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Yom A, Chiang A, Lewis NE. Boltzmann Model Predicts Glycan Structures from Lectin Binding. Anal Chem 2024. [PMID: 38720429 DOI: 10.1021/acs.analchem.3c04992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Glycans are complex oligosaccharides that are involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese hamster ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego, California 92093, United States
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Immunology Center of Georgia, Augusta University, Augusta, Georgia 30912, United States
- Department of Medicine, Augusta University, Augusta, Georgia 30912, United States
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Department of Bioengineering, University of California, San Diego, California 92093, United States
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2
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Yom A, Chiang A, Lewis NE. A Boltzmann model predicts glycan structures from lectin binding. bioRxiv 2024:2023.06.03.543532. [PMID: 37333412 PMCID: PMC10274649 DOI: 10.1101/2023.06.03.543532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Glycans are complex oligosaccharides involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese Hamster Ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego. CA 92093, USA
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
- Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Medicine, Augusta University, Augusta, GA 30912, USA
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego. CA 92093, USA
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
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3
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Wang YE, Zeng WL, Cao ST, Zou JP, Liu CT, Shi JM, Li J, Qiu F, Wang Y. Development of a sample preparation method for micro-proteomics analysis of the formaldehyde-fixed paraffin-embedded liver tissue samples. Talanta 2024; 266:125106. [PMID: 37639870 DOI: 10.1016/j.talanta.2023.125106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Liver micro-proteomics based on the routinely used formaldehyde-fixed paraffin-embedded (FFPE) samples is valuable for innovative research, but the technical approach for sample preparation is often challenging. In this study, we aimed to develop a method for sample preparation for micro-proteomics on using the FFPE liver samples. We collected 2000 individual cells per batch from FFPE liver slices with laser capture microdissection and used them as test samples. We used the microscale fresh-frozen liver samples or HepG2 cells as control samples. For the FFPE samples, we first established a procedure for protein extraction. 2 h incubation at 95 °C in alkaline amine buffer supplemented with 4% sodium dodecyl sulfate allows improved production, efficiency, and quality of protein extraction. Then, we developed a dedicated protocol HDMSP for the micro-concentrated (<0.05 μg/μL) protein preparation for mass spectrometry (MS) based analysis, in which 2 μg/μL carboxyl magnetic beads and 70% acetonitrile are used to induce protein precipitation. For the 0.01 μg/μL protein control samples, protein recovery rate (PRR) by HDMSP is 72.1%, while the PRR is 5.9% if using a standard method solid phase-enhanced sample preparation. For the FFPE samples, the HDMSP PRR is 88.8%, and the subsequent MS analysis demonstrates increased depth, robustness, and quantitation accuracy for HDMSP relative to the control of in-gel digestion. Moreover, the physicochemical properties and subcellular location of the FFPE liver micro-proteome are comparable to those of the fresh-frozen control samples processed with filter-aided sample preparation (FASP). HDMSP is also comparable to FASP in terms of reproducibility and physicochemical properties in liver subcellular proteomes, and meanwhile reduces the sample preparation time by 15.9% and the experimental cost by 30.8%. Overall, the new method is simple and highly effective for preparing the microscale FFPE liver protein samples for MS analysis. This study provides a useful solution for FFPE liver micro-proteomics.
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Affiliation(s)
- Yong-Er Wang
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Wei-Lan Zeng
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Sheng-Tian Cao
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Jun-Peng Zou
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Cui-Ting Liu
- Biomedical Research Center, Southern Medical University, Guangzhou, China
| | - Jun-Min Shi
- Biomedical Research Center, Southern Medical University, Guangzhou, China
| | - Jing Li
- Biomedical Research Center, Southern Medical University, Guangzhou, China
| | - Feng Qiu
- The Seventh Affiliated Hospital of Southern Medical University, Foshan, China.
