicate disease initiation and progression. However, a thorough and translational survey of urinary glycosylation in diseases has not been performed. In this article, we evaluate the clinical applications of urine, introduce methods for urine glycosylation analysis, and discuss urine glycoprotein biomarkers. We emphasize the importance of mining urinary glycoproteins and searching for disease-specific glycosylation in various diseases (including cancer, neurodegenerative diseases, diabetes, and viral infections). With advances in mass spectrometry-based glycomics/glycoproteomics/glycopeptidomics, characterization of disease-specific glycosylation will optimistically lead to the discovery of disease-related urinary biomarkers with better sensitivity and specificity in the near future.
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Affiliation(s)
- Mingming Xu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Arthur Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Jun Xia
- Clinical Laboratory Center, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Junhong Jiang
- Department of Pulmonary and Critical Care Medicine, Dushu Lake Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chun-Feng Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhenyu Ye
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, District of Columbia.
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China.
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8
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Sato Y, Kawashima K, Fukui E, Matsumoto H, Yoshizawa F, Sato Y. Functional analysis reveals that Tinagl1 is required for normal muscle development in mice through the activation of ERK signaling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119294. [PMID: 35597451 DOI: 10.1016/j.bbamcr.2022.119294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/21/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Tinagl1 (tubulointerstitial nephritis antigen-like 1) is a matricellular protein involved in female infertility and breast cancer tumorigenesis. In this study, we analyzed the function of Tinagl1 in skeletal muscle using knockout mice and cell experiments. Although primary myoblasts isolated from Tinagl1-decifient (Tinagl1-/-) mice differentiated into normal myotubes, and treatment with recombinant Tinagl1 did not affect the proliferation or differentiation of C2C12 myoblasts, Tinagl1-/- mice exhibited reduced body mass and calf muscle weights compared to the control group (Tinagl1flox/flox). Furthermore, Tinagl1-/- mice showed myofibers with centrally located nuclei, which is a morphological marker of regenerating muscle or myopathy. In addition, the capillary density in the soleus muscle of Tinagl1-/- mice showed a decreasing trend compared to that of the control group. Importantly, si-RNA-mediated knockdown of TINAGL1 resulted in reduced tube formation in human umbilical vein endothelial cells (HUVECs), whereas treatment with Tinagl1 promoted tube formation. Immunoblot analysis revealed that Tinagl1 activates ERK signaling in both HUVECs and C2C12 myoblasts and myotubes, which are involved in the regulation of myogenic differentiation, proliferation, metabolism, and angiogenesis. Our results demonstrate that Tinagl1 may be required for normal muscle and capillary development through the activation of ERK signaling.
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Affiliation(s)
- Yoriko Sato
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto 8628652, Japan
| | - Keisuke Kawashima
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, 3218505, Japan
| | - Emiko Fukui
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, 3218505, Japan
| | - Hiromichi Matsumoto
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, 3218505, Japan
| | - Fumiaki Yoshizawa
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, 3218505, Japan
| | - Yusuke Sato
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto 8628652, Japan.
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9
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Mackay S, Hitefield NL, Oduor IO, Roberts AB, Burch TC, Lance RS, Cunningham TD, Troyer DA, Semmes OJ, Nyalwidhe JO. Site-Specific Intact N-Linked Glycopeptide Characterization of Prostate-Specific Membrane Antigen from Metastatic Prostate Cancer Cells. ACS OMEGA 2022; 7:29714-29727. [PMID: 36061737 PMCID: PMC9435049 DOI: 10.1021/acsomega.2c02265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
The composition of N-linked glycans that are conjugated to the prostate-specific membrane antigen (PSMA) and their functional significance in prostate cancer progression have not been fully characterized. PSMA was isolated from two metastatic prostate cancer cell lines, LNCaP and MDAPCa2b, which have different tissue tropism and localization. Isolated PSMA was trypsin-digested, and intact glycopeptides were subjected to LC-HCD-EThcD-MS/MS analysis on a Tribrid Orbitrap Fusion Lumos mass spectrometer. Differential qualitative and quantitative analysis of site-specific N-glycopeptides was performed using Byonic and Byologic software. Comparative quantitative analysis demonstrates that multiple glycopeptides at asparagine residues 51, 76, 121, 195, 336, 459, 476, and 638 were in significantly different abundance in the two cell lines (p < 0.05). Biochemical analysis using endoglycosidase treatment and lectin capture confirm the MS and site occupancy data. The data demonstrate the effectiveness of the strategy for comprehensive analysis of PSMA glycopeptides. This approach will form the basis of ongoing experiments to identify site-specific glycan changes in PSMA isolated from disease-stratified clinical samples to uncover targets that may be associated with disease progression and metastatic phenotypes.
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Affiliation(s)
- Stephen Mackay
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
- University
of North Carolina, Chapel Hill, North Carolina 27516, United States
| | - Naomi L. Hitefield
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
- University
of Georgia, Athens, Georgia 30602, United
States
| | - Ian O. Oduor
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
| | - Autumn B. Roberts
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
| | - Tanya C. Burch
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
| | - Raymond S. Lance
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Spokane
Urology, Spokane, Washington 99202, United States
| | - Tina D. Cunningham
- School of
Health Professions, Eastern Virginia Medical
School, Norfolk, Virginia 23507, United States
| | - Dean A. Troyer
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
| | - Oliver J. Semmes
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
| | - Julius O. Nyalwidhe
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23507, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, United States
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10
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Zeng W, Zheng S, Su T, Cheng J, Mao Y, Zhong Y, Liu Y, Chen J, Zhao W, Lin T, Liu F, Li G, Yang H, Zhang Y. Comparative N-Glycoproteomics Analysis of Clinical Samples Via Different Mass Spectrometry Dissociation Methods. Front Chem 2022; 10:839470. [PMID: 35281567 PMCID: PMC8907888 DOI: 10.3389/fchem.2022.839470] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Site-specific N-glycosylation characterization requires intact N-glycopeptide analysis based on suitable tandem mass spectrometry (MS/MS) method. Electron-transfer/higher-energy collisional dissociation (EThcD), stepped collision energy/higher-energy collisional dissociation (sceHCD), higher-energy collisional dissociation-product-dependent electron-transfer dissociation (HCD-pd-ETD), and a hybrid mass spectrometry fragmentation method EThcD-sceHCD have emerged as valuable approaches for glycoprotein analysis. However, each of them incurs some compromise, necessitating the systematic performance comparisons when applied to the analysis of complex clinical samples (e.g., plasma, urine, cells, and tissues). Herein, we compared the performance of EThcD-sceHCD with those previous approaches (EThcD, sceHCD, HCD-pd-ETD, and sceHCD-pd-ETD) in the intact N-glycopeptide analysis, and determined its applicability for clinical N-glycoproteomic study. The intact N-glycopeptides of distinct samples, namely, plasma from prostate cancer (PCa) patients, urine from immunoglobulin A nephropathy (IgAN) patients, human hepatocarcinoma cell line (HepG2), and thyroid tissues from thyroid cancer (TC) patients were analyzed by these methods. We found that EThcD-sceHCD outperformed other methods in the balance of depth and accuracy of intact N-glycopeptide identification, and sceHCD and EThcD-sceHCD have good complementarity. EThcD-sceHCD holds great potential for biomarker discovery from clinical samples.
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Affiliation(s)
- Wenjuan Zeng
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Shanshan Zheng
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Su
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiahan Cheng
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhong
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yueqiu Liu
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Jianhai Chen
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Tianhai Lin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Fang Liu
- Division of Nephrology, West China Hospital, Sichuan University, Chengdu, China
| | - Guisen Li
- Renal Department and Institute of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu, China
| | - Hao Yang
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Hao Yang, ; Yong Zhang,
| | - Yong Zhang
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Hao Yang, ; Yong Zhang,
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11
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Multimerin-1 and cancer: a review. Biosci Rep 2022; 42:230760. [PMID: 35132992 PMCID: PMC8881648 DOI: 10.1042/bsr20211248] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Multimerin-1 (MMRN1) is a platelet protein with a role in haemostasis and coagulation. It is also present in endothelial cells (ECs) and the extracellular matrix (ECM), where it may be involved in cell adhesion, but its molecular functions and protein–protein interactions in these cellular locations have not been studied in detail yet. In recent years, MMRN1 has been identified as a differentially expressed gene (DEG) in various cancers and it has been proposed as a possible cancer biomarker. Some evidence suggest that MMRN1 expression is regulated by methylation, protein interactions, and non-coding RNAs (ncRNAs) in different cancers. This raises the questions if a functional role of MMRN1 is being targeted during cancer development, and if MMRN1’s differential expression pattern correlates with cancer progression. As a result, it is timely to review the current state of what is known about MMRN1 to help inform future research into MMRN1’s molecular mechanisms in cancer.