| | - Yan Wang
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China; The Seventh Affiliated Hospital of Southern Medical University, Foshan, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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4
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Downs M, Zaia J, Sethi MK. Mass spectrometry methods for analysis of extracellular matrix components in neurological diseases. Mass Spectrom Rev 2023; 42:1848-1875. [PMID: 35719114 PMCID: PMC9763553 DOI: 10.1002/mas.21792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/12/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The brain extracellular matrix (ECM) is a highly glycosylated environment and plays important roles in many processes including cell communication, growth factor binding, and scaffolding. The formation of structures such as perineuronal nets (PNNs) is critical in neuroprotection and neural plasticity, and the formation of molecular networks is dependent in part on glycans. The ECM is also implicated in the neuropathophysiology of disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and Schizophrenia (SZ). As such, it is of interest to understand both the proteomic and glycomic makeup of healthy and diseased brain ECM. Further, there is a growing need for site-specific glycoproteomic information. Over the past decade, sample preparation, mass spectrometry, and bioinformatic methods have been developed and refined to provide comprehensive information about the glycoproteome. Core ECM molecules including versican, hyaluronan and proteoglycan link proteins, and tenascin are dysregulated in AD, PD, and SZ. Glycomic changes such as differential sialylation, sulfation, and branching are also associated with neurodegeneration. A more thorough understanding of the ECM and its proteomic, glycomic, and glycoproteomic changes in brain diseases may provide pathways to new therapeutic options.
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Affiliation(s)
- Margaret Downs
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Manveen K Sethi
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
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Balbisi M, Sugár S, Schlosser G, Szeitz B, Fillinger J, Moldvay J, Drahos L, Szász AM, Tóth G, Turiák L. Inter- and intratumoral proteomics and glycosaminoglycan characterization of ALK rearranged lung adenocarcinoma tissues: a pilot study. Sci Rep 2023; 13:6268. [PMID: 37069213 PMCID: PMC10110559 DOI: 10.1038/s41598-023-33435-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023] Open
Abstract
Lung cancer is one of the most common types of cancer with limited therapeutic options, therefore a detailed understanding of the underlying molecular changes is of utmost importance. In this pilot study, we investigated the proteomic and glycosaminoglycan (GAG) profile of ALK rearranged lung tumor tissue regions based on the morphological classification, mucin and stromal content. Principal component analysis and hierarchical clustering revealed that both the proteomic and GAG-omic profiles are highly dependent on mucin content and to a lesser extent on morphology. We found that differentially expressed proteins between morphologically different tumor types are primarily involved in the regulation of protein synthesis, whereas those between adjacent normal and different tumor regions take part in several other biological processes (e.g. extracellular matrix organization, oxidation-reduction processes, protein folding) as well. The total amount and the sulfation profile of heparan sulfate and chondroitin sulfate showed small differences based on morphology and larger differences based on mucin content of the tumor, while an increase was observed in both the total amount and the average rate of sulfation in tumors compared to adjacent normal regions.
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Affiliation(s)
- Mirjam Balbisi
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, 1117, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Simon Sugár
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, 1117, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Eötvös Loránd University, Pázmány Péter sétány 1, Budapest, 1117, Hungary
| | - Beáta Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - János Fillinger
- Department of Pathology, National Korányi Institute of Pulmonology, Korányi Frigyes út 1., Budapest, 1121, Hungary
| | - Judit Moldvay
- 1st Department of Pulmonology, National Korányi Institute of Pulmonology, Korányi Frigyes út 1., Budapest, 1121, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, 1117, Hungary
| | - A Marcell Szász
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, 1117, Hungary.
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, 1117, Hungary.
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary.