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12
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- 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, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, 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, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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13
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Künzel SR, Hoffmann M, Weber S, Künzel K, Kämmerer S, Günscht M, Klapproth E, Rausch JS, Sadek MS, Kolanowski T, Meyer-Roxlau S, Piorkowski C, Tugtekin SM, Rose-John S, Yin X, Mayr M, Kuhlmann JD, Wimberger P, Grützmann K, Herzog N, Küpper JH, O’Reilly M, Kabir SN, Sommerfeld LC, Guan K, Wielockx B, Fabritz L, Nattel S, Ravens U, Dobrev D, Wagner M, El-Armouche A. Diminished PLK2 Induces Cardiac Fibrosis and Promotes Atrial Fibrillation. Circ Res 2021; 129:804-820. [PMID: 34433292 PMCID: PMC8487716 DOI: 10.1161/circresaha.121.319425] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 12/19/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Stephan R. Künzel
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
- Department of Dermatology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K.)
| | - Maximilian Hoffmann
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
| | - Silvio Weber
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
| | - Karolina Künzel
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
| | - Susanne Kämmerer
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
| | - Mario Günscht
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
| | - Erik Klapproth
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
| | - Johanna S.E. Rausch
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
| | - Mirna S. Sadek
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
| | - Tomasz Kolanowski
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
| | - Stefanie Meyer-Roxlau
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
| | - Christopher Piorkowski
- Department of Rhythmology (C.P., M.W.), Clinic for Internal Medicine and Cardiology, Heart Center Dresden GmbH, Dresden, Technische Universität Dresden
| | - Sems M. Tugtekin
- Department of Cardiac Surgery (S.M.T.), Clinic for Internal Medicine and Cardiology, Heart Center Dresden GmbH, Dresden, Technische Universität Dresden
| | - Stefan Rose-John
- Unit for Degradomics of the Protease Web, Institute of Biochemistry, University of Kiel (S.R.-J.)
| | - Xiaoke Yin
- The James Black Centre, King’s College, University of London (X.Y., M.M.)
| | - Manuel Mayr
- The James Black Centre, King’s College, University of London (X.Y., M.M.)
- Internal Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden (M.M.)
| | - Jan Dominik Kuhlmann
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden (J.D.K., P.W.)
- German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg (J.D.K., P.W.)
- National Center for Tumor Diseases (NCT), Partner Site Dresden (J.D.K., P.W., K.G.)
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden (J.D.K., P.W.)
- German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg (J.D.K., P.W.)
- National Center for Tumor Diseases (NCT), Partner Site Dresden (J.D.K., P.W., K.G.)
| | - Konrad Grützmann
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
- National Center for Tumor Diseases (NCT), Partner Site Dresden (J.D.K., P.W., K.G.)
| | - Natalie Herzog
- Brandenburg University of Technology, Senftenberg (N.H., J.-H.K.)
| | | | - Molly O’Reilly
- Institute of Cardiovascular Sciences, University of Birmingham (M.O., S.N.K., L.C.S.)
| | - S. Nashitha Kabir
- Institute of Cardiovascular Sciences, University of Birmingham (M.O., S.N.K., L.C.S.)
| | - Laura C. Sommerfeld
- Institute of Cardiovascular Sciences, University of Birmingham (M.O., S.N.K., L.C.S.)
- University Center of Cardiovascular Science and Department of Cardiology, University Heart and Vascular Center Hamburg (L.F., L.C.S.)
| | - Kaomei Guan
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
- Department of Rhythmology (C.P., M.W.), Clinic for Internal Medicine and Cardiology, Heart Center Dresden GmbH, Dresden, Technische Universität Dresden
- Department of Cardiac Surgery (S.M.T.), Clinic for Internal Medicine and Cardiology, Heart Center Dresden GmbH, Dresden, Technische Universität Dresden
- Unit for Degradomics of the Protease Web, Institute of Biochemistry, University of Kiel (S.R.-J.)
- The James Black Centre, King’s College, University of London (X.Y., M.M.)
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden (J.D.K., P.W.)
- German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg (J.D.K., P.W.)
- National Center for Tumor Diseases (NCT), Partner Site Dresden (J.D.K., P.W., K.G.)
- Brandenburg University of Technology, Senftenberg (N.H., J.-H.K.)
- Institute of Cardiovascular Sciences, University of Birmingham (M.O., S.N.K., L.C.S.)
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden (B.W.)
- Department of Cardiology, University Hospitals Birmingham (L.F.)
- Department of Medicine, Montreal Heart Institute and Université de Montréal, Quebec, Canada (S.N., D.D.)
- Institut für Experimentelle Kardiovaskuläre Medizin, Universitäts Herzzentrum, Freiburg Bad Krotzingen, Freiburg im Breisgau (U.R.)
- Institute of Pharmacology, West German Heart and Vascular Center, University Duisburg-Essen (S.N., D.D.)
- IHU Liryc, Electrophysiology and Heart Modeling Institute, Fondation Bordeaux Université (S.N.)
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine (D.D.)
- Department of Dermatology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K.)
- Internal Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden (M.M.)
- University Center of Cardiovascular Science and Department of Cardiology, University Heart and Vascular Center Hamburg (L.F., L.C.S.)
| | - Ben Wielockx
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden (B.W.)
| | - Larissa Fabritz
- Department of Cardiology, University Hospitals Birmingham (L.F.)
- University Center of Cardiovascular Science and Department of Cardiology, University Heart and Vascular Center Hamburg (L.F., L.C.S.)
| | - Stanley Nattel
- Department of Medicine, Montreal Heart Institute and Université de Montréal, Quebec, Canada (S.N., D.D.)
- Institute of Pharmacology, West German Heart and Vascular Center, University Duisburg-Essen (S.N., D.D.)
- IHU Liryc, Electrophysiology and Heart Modeling Institute, Fondation Bordeaux Université (S.N.)
| | - Ursula Ravens
- Institut für Experimentelle Kardiovaskuläre Medizin, Universitäts Herzzentrum, Freiburg Bad Krotzingen, Freiburg im Breisgau (U.R.)
| | - Dobromir Dobrev
- Department of Medicine, Montreal Heart Institute and Université de Montréal, Quebec, Canada (S.N., D.D.)
- Institute of Pharmacology, West German Heart and Vascular Center, University Duisburg-Essen (S.N., D.D.)
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine (D.D.)
| | - Michael Wagner
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
- Department of Rhythmology (C.P., M.W.), Clinic for Internal Medicine and Cardiology, Heart Center Dresden GmbH, Dresden, Technische Universität Dresden
| | - Ali El-Armouche
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (S.R.K., M.H., S.W., K.K., S.K., M.G., E.K., J.S.E.R., M.S.S., T.K., S.M.-R., K.G., M.W., A.E.-A.)
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14
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De Hert E, Bracke A, Pintelon I, Janssens E, Lambeir AM, Van Der Veken P, De Meester I. Prolyl Carboxypeptidase Mediates the C-Terminal Cleavage of (Pyr)-Apelin-13 in Human Umbilical Vein and Aortic Endothelial Cells. Int J Mol Sci 2021; 22:ijms22136698. [PMID: 34206648 PMCID: PMC8268575 DOI: 10.3390/ijms22136698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/18/2021] [Accepted: 06/18/2021] [Indexed: 12/20/2022] Open
Abstract
The aim of this study was to investigate the C-terminal cleavage of (pyr)-apelin-13 in human endothelial cells with respect to the role and subcellular location of prolyl carboxypeptidase (PRCP). Human umbilical vein and aortic endothelial cells, pre-treated with prolyl carboxypeptidase-inhibitor compound 8o and/or angiotensin converting enzyme 2 (ACE2)-inhibitor DX600, were incubated with (pyr)-apelin-13 for different time periods. Cleavage products of (pyr)-apelin-13 in the supernatant were identified by mass spectrometry. The subcellular location of PRCP was examined via immunocytochemistry. In addition, PRCP activity was measured in supernatants and cell lysates of LPS-, TNFα-, and IL-1β-stimulated cells. PRCP cleaved (pyr)-apelin-13 in human umbilical vein and aortic endothelial cells, while ACE2 only contributed to this cleavage in aortic endothelial cells. PRCP was found in endothelial cell lysosomes. Pro-inflammatory stimulation induced the secretion of PRCP in the extracellular environment of endothelial cells, while its intracellular level remained intact. In conclusion, PRCP, observed in endothelial lysosomes, is responsible for the C-terminal cleavage of (pyr)-apelin-13 in human umbilical vein endothelial cells, while in aortic endothelial cells ACE2 also contributes to this cleavage. These results pave the way to further elucidate the relevance of the C-terminal Phe of (pyr)-apelin-13.
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Affiliation(s)
- Emilie De Hert
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (E.D.H.); (A.B.); (E.J.); (A.-M.L.)
| | - An Bracke
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (E.D.H.); (A.B.); (E.J.); (A.-M.L.)
| | - Isabel Pintelon
- Laboratory of Cell Biology and Histology, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences; Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk, Belgium;
| | - Eline Janssens
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (E.D.H.); (A.B.); (E.J.); (A.-M.L.)
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk, Belgium
| | - Anne-Marie Lambeir
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (E.D.H.); (A.B.); (E.J.); (A.-M.L.)
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium;
| | - Ingrid De Meester
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (E.D.H.); (A.B.); (E.J.); (A.-M.L.)
- Correspondence: ; Tel.: +32-3265-2741
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15
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In silico approach to predict pancreatic β-cells classically secreted proteins. Biosci Rep 2021; 40:222021. [PMID: 32003782 PMCID: PMC7024845 DOI: 10.1042/bsr20193708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic β-cells, residents of the islets of Langerhans, are the unique insulin-producers in the body. Their physiology is a topic of intensive studies aiming to understand the biology of insulin production and its role in diabetes pathology. However, investigations about these cells' subset of secreted proteins, the secretome, are surprisingly scarce and a list describing islet/β-cell secretome upon glucose-stimulation is not yet available. In silico predictions of secretomes are an interesting approach that can be employed to forecast proteins likely to be secreted. In this context, using the rationale behind classical secretion of proteins through the secretory pathway, a Python tool capable of predicting classically secreted proteins was developed. This tool was applied to different available proteomic data (human and rodent islets, isolated β-cells, β-cell secretory granules, and β-cells supernatant), filtering them in order to selectively list only classically secreted proteins. The method presented here can retrieve, organize, search and filter proteomic lists using UniProtKB as a central database. It provides analysis by overlaying different sets of information, filtering out potential contaminants and clustering the identified proteins into functional groups. A range of 70-92% of the original proteomes analyzed was reduced generating predicted secretomes. Islet and β-cell signal peptide-containing proteins, and endoplasmic reticulum-resident proteins were identified and quantified. From the predicted secretomes, exemplary conservational patterns were inferred, as well as the signaling pathways enriched within them. Such a technique proves to be an effective approach to reduce the horizon of plausible targets for drug development or biomarkers identification.
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16
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Barallobre-Barreiro J, Loeys B, Mayr M, Rienks M, Verstraeten A, Kovacic JC. Extracellular Matrix in Vascular Disease, Part 2/4: JACC Focus Seminar. J Am Coll Cardiol 2020; 75:2189-2203. [PMID: 32354385 DOI: 10.1016/j.jacc.2020.03.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 02/26/2020] [Accepted: 03/03/2020] [Indexed: 01/01/2023]
Abstract
Medium-sized and large arteries consist of 3 layers: the tunica intima, tunica media, and tunica adventitia. The tunica media accounts for the bulk of the vessel wall and is the chief determinant of mechanical compliance. It is primarily composed of circumferentially arranged layers of vascular smooth muscle cells that are separated by concentrically arranged elastic lamellae; a form of extracellular matrix (ECM). The tunica media is separated from the tunica intima and tunica adventitia, the innermost and outermost layers, respectively, by the internal and external elastic laminae. This second part of a 4-part JACC Focus Seminar discusses the contributions of the ECM to vascular homeostasis and pathology. Advances in genetics and proteomics approaches have fostered significant progress in our understanding of vascular ECM. This review highlights the important role of the ECM in vascular disease and the prospect of translating these discoveries into clinical disease biomarkers and potential future therapies.
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Affiliation(s)
| | - Bart Loeys
- Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp, Belgium; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, United Kingdom; The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Marieke Rienks
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Aline Verstraeten
- Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp, Belgium
| | - Jason C Kovacic
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia; St. Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia.
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17
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Zhou S, Yin X, Mayr M, Noor M, Hylands PJ, Xu Q. Proteomic landscape of TGF-β1-induced fibrogenesis in renal fibroblasts. Sci Rep 2020; 10:19054. [PMID: 33149203 PMCID: PMC7642370 DOI: 10.1038/s41598-020-75989-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/22/2020] [Indexed: 01/09/2023] Open
Abstract
Transforming growth factor-β1 (TGF-β1) plays a premier role in fibrosis. To understand the molecular events underpinning TGF-β1-induced fibrogenesis, we examined the proteomic profiling of a TGF-β1-induced in vitro model of fibrosis in NRK-49F normal rat kidney fibroblasts. Mass spectrometric analysis indicated that 628 cell-lysate proteins enriched in 44 cellular component clusters, 24 biological processes and 27 molecular functions were regulated by TGF-β1. Cell-lysate proteins regulated by TGF-β1 were characterised by increased ribosomal proteins and dysregulated proteins involved in multiple metabolic pathways, including reduced Aldh3a1 and induced Enpp1 and Impdh2, which were validated by enzyme-linked immunosorbent assays (ELISA). In conditioned media, 62 proteins enriched in 20 cellular component clusters, 40 biological processes and 7 molecular functions were regulated by TGF-β1. Secretomic analysis and ELISA uncovered dysregulated collagen degradation regulators (induced PAI-1 and reduced Mmp3), collagen crosslinker (induced Plod2), signalling molecules (induced Ccn1, Ccn2 and Tsku, and reduced Ccn3) and chemokines (induced Ccl2 and Ccl7) in the TGF-β1 group. We conclude that TGF-β1-induced fibrogenesis in renal fibroblasts is an intracellular metabolic disorder and is inherently coupled with inflammation mediated by chemokines. Proteomic profiling established in this project may guide development of novel anti-fibrotic therapies in a network pharmacology approach.
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Affiliation(s)
- Shujun Zhou
- Renal Science and Integrative Chinese Medicine Laboratory, Department of Inflammation Biology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Xiaoke Yin
- School of Cardiovascular Medicine and Sciences, King's BHF Centre of Research Excellence, King's College London, London, UK
| | - Manuel Mayr
- School of Cardiovascular Medicine and Sciences, King's BHF Centre of Research Excellence, King's College London, London, UK
| | - Mazhar Noor
- Renal Science and Integrative Chinese Medicine Laboratory, Department of Inflammation Biology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Peter J Hylands
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Qihe Xu
- Renal Science and Integrative Chinese Medicine Laboratory, Department of Inflammation Biology, School of Immunology and Microbial Sciences, King's College London, London, UK.
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18
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Robin T, Mariethoz J, Lisacek F. Examining and Fine-tuning the Selection of Glycan Compositions with GlyConnect Compozitor. Mol Cell Proteomics 2020; 19:1602-1618. [PMID: 32636234 PMCID: PMC8014996 DOI: 10.1074/mcp.ra120.002041] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/01/2020] [Indexed: 01/22/2023] Open
Abstract
A key point in achieving accurate intact glycopeptide identification is the definition of the glycan composition file that is used to match experimental with theoretical masses by a glycoproteomics search engine. At present, these files are mainly built from searching the literature and/or querying data sources focused on posttranslational modifications. Most glycoproteomics search engines include a default composition file that is readily used when processing MS data. We introduce here a glycan composition visualizing and comparative tool associated with the GlyConnect database and called GlyConnect Compozitor. It offers a web interface through which the database can be queried to bring out contextual information relative to a set of glycan compositions. The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarizing information searched in the database. These results provide a guide for selecting or deselecting compositions in a file in order to reflect the context of a study as closely as possible. They also confirm the consistency of a set of compositions based on the content of the GlyConnect database. As part of the tool collection of the Glycomics@ExPASy initiative, Compozitor is hosted at https://glyconnect.expasy.org/compozitor/ where it can be run as a web application. It is also directly accessible from the GlyConnect database.
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Affiliation(s)
- Thibault Robin
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland; Computer Science Dept., Faculty of Science, University of Geneva, Switzerland; CALIPHO Group, SIB Swiss Institute of BioinformaticsCMU, Geneva, Switzerland; Microbiology and Molecular Medicine Dept., Faculty of Medicine, University of Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland; Computer Science Dept., Faculty of Science, University of Geneva, Switzerland
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland; Computer Science Dept., Faculty of Science, University of Geneva, Switzerland; Section of Biology, Faculty of Science, University of Geneva, Switzerland.
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19
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Zhu R, Huang Y, Zhao J, Zhong J, Mechref Y. Isomeric Separation of N-Glycopeptides Derived from Glycoproteins by Porous Graphitic Carbon (PGC) LC-MS/MS. Anal Chem 2020; 92:9556-9565. [PMID: 32544320 PMCID: PMC7815195 DOI: 10.1021/acs.analchem.0c00668] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein glycosylation is involved in many biological processes and physiological functions. Despite the recent advances in LC-MS/MS methodologies, the profiling of site-specific glycosylation is one of the major analytical challenges of glycoprotein analysis. Herein, we report that the separation of glycopeptide isomers on porous graphitic carbon (PGC)-LC was significantly improved by elevating the separation temperature under basic mobile phases. These findings permitted the isomeric separation of glycopeptides resulting from highly specific enzymatic digestions. The selectivity for different glycan types was studied using bovine fetuin, asialofetuin, IgG, ribonuclease B, and alpha-1 acid glycoprotein (AGP) by PGC-LC-MS. Comprehensive structural isomeric separation of glycopeptides was observed by high-resolution MS and confirmed by MS/MS. The specific structures of the glycopeptide isomers were identified and confirmed through exoglycosidase digestions. Glycosylation analysis of human AGP revealed the potential use of PGC-LC-MS for extensive glycoprotein analysis for biomarker discovery. This newly developed separation technique was shown as a reproducible and useful analytical method to study site-specific isomeric glycosylation.