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Pál D, Tóth G, Sugár S, Fügedi KD, Szabó D, Kovalszky I, Papp D, Schlosser G, Tóth C, Tornóczky T, Drahos L, Turiák L. Compositional Analysis of Glycosaminoglycans in Different Lung Cancer Types-A Pilot Study. Int J Mol Sci 2023; 24:ijms24087050. [PMID: 37108213 PMCID: PMC10138872 DOI: 10.3390/ijms24087050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Lung cancer is one of the most commonly diagnosed cancer types. Studying the molecular changes that occur in lung cancer is important to understand tumor formation and identify new therapeutic targets and early markers of the disease to decrease mortality. Glycosaminoglycan chains play important roles in various signaling events in the tumor microenvironment. Therefore, we have determined the quantity and sulfation characteristics of chondroitin sulfate and heparan sulfate in formalin-fixed paraffin-embedded human lung tissue samples belonging to different lung cancer types as well as tumor adjacent normal areas. Glycosaminoglycan disaccharide analysis was performed using HPLC-MS following on-surface lyase digestion. Significant changes were identified predominantly in the case of chondroitin sulfate; for example, the total amount was higher in tumor tissue compared to the adjacent normal tissue. We also observed differences in the degree of sulfation and relative proportions of individual chondroitin sulfate disaccharides between lung cancer types and adjacent normal tissue. Furthermore, the differences in the 6-O-/4-O-sulfation ratio of chondroitin sulfate were different between the lung cancer types. Our pilot study revealed that further investigation of the role of chondroitin sulfate chains and enzymes involved in their biosynthesis is an important aspect of lung cancer research.
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Affiliation(s)
- Domonkos Pál
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, H-1085 Budapest, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Simon Sugár
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, H-1085 Budapest, Hungary
| | - Kata Dorina Fügedi
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary
| | - Dávid Papp
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Csaba Tóth
- Teaching Hospital Markusovszky, University of Pécs, H-9700 Szombathely, Hungary
| | - Tamás Tornóczky
- Department of Pathology, Faculty of Medicine and Clinical Center, University of Pécs, H-7624 Pécs, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
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Tóth G, Pál D, Sugár S, Kovalszky I, Dezső K, Schlosser G, Drahos L, Turiák L. Expression of glycosaminoglycans in cirrhotic liver and hepatocellular carcinoma-a pilot study including etiology. Anal Bioanal Chem 2022; 414:3837-3846. [PMID: 35344068 PMCID: PMC8958808 DOI: 10.1007/s00216-022-04025-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/08/2022] [Accepted: 03/15/2022] [Indexed: 11/25/2022]
Abstract
Chronic liver diseases have both high incidence and mortality rates; therefore, a deeper understanding of the underlying molecular mechanisms is essential. We have determined the content and sulfation pattern of chondroitin sulfate (CS) and heparan sulfate (HS) in human hepatocellular carcinoma and cirrhotic liver tissues, considering the etiology of the diseases. A variety of pathological conditions such as alcoholic liver disease, hepatitis B and C virus infections, and primary sclerosing cholangitis were studied. Major differences were observed in the total abundance and sulfation pattern of CS and HS chains. For example, the 6-O-sulfation of CS is fundamentally different regarding etiologies of cirrhosis, and a 2-threefold increase in HS N-sulfation/O-sulfation ratio was observed in hepatocellular carcinoma compared to cirrhotic tissues.
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Affiliation(s)
- Gábor Tóth
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117, Budapest, Hungary.,Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111, Budapest, Hungary
| | - Domonkos Pál
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117, Budapest, Hungary
| | - Simon Sugár
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117, Budapest, Hungary.,Ph.D. School of Pharmaceutical Sciences, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Katalin Dezső
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Eötvös Loránd University, Pázmány Péter sétány 1, 1117, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117, Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117, Budapest, Hungary.
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Sugár S, Tóth G, Bugyi F, Vékey K, Karászi K, Drahos L, Turiák L. Alterations in protein expression and site-specific N-glycosylation of prostate cancer tissues. Sci Rep 2021; 11:15886. [PMID: 34354152 PMCID: PMC8342536 DOI: 10.1038/s41598-021-95417-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/23/2021] [Indexed: 02/07/2023] Open
Abstract
Identifying molecular alterations occurring during cancer progression is essential for a deeper understanding of the underlying biological processes. Here we have analyzed cancerous and healthy prostate biopsies using nanoLC-MS(MS) to detect proteins with altered expression and N-glycosylation. We have identified 75 proteins with significantly changing expression during disease progression. The biological processes involved were assigned based on protein-protein interaction networks. These include cellular component organization, metabolic and localization processes. Multiple glycoproteins were identified with aberrant glycosylation in prostate cancer, where differences in glycosite-specific sialylation, fucosylation, and galactosylation were the most substantial. Many of the glycoproteins with altered N-glycosylation were extracellular matrix constituents, and are heavily involved in the establishment of the tumor microenvironment.
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Affiliation(s)
- Simon Sugár
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary ,grid.11804.3c0000 0001 0942 9821Semmelweis University, Ph.D. School of Pharmaceutical Sciences, Üllői út 26, 1085 Budapest, Hungary
| | - Gábor Tóth
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary ,grid.6759.d0000 0001 2180 0451Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rakpart 3, 1111 Budapest, Hungary
| | - Fanni Bugyi
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary ,grid.5591.80000 0001 2294 6276Eötvös Loránd University, Hevesy György Ph.D. School of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Károly Vékey
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Katalin Karászi
- grid.11804.3c0000 0001 0942 98211St Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary
| | - László Drahos
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Lilla Turiák
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary ,grid.11804.3c0000 0001 0942 9821Semmelweis University, Ph.D. School of Pharmaceutical Sciences, Üllői út 26, 1085 Budapest, Hungary
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9
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Barboza M, Solakyildirim K, Knotts TA, Luke J, Gareau MG, Raybould HE, Lebrilla CB. Region-Specific Cell Membrane N-Glycome of Functional Mouse Brain Areas Revealed by nanoLC-MS Analysis. Mol Cell Proteomics 2021; 20:100130. [PMID: 34358619 PMCID: PMC8426282 DOI: 10.1016/j.mcpro.2021.100130] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/21/2022] Open
Abstract
N-glycosylation is a ubiquitous posttranslational modification that affects protein structure and function, including those of the central nervous system. N-glycans attached to cell membrane proteins play crucial roles in all aspects of biology, including embryogenesis, development, cell-cell recognition and adhesion, and cell signaling and communication. Although brain function and behavior are known to be regulated by the N-glycosylation state of numerous cell surface glycoproteins, our current understanding of brain glycosylation is limited, and glycan variations associated with functional brain regions remain largely unknown. In this work, we used a well-established cell surface glycomic nanoLC-Chip-Q-TOF platform developed in our laboratory to characterize the N-glycome of membrane fractions enriched in cell surface glycoproteins obtained from specific functional brain areas. We report the cell membrane N-glycome of two major developmental divisions of mice brain with specific and distinctive functions, namely the forebrain and hindbrain. Region-specific glycan maps were obtained with ∼120 N-glycan compositions in each region, revealing significant differences in "brain-type" glycans involving high mannose, bisecting, and core and antenna fucosylated species. Additionally, the cell membrane N-glycome of three functional regions of the forebrain and hindbrain, the cerebral cortex, hippocampus, and cerebellum, was characterized. In total, 125 N-glycan compositions were identified, and their region-specific expression profiles were characterized. Over 70 N-glycans contributed to the differentiation of the cerebral cortex, hippocampus, and cerebellum N-glycome, including bisecting and branched glycans with varying degrees of core and antenna fucosylation and sialylation. This study presents a comprehensive spatial distribution of the cell-membrane enriched N-glycomes associated with five discrete anatomical and functional brain areas, providing evidence for the presence of a previously unknown brain glyco-architecture. The region-specific molecular glyco fingerprints identified here will enable a better understanding of the critical biological roles that N-glycans play in the specialized functional brain areas in health and disease.
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Affiliation(s)
- Mariana Barboza
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, California, USA; Department of Chemistry, University of California Davis, Davis, California, USA.