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Affiliation(s)
| | | | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
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20
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Cipollo JF, Parsons LM. Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships. MASS SPECTROMETRY REVIEWS 2020; 39:371-409. [PMID: 32350911 PMCID: PMC7318305 DOI: 10.1002/mas.21629] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/05/2020] [Indexed: 05/21/2023]
Abstract
The advancement of viral glycomics has paralleled that of the mass spectrometry glycomics toolbox. In some regard the glycoproteins studied have provided the impetus for this advancement. Viral proteins are often highly glycosylated, especially those targeted by the host immune system. Glycosylation tends to be dynamic over time as viruses propagate in host populations leading to increased number of and/or "movement" of glycosylation sites in response to the immune system and other pressures. This relationship can lead to highly glycosylated, difficult to analyze glycoproteins that challenge the capabilities of modern mass spectrometry. In this review, we briefly discuss five general areas where glycosylation is important in the viral niche and how mass spectrometry has been used to reveal key information regarding structure-function relationships between viral glycoproteins and host cells. We describe the recent past and current glycomics toolbox used in these analyses and give examples of how the requirement to analyze these complex glycoproteins has provided the incentive for some advances seen in glycomics mass spectrometry. A general overview of viral glycomics, special cases, mass spectrometry methods and work-flows, informatics and complementary chemical techniques currently used are discussed. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- John F. Cipollo
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
| | - Lisa M. Parsons
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
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21
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Lipphardt M, Dihazi H, Jeon NL, Dadafarin S, Ratliff BB, Rowe DW, Müller GA, Goligorsky MS. Dickkopf-3 in aberrant endothelial secretome triggers renal fibroblast activation and endothelial-mesenchymal transition. Nephrol Dial Transplant 2019; 34:49-62. [PMID: 29726981 DOI: 10.1093/ndt/gfy100] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 03/18/2018] [Indexed: 01/22/2023] Open
Abstract
Background Our laboratory has previously demonstrated that Sirt1endo-/- mice show endothelial dysfunction and exaggerated renal fibrosis, whereas mice with silenced endothelial transforming growth factor beta (TGF-β) signaling are resistant to fibrogenic signals. Considering the fact that the only difference between these mutant mice is confined to the vascular endothelium, this indicates that secreted substances contribute to these contrasting responses. Methods We performed an unbiased proteomic analysis of the secretome of renal microvascular endothelial cells (RMVECs) isolated from these two mutants. We cultured renal fibroblasts and RMVECs and used microfluidic devices for coculturing. Results Dickkopf-3 (DKK3), a putative ligand of the Wnt/β-catenin pathway, was present exclusively in the fibrogenic secretome. In cultured fibroblasts, DKK3 potently induced myofibroblast activation. In addition, DKK3 antagonized effects of DKK1, a known inhibitor of the Wnt pathway, in conversion of fibroblasts to myofibroblasts. In RMVECs, DKK3 induced endothelial-mesenchymal transition and impaired their angiogenic competence. The inhibition of endothelial outgrowth, enhanced myofibroblast formation and endothelial-mesenchymal transition were confirmed in coculture. In reporter DKK3-eGFP × Col3.6-GFPcyan mice, DKK3 was marginally expressed under basal conditions. Adriamycin-induced nephropathy resulted in upregulation of DKK3 expression in tubular and, to a lesser degree, endothelial compartments. Sulindac sulfide was found to exhibit superior Wnt pathway-suppressive action and decreased DKK3 signals and the extent of renal fibrosis. Conclusions In conclusion, this unbiased proteomic screen of the profibrogenic endothelial secretome revealed DKK3 acting as an agonist of the Wnt pathway, enhancing formation of myofibroblasts and endothelial-mesenchymal transition and impairing angiogenesis. A potent inhibitor of the Wnt pathway, sulindac sulfide, suppressed nephropathy-induced DKK3 expression and renal fibrosis.
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Affiliation(s)
- Mark Lipphardt
- Departments of Medicine, Pharmacology and Physiology, Renal Research Institute, New York Medical College at Touro University, Valhalla, NY, USA.,Department of Nephrology and Rheumatology, Göttingen University Medical School, Göttingen, Germany
| | - Hassan Dihazi
- Department of Nephrology and Rheumatology, Göttingen University Medical School, Göttingen, Germany
| | - Noo Li Jeon
- Division of WCU Multiscale Mechanical Design, School of Mechanical and Aerospace Engineering, Institute of Advanced Machinery and Design, Seoul National University, Seoul, Korea
| | - Sina Dadafarin
- Departments of Medicine, Pharmacology and Physiology, Renal Research Institute, New York Medical College at Touro University, Valhalla, NY, USA
| | - Brian B Ratliff
- Departments of Medicine, Pharmacology and Physiology, Renal Research Institute, New York Medical College at Touro University, Valhalla, NY, USA
| | - David W Rowe
- Department of Reconstructive Sciences, Biomaterials and Skeletal Development, Center for Regenerative Medicine and Skeletal Development, School of Dental Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Gerhard A Müller
- Department of Nephrology and Rheumatology, Göttingen University Medical School, Göttingen, Germany
| | - Michael S Goligorsky
- Departments of Medicine, Pharmacology and Physiology, Renal Research Institute, New York Medical College at Touro University, Valhalla, NY, USA
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22
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Fert-Bober J, Murray CI, Parker SJ, Van Eyk JE. Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way. Circ Res 2019; 122:1221-1237. [PMID: 29700069 DOI: 10.1161/circresaha.118.310966] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is an exponential increase in biological complexity as initial gene transcripts are spliced, translated into amino acid sequence, and post-translationally modified. Each protein can exist as multiple chemical or sequence-specific proteoforms, and each has the potential to be a critical mediator of a physiological or pathophysiological signaling cascade. Here, we provide an overview of how different proteoforms come about in biological systems and how they are most commonly measured using mass spectrometry-based proteomics and bioinformatics. Our goal is to present this information at a level accessible to every scientist interested in mass spectrometry and its application to proteome profiling. We will specifically discuss recent data linking various protein post-translational modifications to cardiovascular disease and conclude with a discussion for enablement and democratization of proteomics across the cardiovascular and scientific community. The aim is to inform and inspire the readership to explore a larger breadth of proteoform, particularity post-translational modifications, related to their particular areas of expertise in cardiovascular physiology.
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Affiliation(s)
- Justyna Fert-Bober
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Christopher I Murray
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Sarah J Parker
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA.
| | - Jennifer E Van Eyk
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
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23
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Sun S, Hu Y, Ao M, Shah P, Chen J, Yang W, Jia X, Tian Y, Thomas S, Zhang H. N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping. Clin Proteomics 2019; 16:35. [PMID: 31516400 PMCID: PMC6731604 DOI: 10.1186/s12014-019-9254-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. The large-scale characterization of N-linked glycoproteins accomplished by mass spectrometry-based glycoproteomics has provided valuable insights into the interdependence of glycoprotein structure and protein function. However, these studies focused mainly on the analysis of specific sample type, and lack the integration of glycoproteomic data from different tissues, body fluids or cell types. METHODS In this study, we collected the human glycosite-containing peptides identified through their de-glycosylated forms by mass spectrometry from over 100 publications and unpublished datasets generated from our laboratory. A database resource termed N-GlycositeAtlas was created and further used for the distribution analyses of glycoproteins among different human cells, tissues and body fluids. Finally, a web interface of N-GlycositeAtlas was created to maximize the utility and value of the database. RESULTS The N-GlycositeAtlas database contains more than 30,000 glycosite-containing peptides (representing > 14,000 N-glycosylation sites) from more than 7200 N-glycoproteins from different biological sources including human-derived tissues, body fluids and cell lines from over 100 studies. CONCLUSIONS The entire human N-glycoproteome database as well as 22 sub-databases associated with individual tissues or body fluids can be downloaded from the N-GlycositeAtlas website at http://nglycositeatlas.biomarkercenter.org.
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Affiliation(s)
- Shisheng Sun
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
- College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Minghui Ao
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Punit Shah
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Jing Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Xingwang Jia
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Yuan Tian
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Stefani Thomas
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
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Chen Z, Huang J, Li L. Recent advances in mass spectrometry (MS)-based glycoproteomics in complex biological samples. Trends Analyt Chem 2019; 118:880-892. [PMID: 31579312 PMCID: PMC6774629 DOI: 10.1016/j.trac.2018.10.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein glycosylation plays a key role in various biological processes and disease-related pathological progression. Mass spectrometry (MS)-based glycoproteomics is a powerful approach that provides a system-wide profiling of the glycoproteome in a high-throughput manner. There have been numerous significant technological advances in this field, including improved glycopeptide enrichment, hybrid fragmentation techniques, emerging specialized software packages, and effective quantitation strategies, as well as more dedicated workflows. With increasingly sophisticated glycoproteomics tools on hand, researchers have extensively adapted this approach to explore different biological systems both in terms of in-depth glycoproteome profiling and comparative glycoproteome analysis. Quantitative glycoproteomics enables researchers to discover novel glycosylation-based biomarkers in various diseases with potential to offer better sensitivity and specificity for disease diagnosis. In this review, we present recent methodological developments in MS-based glycoproteomics and highlight its utility and applications in answering various questions in complex biological systems.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
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25
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Chen Z, Huang J, Li L. Recent advances in mass spectrometry (MS)-based glycoproteomics in complex biological samples. Trends Analyt Chem 2019. [PMID: 31579312 DOI: 10.1016/jtrac.2018.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Protein glycosylation plays a key role in various biological processes and disease-related pathological progression. Mass spectrometry (MS)-based glycoproteomics is a powerful approach that provides a system-wide profiling of the glycoproteome in a high-throughput manner. There have been numerous significant technological advances in this field, including improved glycopeptide enrichment, hybrid fragmentation techniques, emerging specialized software packages, and effective quantitation strategies, as well as more dedicated workflows. With increasingly sophisticated glycoproteomics tools on hand, researchers have extensively adapted this approach to explore different biological systems both in terms of in-depth glycoproteome profiling and comparative glycoproteome analysis. Quantitative glycoproteomics enables researchers to discover novel glycosylation-based biomarkers in various diseases with potential to offer better sensitivity and specificity for disease diagnosis. In this review, we present recent methodological developments in MS-based glycoproteomics and highlight its utility and applications in answering various questions in complex biological systems.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
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26
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Lin N, Li J, Shao R, Zhang H. Site-Specific Analysis of N-Linked Glycosylation Heterogeneity from Royal Jelly Glycoproteins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9411-9422. [PMID: 31393126 DOI: 10.1021/acs.jafc.9b03080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Royal jelly (RJ) is secreted by young worker bees, and it plays key roles in the development and physiological function in honeybees and can improve human health. Although there have been analyses on the glycosylation modification of RJ proteins, none of these methods have been conducted on a site-specific analysis of glycosylation from these glycoproteins. Here, a combined glycomics and glycoproteomics strategy was developed for the site-specific analysis of N-linked glycosylation heterogeneity of RJ glycoproteins. First, global characterization of the N-glycome of RJ was performed using a direct infusion ion trap-sequential mass spectrometry (IT-MSn) method. Second, tryptic glycopeptides were enriched and separated by hydrophilic interaction liquid chromatography-ion trap-sequential mass spectrometry (HILIC-IT-MSn). A total of 50 N-glycopeptides and 30 N-glycans have been site-specific glycosylation profiled in major royal jelly protein 1 (MRJP1) and MRJP2 of RJ for the first time. Eighteen of the identified N-glycans have been structurally characterized by IT-MSn, including oligosaccharide composition, sequence, branching, and linkage. Two N-glycosylation sites (N177 and N394), 3 sites (N145, N178, and N92), and 1 site of N183 were identified in MRJP1, MRJP2, and MRJP3, respectively. There were 18, 17, and 2 N-glycans attached to MRJP1, MRJP2, and MRJP3, respectively. The diversity of N-glycans attached to each single glycosylation site of these glycoproteins confirmed that MRJP1 and MRJP2 heterogeneity was mostly associated with their glycoform populations. Understanding the properties of the site-specific glycosylation heterogeneity of the RJ glycoproteins can be potentially useful for producing a glycoprotein with desirable pharmacokinetic and biological activity.