| | - Kemal Solakyildirim
- Department of Chemistry, University of California Davis, Davis, California, USA; Department of Chemistry, Erzincan Binali Yildirim University, Erzincan, Turkey
| | - Trina A Knotts
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Jonathan Luke
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Melanie G Gareau
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Helen E Raybould
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, Davis, California, USA; Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, USA
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10
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Tabang DN, Ford M, Li L. Recent Advances in Mass Spectrometry-Based Glycomic and Glycoproteomic Studies of Pancreatic Diseases. Front Chem 2021; 9:707387. [PMID: 34368082 PMCID: PMC8342852 DOI: 10.3389/fchem.2021.707387] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Modification of proteins by glycans plays a crucial role in mediating biological functions in both healthy and diseased states. Mass spectrometry (MS) has emerged as the most powerful tool for glycomic and glycoproteomic analyses advancing knowledge of many diseases. Such diseases include those of the pancreas which affect millions of people each year. In this review, recent advances in pancreatic disease research facilitated by MS-based glycomic and glycoproteomic studies will be examined with a focus on diabetes and pancreatic cancer. The last decade, and especially the last five years, has witnessed developments in both discovering new glycan or glycoprotein biomarkers and analyzing the links between glycans and disease pathology through MS-based studies. The strength of MS lies in the specificity and sensitivity of liquid chromatography-electrospray ionization MS for measuring a wide range of biomolecules from limited sample amounts from many sample types, greatly enhancing and accelerating the biomarker discovery process. Furthermore, imaging MS of glycans enabled by matrix-assisted laser desorption/ionization has proven useful in complementing histology and immunohistochemistry to monitor pancreatic disease progression. Advances in biological understanding and analytical techniques, as well as challenges and future directions for the field, will be discussed.
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Affiliation(s)
- Dylan Nicholas Tabang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Megan Ford
- Department of Chemical and Biological Engineering, 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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11
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Zhan W, Muhuri M, Tai PWL, Gao G. Vectored Immunotherapeutics for Infectious Diseases: Can rAAVs Be The Game Changers for Fighting Transmissible Pathogens? Front Immunol 2021; 12:673699. [PMID: 34046041 PMCID: PMC8144494 DOI: 10.3389/fimmu.2021.673699] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
Conventional vaccinations and immunotherapies have encountered major roadblocks in preventing infectious diseases like HIV, influenza, and malaria. These challenges are due to the high genomic variation and immunomodulatory mechanisms inherent to these diseases. Passive transfer of broadly neutralizing antibodies may offer partial protection, but these treatments require repeated dosing. Some recombinant viral vectors, such as those based on lentiviruses and adeno-associated viruses (AAVs), can confer long-term transgene expression in the host after a single dose. Particularly, recombinant (r)AAVs have emerged as favorable vectors, given their high in vivo transduction efficiency, proven clinical efficacy, and low immunogenicity profiles. Hence, rAAVs are being explored to deliver recombinant antibodies to confer immunity against infections or to diminish the severity of disease. When used as a vaccination vector for the delivery of antigens, rAAVs enable de novo synthesis of foreign proteins with the conformation and topology that resemble those of natural pathogens. However, technical hurdles like pre-existing immunity to the rAAV capsid and production of anti-drug antibodies can reduce the efficacy of rAAV-vectored immunotherapies. This review summarizes rAAV-based prophylactic and therapeutic strategies developed against infectious diseases that are currently being tested in pre-clinical and clinical studies. Technical challenges and potential solutions will also be discussed.