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Affiliation(s)
- Na Lin
- School of Food Science and Biological Engineering , Zhejiang Gongshang University , Hangzhou , Zhejiang Province 310018 , P. R. China
| | - Junmin Li
- School of Food Science and Biological Engineering , Zhejiang Gongshang University , Hangzhou , Zhejiang Province 310018 , P. R. China
| | - Rouming Shao
- School of Food Science and Biological Engineering , Zhejiang Gongshang University , Hangzhou , Zhejiang Province 310018 , P. R. China
| | - Hong Zhang
- School of Food Science and Biological Engineering , Zhejiang Gongshang University , Hangzhou , Zhejiang Province 310018 , P. R. China
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27
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Abstract
Glycosylation is one of the most ubiquitous and complex post-translational modifications (PTMs). It plays pivotal roles in various biological processes. Studies at the glycopeptide level are typically considered as a downstream work resulting from enzymatic digested glycoproteins. Less attention has been focused on glycosylated endogenous signaling peptides due to their low abundance, structural heterogeneity and the lack of enabling analytical tools. Here, protocols are presented to isolate and characterize glycosylated neuropeptides utilizing nanoflow liquid chromatography coupled with mass spectrometry (LC-MS). We first demonstrate how to extract neuropeptides from raw tissues and perform further separation/cleanup before MS analysis. Then we describe hybrid MS methods for glycosylated neuropeptide profiling and site-specific analysis. We also include recommendations for data analysis to identify glycosylated neuropeptides in crustaceans where a complete neuropeptide database is still lacking. Other strategies and future directions are discussed to provide readers with alternative approaches and further unravel biological complexity rendered by glycosylation.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Qinjingwen Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States; School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States.
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28
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Xiao H, Sun F, Suttapitugsakul S, Wu R. Global and site-specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:356-379. [PMID: 30605224 PMCID: PMC6610820 DOI: 10.1002/mas.21586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/27/2018] [Indexed: 05/16/2023]
Abstract
Protein glycosylation is ubiquitous in biological systems and plays essential roles in many cellular events. Global and site-specific analysis of glycoproteins in complex biological samples can advance our understanding of glycoprotein functions and cellular activities. However, it is extraordinarily challenging because of the low abundance of many glycoproteins and the heterogeneity of glycan structures. The emergence of mass spectrometry (MS)-based proteomics has provided us an excellent opportunity to comprehensively study proteins and their modifications, including glycosylation. In this review, we first summarize major methods for glycopeptide/glycoprotein enrichment, followed by the chemical and enzymatic methods to generate a mass tag for glycosylation site identification. We next discuss the systematic and quantitative analysis of glycoprotein dynamics. Reversible protein glycosylation is dynamic, and systematic study of glycoprotein dynamics helps us gain insight into glycoprotein functions. The last part of this review focuses on the applications of MS-based proteomics to study glycoproteins in different biological systems, including yeasts, plants, mice, human cells, and clinical samples. Intact glycopeptide analysis is also included in this section. Because of the importance of glycoproteins in complex biological systems, the field of glycoproteomics will continue to grow in the next decade. Innovative and effective MS-based methods will exponentially advance glycoscience, and enable us to identify glycoproteins as effective biomarkers for disease detection and drug targets for disease treatment. © 2019 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2019.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
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29
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Yin 殷晓科 X, Wanga S, Fellows AL, Barallobre-Barreiro J, Lu R, Davaapil H, Franken R, Fava M, Baig F, Skroblin P, Xing Q, Koolbergen DR, Groenink M, Zwinderman AH, Balm R, de Vries CJM, Mulder BJM, Viner R, Jahangiri M, Reinhardt DP, Sinha S, de Waard V, Mayr M. Glycoproteomic Analysis of the Aortic Extracellular Matrix in Marfan Patients. Arterioscler Thromb Vasc Biol 2019; 39:1859-1873. [PMID: 31315432 PMCID: PMC6727943 DOI: 10.1161/atvbaha.118.312175] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Supplemental Digital Content is available in the text. Marfan syndrome (MFS) is caused by mutations in FBN1 (fibrillin-1), an extracellular matrix (ECM) component, which is modified post-translationally by glycosylation. This study aimed to characterize the glycoproteome of the aortic ECM from patients with MFS and relate it to aortopathy.
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Affiliation(s)
- Xiaoke Yin 殷晓科
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., A.L.F., J.B.-B., R.L., M.F., F.B., P.S., Q.X., M.M.)
| | - Shaynah Wanga
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (S.W., C.J.M.d.V., V.d.W.), Amsterdam UMC, University of Amsterdam, the Netherlands.,Department of Cardiology (S.W., R.F., M.G., B.J.M.M.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Adam L Fellows
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., A.L.F., J.B.-B., R.L., M.F., F.B., P.S., Q.X., M.M.)
| | - Javier Barallobre-Barreiro
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., A.L.F., J.B.-B., R.L., M.F., F.B., P.S., Q.X., M.M.)
| | - Ruifang Lu
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., A.L.F., J.B.-B., R.L., M.F., F.B., P.S., Q.X., M.M.)
| | - Hongorzul Davaapil
- Department of Medicine, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, United Kingdom (H.D., S.S.)
| | - Romy Franken
- Department of Cardiology (S.W., R.F., M.G., B.J.M.M.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Marika Fava
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., A.L.F., J.B.-B., R.L., M.F., F.B., P.S., Q.X., M.M.)
| | - Ferheen Baig
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., A.L.F., J.B.-B., R.L., M.F., F.B., P.S., Q.X., M.M.)
| | - Philipp Skroblin
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., A.L.F., J.B.-B., R.L., M.F., F.B., P.S., Q.X., M.M.)
| | - Qiuru Xing
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., A.L.F., J.B.-B., R.L., M.F., F.B., P.S., Q.X., M.M.)
| | - David R Koolbergen
- Department of Cardiothoracic Surgery (D.R.K.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Maarten Groenink
- Department of Cardiology (S.W., R.F., M.G., B.J.M.M.), Amsterdam UMC, University of Amsterdam, the Netherlands.,Department of Radiology (M.G.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics (A.H.Z.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Ron Balm
- Department of Surgery (R.B.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Carlie J M de Vries
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (S.W., C.J.M.d.V., V.d.W.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Barbara J M Mulder
- Department of Cardiology (S.W., R.F., M.G., B.J.M.M.), Amsterdam UMC, University of Amsterdam, the Netherlands.,Netherlands Heart Institute, Utrecht (B.J.M.M.)
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA (R.V.)
| | | | - Dieter P Reinhardt
- Faculty of Medicine, Department of Anatomy and Cell Biology and Faculty of Dentistry, McGill University, Montreal, Canada (D.P.R.)
| | - Sanjay Sinha
- Department of Medicine, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, United Kingdom (H.D., S.S.)
| | - Vivian de Waard
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (S.W., C.J.M.d.V., V.d.W.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Manuel Mayr
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., A.L.F., J.B.-B., R.L., M.F., F.B., P.S., Q.X., M.M.)