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Affiliation(s)
- Wei Zhan
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, United States
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, United States
| | - Manish Muhuri
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, United States
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, United States
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
| | - Phillip W. L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, United States
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, United States
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, United States
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, United States
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, United States
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12
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Reszegi A, Karászi K, Tóth G, Rada K, Váncza L, Turiák L, Schaff Z, Kiss A, Szilák L, Szabó G, Petővári G, Sebestyén A, Dezső K, Regős E, Tátrai P, Baghy K, Kovalszky I. Overexpression of Human Syndecan-1 Protects against the Diethylnitrosamine-Induced Hepatocarcinogenesis in Mice. Cancers (Basel) 2021; 13:1548. [PMID: 33801718 DOI: 10.3390/cancers13071548] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Syndecan-1 is a Janus-faced proteoglycan: depending on the type of cancer, it can promote or inhibit the development of tumors. Our previous in vitro experiments revealed that transfection of human syndecan-1 (hSDC1) into hepatoma cells, initiating hepatocyte-like differentiation. To further confirm the antitumor action of hSDC1 in the context of liver carcinogenesis, mice transgenic for albumin promoter-driven hSDC1 were created with exclusive expression of hSDC1 in the liver. Indeed, hSDC1 interfered with the development of liver cancer in diethylnitrosamine (DEN)-induced hepatocarcinogenesis experiments. The mechanism was found to be related to lipid metabolism that plays an important role in the induction of nonalcoholic liver cirrhosis. Nonalcoholic fatty liver disease is known to promote the development of cancer; therefore, the oncoprotective effect of hSDC1 may be mediated by a beneficial modulation of lipid metabolism. Abstract Although syndecan-1 (SDC1) is known to be dysregulated in various cancer types, its implication in tumorigenesis is poorly understood. Its effect may be detrimental or protective depending on the type of cancer. Our previous data suggest that SDC1 is protective against hepatocarcinogenesis. To further verify this notion, human SDC1 transgenic (hSDC1+/+) mice were generated that expressed hSDC1 specifically in the liver under the control of the albumin promoter. Hepatocarcinogenesis was induced by a single dose of diethylnitrosamine (DEN) at an age of 15 days after birth, which resulted in tumors without cirrhosis in wild-type and hSDC1+/+ mice. At the experimental endpoint, livers were examined macroscopically and histologically, as well as by immunohistochemistry, Western blot, receptor tyrosine kinase array, phosphoprotein array, and proteomic analysis. Liver-specific overexpression of hSDC1 resulted in an approximately six month delay in tumor formation via the promotion of SDC1 shedding, downregulation of lipid metabolism, inhibition of the mTOR and the β-catenin pathways, and activation of the Foxo1 and p53 transcription factors that lead to the upregulation of the cell cycle inhibitors p21 and p27. Furthermore, both of them are implicated in the regulation of intermediary metabolism. Proteomic analysis showed enhanced lipid metabolism, activation of motor proteins, and loss of mitochondrial electron transport proteins as promoters of cancer in wild-type tumors, inhibited in the hSDC1+/+ livers. These complex mechanisms mimic the characteristics of nonalcoholic steatohepatitis (NASH) induced human liver cancer successfully delayed by syndecan-1.
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13
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Pepi LE, Sanderson P, Stickney M, Amster IJ. Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review. Mol Cell Proteomics 2021; 20:100025. [PMID: 32938749 PMCID: PMC8724624 DOI: 10.1074/mcp.r120.002267] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
This review covers recent developments in glycosaminoglycan (GAG) analysis via mass spectrometry (MS). GAGs participate in a variety of biological functions, including cellular communication, wound healing, and anticoagulation, and are important targets for structural characterization. GAGs exhibit a diverse range of structural features due to the variety of O- and N-sulfation modifications and uronic acid C-5 epimerization that can occur, making their analysis a challenging target. Mass spectrometry approaches to the structure assignment of GAGs have been widely investigated, and new methodologies remain the subject of development. Advances in sample preparation, tandem MS techniques (MS/MS), online separations, and automated analysis software have advanced the field of GAG analysis. These recent developments have led to remarkable improvements in the precision and time efficiency for the structural characterization of GAGs.
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Affiliation(s)
- Lauren E Pepi
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | | | - Morgan Stickney
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, Georgia, USA.