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30
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Gerhardt MJ, Marsh JA, Morrison M, Kazlauskas A, Khadka A, Rosenkranz S, DeAngelis MM, Saint-Geniez M, Jacobo SMP. ER stress-induced aggresome trafficking of HtrA1 protects against proteotoxicity. J Mol Cell Biol 2019; 9:516-532. [PMID: 28992183 PMCID: PMC5823240 DOI: 10.1093/jmcb/mjx024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 07/08/2017] [Indexed: 01/13/2023] Open
Abstract
High temperature requirement A1 (HtrA1) belongs to an ancient protein family that is linked to various human disorders. The precise role of exon 1-encoded N-terminal domains and how these influence the biological functions of human HtrA1 remain elusive. In this study, we traced the evolutionary origins of these N-terminal domains to a single gene fusion event in the most recent common ancestor of vertebrates. We hypothesized that human HtrA1 is implicated in unfolded protein response. In highly secretory cells of the retinal pigmented epithelia, endoplasmic reticulum (ER) stress upregulated HtrA1. HtrA1 co-localized with vimentin intermediate filaments in highly arborized fashion. Upon ER stress, HtrA1 tracked along intermediate filaments, which collapsed and bundled in an aggresome at the microtubule organizing center. Gene silencing of HtrA1 altered the schedule and amplitude of adaptive signaling and concomitantly resulted in apoptosis. Restoration of wild-type HtrA1, but not its protease inactive mutant, was necessary and sufficient to protect from apoptosis. A variant of HtrA1 that harbored exon 1 substitutions displayed reduced efficacy in rescuing cells from proteotoxicity. Our results illuminate the integration of HtrA1 in the toolkit of mammalian cells against protein misfolding and the implications of defects in HtrA1 in proteostasis.
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Affiliation(s)
- Maximilian J Gerhardt
- Department of Ophthalmology, Harvard Medical School, The Schepens Eye Research Institute and Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA.,Department III of Internal Medicine, Cologne University Heart Center, Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Margaux Morrison
- Department of Ophthalmology and Visual Sciences, University of Utah and John A. Moran Eye Center, Salt Lake City, UT 84132, USA
| | - Andrius Kazlauskas
- Department of Ophthalmology, Harvard Medical School, The Schepens Eye Research Institute and Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Arogya Khadka
- Department of Ophthalmology, Harvard Medical School, The Schepens Eye Research Institute and Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Stephan Rosenkranz
- Department III of Internal Medicine, Cologne University Heart Center, Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany
| | - Margaret M DeAngelis
- Department of Ophthalmology and Visual Sciences, University of Utah and John A. Moran Eye Center, Salt Lake City, UT 84132, USA
| | - Magali Saint-Geniez
- Department of Ophthalmology, Harvard Medical School, The Schepens Eye Research Institute and Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Sarah Melissa P Jacobo
- Department of Ophthalmology, Harvard Medical School, The Schepens Eye Research Institute and Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
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31
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Delfín DA, DeAguero JL, McKown EN. The Extracellular Matrix Protein ABI3BP in Cardiovascular Health and Disease. Front Cardiovasc Med 2019; 6:23. [PMID: 30923710 PMCID: PMC6426741 DOI: 10.3389/fcvm.2019.00023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/20/2019] [Indexed: 01/31/2023] Open
Abstract
ABI3BP is a relatively newly identified protein whose general biological functions are not yet fully defined. It is implicated in promoting cellular senescence and cell-extracellular matrix interactions, both of which are of vital importance in the cardiovascular system. ABI3BP has been shown in multiple studies to be expressed in the heart and vasculature, and to have a role in normal cardiovascular function and disease. However, its precise role in the cardiovascular system is not known. Because ABI3BP is present in the cardiovascular system and is altered in cardiovascular disease states, further investigation into ABI3BP's biological and biochemical importance in cardiovascular health and disease is warranted.
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Affiliation(s)
- Dawn A. Delfín
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States
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32
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Belczacka I, Pejchinovski M, Krochmal M, Magalhães P, Frantzi M, Mullen W, Vlahou A, Mischak H, Jankowski V. Urinary Glycopeptide Analysis for the Investigation of Novel Biomarkers. Proteomics Clin Appl 2018; 13:e1800111. [PMID: 30334612 DOI: 10.1002/prca.201800111] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/16/2018] [Indexed: 12/20/2022]
Abstract
PURPOSE Urine is a rich source of potential biomarkers, including glycoproteins. Glycoproteomic analysis remains difficult due to the high heterogeneity of glycans. Nevertheless, recent advances in glycoproteomics software solutions facilitate glycopeptide identification and characterization. The aim is to investigate intact glycopeptides in the urinary peptide profiles of normal subjects using a novel PTM-centric software-Byonic. EXPERIMENTAL DESIGN The urinary peptide profiles of 238 normal subjects, previously analyzed using CE-MS and CE-MS/MS and/or LC-MS/MS, are subjected to glycopeptide analysis. Additionally, glycopeptide distribution is assessed in a set of 969 patients with five different cancer types: bladder, prostate and pancreatic cancer, cholangiocarcinoma, and renal cell carcinoma. RESULTS A total of 37 intact O-glycopeptides and 23 intact N-glycopeptides are identified in the urinary profiles of 238 normal subjects. Among the most commonly identified O-glycoproteins are Apolipoprotein C-III and insulin-like growth factor II, while titin among the N-glycoproteins. Further statistical analysis reveals that three O-glycopeptides and five N-glycopeptides differed significantly in their abundance among the different cancer types, comparing to normal subjects. CONCLUSIONS AND CLINICAL RELEVANCE Through the established glycoproteomics workflow, intact O- and N-glycopeptides in human urine are identified and characterized, providing novel insights for further exploration of the glycoproteome with respect to specific diseases.
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Affiliation(s)
- Iwona Belczacka
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany.,University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), 52074 Aachen, Germany
| | | | | | | | | | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, G128QQ Glasgow, UK
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens (BRFAA), 11527 Athens, Greece
| | | | - Vera Jankowski
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), 52074 Aachen, Germany
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33
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Sung HJ, Ahn JM, Yoon YH, Na SS, Choi YJ, Kim YI, Lee SY, Lee EB, Cho S, Cho JY. Quiescin Sulfhydryl Oxidase 1 (QSOX1) Secreted by Lung Cancer Cells Promotes Cancer Metastasis. Int J Mol Sci 2018; 19:ijms19103213. [PMID: 30336636 PMCID: PMC6214099 DOI: 10.3390/ijms19103213] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 01/16/2023] Open
Abstract
As lung cancer shows the highest mortality in cancer-related death, serum biomarkers are demanded for lung cancer diagnosis and its treatment. To discover lung cancer protein biomarkers, secreted proteins from primary cultured lung cancer and adjacent normal tissues from patients were subjected to LC/MS⁻MS proteomic analysis. Quiescin sulfhydryl oxidase (QSOX1) was selected as a biomarker candidate from the enriched proteins in the secretion of lung cancer cells. QSOX1 levels were higher in 82% (51 of 62 tissues) of lung cancer tissues compared to adjacent normal tissues. Importantly, QSOX1 serum levels were significantly higher in cancer patients (p < 0.05, Area Under curve (AUC) = 0.89) when measured by multiple reaction monitoring (MRM). Higher levels of QSOX1 were also uniquely detected in lung cancer tissues, among several other solid cancers, by immunohistochemistry. QSOX1-knock-downed Lewis lung cancer (LLC) cells were less viable from oxidative stress and reduced migration and invasion. In addition, LLC mouse models with QSOX1 knock-down also proved that QSOX1 functions in promoting cancer metastasis. In conclusion, QSOX1 might be a lung cancer tissue-derived biomarker and be involved in the promotion of lung cancers, and thus can be a therapeutic target for lung cancers.
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Affiliation(s)
- Hye-Jin Sung
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Jung-Mo Ahn
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Yeon-Hee Yoon
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Sang-Su Na
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Young-Jin Choi
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Yong-In Kim
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Soo-Youn Lee
- Departments of Laboratory Medicine & Genetics and Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea.
| | - Eung-Bae Lee
- Department of Thoracic and Cardiovascular Surgery, Kyungpook National University Medical Center, Daegu 41944, Korea.
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seoungnam-si, Gyeonggi-do 13620, Korea.
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
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34
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Gianazza E, Banfi C. Post-translational quantitation by SRM/MRM: applications in cardiology. Expert Rev Proteomics 2018; 15:477-502. [DOI: 10.1080/14789450.2018.1484283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erica Gianazza
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Cristina Banfi
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
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35
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Frost DC, Li L. Recent advances in mass spectrometry-based glycoproteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 95:71-123. [PMID: 24985770 DOI: 10.1016/b978-0-12-800453-1.00003-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein glycosylation plays fundamental roles in many biological processes as one of the most common, and the most complex, posttranslational modification. Alterations in glycosylation profile are now known to be associated with many diseases. As a result, the discovery and detailed characterization of glycoprotein disease biomarkers is a primary interest of biomedical research. Advances in mass spectrometry (MS)-based glycoproteomics and glycomics are increasingly enabling qualitative and quantitative approaches for site-specific structural analysis of protein glycosylation. While the complexity presented by glycan heterogeneity and the wide dynamic range of clinically relevant samples like plasma, serum, cerebrospinal fluid, and tissue make comprehensive analyses of the glycoproteome a challenging task, the ongoing efforts into the development of glycoprotein enrichment, enzymatic digestion, and separation strategies combined with novel quantitative MS methodologies have greatly improved analytical sensitivity, specificity, and throughput. This review summarizes current MS-based glycoproteomics approaches and highlights recent advances in its application to cancer biomarker and neurodegenerative disease research.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA; Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.
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36
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Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B. Large-scale intact glycopeptide identification by Mascot database search. Sci Rep 2018; 8:2117. [PMID: 29391424 PMCID: PMC5795011 DOI: 10.1038/s41598-018-20331-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/15/2018] [Indexed: 01/16/2023] Open
Abstract
Workflows capable of determining glycopeptides in large-scale are missing in the field of glycoproteomics. We present an approach for automated annotation of intact glycopeptide mass spectra. The steps in adopting the Mascot search engine for intact glycopeptide analysis included: (i) assigning one letter codes for monosaccharides, (ii) linearizing glycan sequences and (iii) preparing custom glycoprotein databases. Automated annotation of both N- and O-linked glycopeptides was proven using standard glycoproteins. In a large-scale study, a total of 257 glycoproteins containing 970 unique glycosylation sites and 3447 non-redundant N-linked glycopeptide variants were identified in 24 serum samples. Thus, a single tool was developed that collectively allows the (i) elucidation of N- and O-linked glycopeptide spectra, (ii) matching glycopeptides to known protein sequences, and (iii) high-throughput, batch-wise analysis of large-scale glycoproteomics data sets.
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Affiliation(s)
| | | | - Randi Elin Gislefoss
- Cancer Registry of Norway, Institute of Population-based Cancer Research, Oslo, Norway
| | | | - Bernd Thiede
- Department of Biosciences, University of Oslo, Oslo, Norway.
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37
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Lindsey ML, Jung M, Hall ME, DeLeon-Pennell KY. Proteomic analysis of the cardiac extracellular matrix: clinical research applications. Expert Rev Proteomics 2018; 15:105-112. [PMID: 29285949 DOI: 10.1080/14789450.2018.1421947] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The cardiac extracellular matrix (ECM) provides anatomical, biochemical, and physiological support to the left ventricle. ECM proteins are difficult to detect using unbiased proteomic approaches due to solubility issues and a relatively low abundance compared to cytoplasmic and mitochondrial proteins present in highly prevalent cardiomyocytes. Areas covered: Proteomic capabilities have dramatically improved over the past 20 years, due to enhanced sample preparation protocols and increased capabilities in mass spectrometry (MS), database searching, and bioinformatics analysis. This review summarizes technological advancements made in proteomic applications that make ECM proteomics highly feasible. Expert commentary: Proteomic analysis of the ECM provides an important contribution to our understanding of the molecular and cellular processes associated with cardiovascular disease. Using results generated from proteomics approaches in basic science applications and integrating proteomics templates into clinical research protocols will aid in efforts to personalize medicine.
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Affiliation(s)
- Merry L Lindsey
- a Research Service , G.V. (Sonny) Montgomery Veterans Affairs Medical Center , Jackson , MS , USA.,b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA
| | - Mira Jung
- b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA
| | - Michael E Hall
- b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA.,c Division of Cardiology , University of Mississippi Medical Center , Jackson , MS , USA
| | - Kristine Y DeLeon-Pennell
- a Research Service , G.V. (Sonny) Montgomery Veterans Affairs Medical Center , Jackson , MS , USA.,b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA
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38
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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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39
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Suna G, Wojakowski W, Lynch M, Barallobre-Barreiro J, Yin X, Mayr U, Baig F, Lu R, Fava M, Hayward R, Molenaar C, White SJ, Roleder T, Milewski KP, Gasior P, Buszman PP, Buszman P, Jahangiri M, Shanahan CM, Hill J, Mayr M. Extracellular Matrix Proteomics Reveals Interplay of Aggrecan and Aggrecanases in Vascular Remodeling of Stented Coronary Arteries. Circulation 2017; 137:166-183. [PMID: 29030347 PMCID: PMC5757669 DOI: 10.1161/circulationaha.116.023381] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 09/22/2017] [Indexed: 12/11/2022]
Abstract
Supplemental Digital Content is available in the text. Background: Extracellular matrix (ECM) remodeling contributes to in-stent restenosis and thrombosis. Despite its important clinical implications, little is known about ECM changes post–stent implantation. Methods: Bare-metal and drug-eluting stents were implanted in pig coronary arteries with an overstretch under optical coherence tomography guidance. Stented segments were harvested 1, 3, 7, 14, and 28 days post-stenting for proteomics analysis of the media and neointima. Results: A total of 151 ECM and ECM-associated proteins were identified by mass spectrometry. After stent implantation, proteins involved in regulating calcification were upregulated in the neointima of drug-eluting stents. The earliest changes in the media were proteins involved in inflammation and thrombosis, followed by changes in regulatory ECM proteins. By day 28, basement membrane proteins were reduced in drug-eluting stents in comparison with bare-metal stents. In contrast, the large aggregating proteoglycan aggrecan was increased. Aggrecanases of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) family contribute to the catabolism of vascular proteoglycans. An increase in ADAMTS-specific aggrecan fragments was accompanied by a notable shift from ADAMTS1 and ADAMTS5 to ADAMTS4 gene expression after stent implantation. Immunostaining in human stented coronary arteries confirmed the presence of aggrecan and aggrecan fragments, in particular, at the contacts of the stent struts with the artery. Further investigation of aggrecan presence in the human vasculature revealed that aggrecan and aggrecan cleavage were more abundant in human arteries than in human veins. In addition, aggrecan synthesis was induced on grafting a vein into the arterial circulation, suggesting an important role for aggrecan in vascular plasticity. Finally, lack of ADAMTS-5 activity in mice resulted in an accumulation of aggrecan and a dilation of the thoracic aorta, confirming that aggrecanase activity regulates aggrecan abundance in the arterial wall and contributes to vascular remodeling. Conclusions: Significant differences were identified by proteomics in the ECM of coronary arteries after bare-metal and drug-eluting stent implantation, most notably an upregulation of aggrecan, a major ECM component of cartilaginous tissues that confers resistance to compression. The accumulation of aggrecan coincided with a shift in ADAMTS gene expression. This study provides the first evidence implicating aggrecan and aggrecanases in the vascular injury response after stenting.
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Affiliation(s)
- Gonca Suna
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Wojciech Wojakowski
- 3rd Division of Cardiology, Medical University of Silesia, Katowice, Poland (W.W., T.R., P.G.)
| | - Marc Lynch
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Javier Barallobre-Barreiro
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Xiaoke Yin
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Ursula Mayr
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Ferheen Baig
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Ruifang Lu
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Marika Fava
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Robert Hayward
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Chris Molenaar
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Stephen J White
- Healthcare Science Research Centre, Manchester Metropolitan University, United Kingdom (S.J.W.)
| | - Tomasz Roleder
- 3rd Division of Cardiology, Medical University of Silesia, Katowice, Poland (W.W., T.R., P.G.)
| | - Krzysztof P Milewski
- Centre for Cardiovascular Research and Development, American Heart of Poland, Katowice (K.P.M., P.P.B., P.B.)
| | - Pawel Gasior
- 3rd Division of Cardiology, Medical University of Silesia, Katowice, Poland (W.W., T.R., P.G.)
| | - Piotr P Buszman
- Centre for Cardiovascular Research and Development, American Heart of Poland, Katowice (K.P.M., P.P.B., P.B.)
| | - Pawel Buszman
- Centre for Cardiovascular Research and Development, American Heart of Poland, Katowice (K.P.M., P.P.B., P.B.)
| | - Marjan Jahangiri
- St George's Vascular Institute, St George's Healthcare NHS Trust, London, United Kingdom (M.J.)
| | - Catherine M Shanahan
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
| | - Jonathan Hill
- King's College Hospital and King's Health Partners Academic Health Sciences, London, United Kingdom (J.H.)
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, United Kingdom (G.S., M.L., J.B.-B., X.Y., U.M., F.B., R.L., M.F., R.H., C.M., C.M.S., M.M.)
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40
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Outside-in, inside-out: Proteomic analysis of endothelial stress mediated by 7-ketocholesterol. Chem Phys Lipids 2017; 207:231-238. [DOI: 10.1016/j.chemphyslip.2017.06.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 12/15/2022]
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41
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Comparative glycoproteomics of stem cells identifies new players in ricin toxicity. Nature 2017; 549:538-542. [PMID: 28959962 DOI: 10.1038/nature24015] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/16/2017] [Indexed: 12/16/2022]
Abstract
Glycosylation, the covalent attachment of carbohydrate structures onto proteins, is the most abundant post-translational modification. Over 50% of human proteins are glycosylated, which alters their activities in diverse fundamental biological processes. Despite the importance of glycosylation in biology, the identification and functional validation of complex glycoproteins has remained largely unexplored. Here we develop a novel quantitative approach to identify intact glycopeptides from comparative proteomic data sets, allowing us not only to infer complex glycan structures but also to directly map them to sites within the associated proteins at the proteome scale. We apply this method to human and mouse embryonic stem cells to illuminate the stem cell glycoproteome. This analysis nearly doubles the number of experimentally confirmed glycoproteins, identifies previously unknown glycosylation sites and multiple glycosylated stemness factors, and uncovers evolutionarily conserved as well as species-specific glycoproteins in embryonic stem cells. The specificity of our method is confirmed using sister stem cells carrying repairable mutations in enzymes required for fucosylation, Fut9 and Slc35c1. Ablation of fucosylation confers resistance to the bioweapon ricin, and we discover proteins that carry a fucosylation-dependent sugar code for ricin toxicity. Mutations disrupting a subset of these proteins render cells ricin resistant, revealing new players that orchestrate ricin toxicity. Our comparative glycoproteomics platform, SugarQb, enables genome-wide insights into protein glycosylation and glycan modifications in complex biological systems.
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42
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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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43
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Woo CM, Felix A, Byrd WE, Zuegel DK, Ishihara M, Azadi P, Iavarone AT, Pitteri SJ, Bertozzi CR. Development of IsoTaG, a Chemical Glycoproteomics Technique for Profiling Intact N- and O-Glycopeptides from Whole Cell Proteomes. J Proteome Res 2017; 16:1706-1718. [PMID: 28244757 DOI: 10.1021/acs.jproteome.6b01053] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Protein glycosylation can have an enormous variety of biological consequences, reflecting the molecular diversity encoded in glycan structures. This same structural diversity has imposed major challenges on the development of methods to study the intact glycoproteome. We recently introduced a method termed isotope-targeted glycoproteomics (IsoTaG), which utilizes isotope recoding to characterize azidosugar-labeled glycopeptides bearing fully intact glycans. Here, we describe the broad application of the method to analyze glycoproteomes from a collection of tissue-diverse cell lines. The effort was enabled by a new high-fidelity pattern-searching and glycopeptide validation algorithm termed IsoStamp v2.0, as well as by novel stable isotope probes. Application of the IsoTaG platform to 15 cell lines metabolically labeled with Ac4GalNAz or Ac4ManNAz revealed 1375 N- and 2159 O-glycopeptides, variously modified with 74 discrete glycan structures. Glycopeptide-bound glycans observed by IsoTaG were found to be comparable to released N-glycans identified by permethylation analysis. IsoTaG is therefore positioned to enhance structural understanding of the glycoproteome.
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Affiliation(s)
- Christina M Woo
- Department of Chemistry; §School of Engineering; #Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine; ∇Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States.,School of Computing, University of Utah , Salt Lake City, Utah 84112, United States.,Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States.,QB3Mass Spectrometry, University of California , Berkeley, California 94720, United States
| | - Alejandra Felix
- Department of Chemistry; §School of Engineering; #Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine; ∇Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States.,School of Computing, University of Utah , Salt Lake City, Utah 84112, United States.,Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States.,QB3Mass Spectrometry, University of California , Berkeley, California 94720, United States
| | - William E Byrd
- Department of Chemistry; §School of Engineering; #Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine; ∇Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States.,School of Computing, University of Utah , Salt Lake City, Utah 84112, United States.,Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States.,QB3Mass Spectrometry, University of California , Berkeley, California 94720, United States
| | - Devon K Zuegel
- Department of Chemistry; §School of Engineering; #Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine; ∇Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States.,School of Computing, University of Utah , Salt Lake City, Utah 84112, United States.,Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States.,QB3Mass Spectrometry, University of California , Berkeley, California 94720, United States
| | - Mayumi Ishihara
- Department of Chemistry; §School of Engineering; #Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine; ∇Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States.,School of Computing, University of Utah , Salt Lake City, Utah 84112, United States.,Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States.,QB3Mass Spectrometry, University of California , Berkeley, California 94720, United States
| | - Parastoo Azadi
- Department of Chemistry; §School of Engineering; #Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine; ∇Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States.,School of Computing, University of Utah , Salt Lake City, Utah 84112, United States.,Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States.,QB3Mass Spectrometry, University of California , Berkeley, California 94720, United States
| | - Anthony T Iavarone
- Department of Chemistry; §School of Engineering; #Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine; ∇Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States.,School of Computing, University of Utah , Salt Lake City, Utah 84112, United States.,Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States.,QB3Mass Spectrometry, University of California , Berkeley, California 94720, United States
| | - Sharon J Pitteri
- Department of Chemistry; §School of Engineering; #Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine; ∇Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States.,School of Computing, University of Utah , Salt Lake City, Utah 84112, United States.,Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States.,QB3Mass Spectrometry, University of California , Berkeley, California 94720, United States
| | - Carolyn R Bertozzi
- Department of Chemistry; §School of Engineering; #Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine; ∇Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States.,School of Computing, University of Utah , Salt Lake City, Utah 84112, United States.,Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States.,QB3Mass Spectrometry, University of California , Berkeley, California 94720, United States
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44
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Abstract
Protein glycosylation is one of the most important posttranslational modifications. Numerous biological functions are related to protein glycosylation. However, analytical challenges remain in the glycoprotein analysis. To overcome the challenges associated with glycoprotein analysis, many analytical techniques were developed in recent years. Enrichment methods were used to improve the sensitivity of detection, while HPLC and mass spectrometry methods were developed to facilitate the separation of glycopeptides/proteins and enhance detection, respectively. Fragmentation techniques applied in modern mass spectrometers allow the structural interpretation of glycopeptides/proteins, while automated software tools started replacing manual processing to improve the reliability and throughput of the analysis. In this chapter, the current methodologies of glycoprotein analysis were discussed. Multiple analytical techniques are compared, and advantages and disadvantages of each technique are highlighted.
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45
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Smeekens JM, Xiao H, Wu R. Global Analysis of Secreted Proteins and Glycoproteins in Saccharomyces cerevisiae. J Proteome Res 2016; 16:1039-1049. [PMID: 27933904 DOI: 10.1021/acs.jproteome.6b00953] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein secretion is essential for numerous cellular activities, and secreted proteins in bodily fluids are a promising and noninvasive source of biomarkers for disease detection. Systematic analysis of secreted proteins and glycoproteins will provide insight into protein function and cellular activities. Yeast (Saccharomyces cerevisiae) is an excellent model system for eukaryotic cells, but global analysis of secreted proteins and glycoproteins in yeast is challenging due to the low abundances of secreted proteins and contamination from high-abundance intracellular proteins. Here, by using mild separation of secreted proteins from cells, we comprehensively identified and quantified secreted proteins and glycoproteins through inhibition of glycosylation and mass spectrometry-based proteomics. In biological triplicate experiments, 245 secreted proteins were identified, and comparison with previous experimental and computational results demonstrated that many identified proteins were located in the extracellular space. Most quantified secreted proteins were down-regulated from cells treated with an N-glycosylation inhibitor (tunicamycin). The quantitative results strongly suggest that the secretion of these down-regulated proteins was regulated by glycosylation, while the secretion of proteins with minimal abundance changes was contrarily irrelevant to protein glycosylation, likely being secreted through nonclassical pathways. Glycoproteins in the yeast secretome were globally analyzed for the first time. A total of 27 proteins were quantified in at least two protein and glycosylation triplicate experiments, and all except one were down-regulated under N-glycosylation inhibition, which is solid experimental evidence to further demonstrate that the secretion of these proteins is regulated by their glycosylation. These results provide valuable insight into protein secretion, which will further advance protein secretion and disease studies.
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Affiliation(s)
- Johanna M Smeekens
- School of Chemistry and Biochemistry, and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Haopeng Xiao
- School of Chemistry and Biochemistry, and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry, and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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46
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Site-specific glycosylation of the Newcastle disease virus haemagglutinin-neuraminidase. Glycoconj J 2016; 34:181-197. [DOI: 10.1007/s10719-016-9750-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 12/14/2022]
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47
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Use of a glycosylation site database to improve glycopeptide identification from complex mixtures. Anal Bioanal Chem 2016; 409:571-577. [PMID: 27722944 DOI: 10.1007/s00216-016-9981-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/16/2016] [Accepted: 09/26/2016] [Indexed: 10/20/2022]
Abstract
New mass spectrometry instrumentation, particularly those with electron transfer dissociation fragmentation, has made the analysis of complex glycopeptide mixtures accessible. However, software tools need to be optimized for interpretation of this type of data. Glycopeptide identification is challenging due to the number of different peptide and sugar moieties that can be combined, leading to a large number of potential compositions to consider. In this manuscript, different strategies for reducing the number of peptides and glycopeptides considered in database searching are compared. Adaptation of the software Protein Prospector to support the use of a reference modification site database doubled the number of glycopeptide IDs. The potential of this as an improved analysis strategy is discussed. Graphical abstract This manuscript compares the use of a restricted protein database based on a list of accession numbers of identified proteins to the use of a modification site database for intact glycopeptide analysis. It was found that the modification database is more effective for glycopeptide identification, particularly for larger glycopeptides.
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48
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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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49
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Lindsey ML, Hall ME, Harmancey R, Ma Y. Adapting extracellular matrix proteomics for clinical studies on cardiac remodeling post-myocardial infarction. Clin Proteomics 2016; 13:19. [PMID: 27651752 PMCID: PMC5024439 DOI: 10.1186/s12014-016-9120-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/15/2016] [Indexed: 01/16/2023] Open
Abstract
Following myocardial infarction (MI), the left ventricle (LV) undergoes a series of cardiac wound healing responses that involve stimulation of robust inflammation to clear necrotic myocytes and tissue debris and induction of extracellular matrix (ECM) protein synthesis to generate a scar. Proteomic strategies provide us with a means to index the ECM proteins expressed in the LV, quantify amounts, determine functions, and explore interactions. This review will focus on the efforts taken in the proteomics research field that have expanded our understanding of post-MI LV remodeling, concentrating on the strengths and limitations of different proteomic approaches to glean information that is specific to ECM turnover in the post-MI setting. We will discuss how recent advances in sample preparation and labeling protocols increase our successes at detecting components of the cardiac ECM proteome. We will summarize how proteomic approaches, focusing on the ECM compartment, have progressed over time to current gel-free methods using decellularized fractions or labeling strategies that will be useful for clinical applications. This review will provide an overview of how cardiac ECM proteomics has evolved over the last decade and will provide insight into future directions that will drive forward our understanding of cardiac ECM turnover in the post-MI LV.
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Affiliation(s)
- Merry L Lindsey
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA ; Division of Cardiology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS USA ; Research Service, G.V. (Sonny) Montgomery Veterans Affairs Medical Center, Jackson, MS USA
| | - Michael E Hall
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA ; Division of Cardiology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS USA
| | - Romain Harmancey
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA
| | - Yonggang Ma
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA
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50
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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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