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14
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Lee YR, Briggs MT, Condina MR, Puddy H, Anderson PH, Hoffmann P, Kuliwaba JS. Mass Spectrometry Imaging as a Potential Tool to Investigate Human Osteoarthritis at the Tissue Level. Int J Mol Sci 2020; 21:E6414. [PMID: 32899238 DOI: 10.3390/ijms21176414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/25/2022] Open
Abstract
Osteoarthritis (OA) is the most common degenerative joint disease, predicted to increase in incidence year by year due to an ageing population. Due to the biological complexity of the disease, OA remains highly heterogeneous. Although much work has been undertaken in the past few years, underlying molecular mechanisms leading to joint tissue structural deterioration are not fully understood, with only few validated markers for disease diagnosis and progression being available. Discovery and quantitation of various OA-specific biomarkers is still largely focused on the bodily fluids which does not appear to be reliable and sensitive enough. However, with the advancement of spatial proteomic techniques, several novel peptides and proteins, as well as N-glycans, can be identified and localised in a reliable and sensitive manner. To summarise the important findings from OA biomarker studies, papers published between 2000 and 2020 were searched via Google Scholar and PubMed. Medical subject heading (MeSH) terms ‘osteoarthritis’, ‘biomarker’, ‘synovial fluid’, ‘serum’, ‘urine’, ’matrix-assisted laser desorption/ionisation’, ‘mass spectrometry imaging’, ‘proteomic’, ‘glycomic’, ‘cartilage’, ‘synovium’ AND ‘subchondral bone’ were selectively used. The literature search was restricted to full-text original research articles and written only in English. Two main areas were reviewed for OA biomarker studies: (1) an overview of disease-specific markers detected from different types of OA bio-samples, and (2) an up-to-date summary of the tissue-specific OA studies that have utilised matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI). Overall, these OA biomarkers could provide clinicians with information for better the diagnosis, and prognosis of individual patients, and ultimately help facilitate the development of disease-modifying treatments.
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15
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Raghunathan R, Hogan JD, Labadorf A, Myers RH, Zaia J. A glycomics and proteomics study of aging and Parkinson's disease in human brain. Sci Rep 2020; 10:12804. [PMID: 32733076 PMCID: PMC7393382 DOI: 10.1038/s41598-020-69480-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 05/04/2020] [Indexed: 01/08/2023] Open
Abstract
Previous studies on Parkinson’s disease mechanisms have shown dysregulated extracellular transport of α-synuclein and growth factors in the extracellular space. In the human brain these consist of perineuronal nets, interstitial matrices, and basement membranes, each composed of a set of collagens, non-collagenous glycoproteins, proteoglycans, and hyaluronan. The manner by which amyloidogenic proteins spread extracellularly, become seeded, oligomerize, and are taken up by cells, depends on intricate interactions with extracellular matrix molecules. We sought to assess the alterations to structure of glycosaminoglycans and proteins that occur in PD brain relative to controls of similar age. We found that PD differs markedly from normal brain in upregulation of extracellular matrix structural components including collagens, proteoglycans and glycosaminoglycan binding molecules. We also observed that levels of hemoglobin chains, possibly related to defects in iron metabolism, were enriched in PD brains. These findings shed important new light on disease processes that occur in association with PD.
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Affiliation(s)
- Rekha Raghunathan
- Graduate Program in Molecular and Translational Medicine, Boston University School of Medicine, Boston, 02118, USA
| | - John D Hogan
- Bioinformatics Program, Boston University Graduate School of Arts and Sciences, Boston, 02118, USA
| | - Adam Labadorf
- Bioinformatics Program, Boston University Graduate School of Arts and Sciences, Boston, 02118, USA.,Department of Neurology, Boston University School of Medicine, Boston, 02118, USA
| | - Richard H Myers
- Graduate Program in Molecular and Translational Medicine, Boston University School of Medicine, Boston, 02118, USA.,Bioinformatics Program, Boston University Graduate School of Arts and Sciences, Boston, 02118, USA.,Department of Neurology, Boston University School of Medicine, Boston, 02118, USA
| | - Joseph Zaia
- Graduate Program in Molecular and Translational Medicine, Boston University School of Medicine, Boston, 02118, USA. .,Department of Biochemistry, Boston University School of Medicine, 670 Albany St., Rm. 509, Boston, 02118, USA. .,Bioinformatics Program, Boston University Graduate School of Arts and Sciences, Boston, 02118, USA.
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16
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Abstract
Advancement in mass spectrometry has revolutionized the field of proteomics. However, there remains a gap in the analysis of protein post-translational modifications (PTMs), particularly for glycosylation. Glycosylation, the most common form of PTM, is involved in most biological processes; thus, analysis of glycans along with proteins is crucial to answering important biologically relevant questions. Of particular interest is the brain extracellular matrix (ECM), which has been called the "final Frontier" in neuroscience, which consists of highly glycosylated proteins. Among these, proteoglycans (PGs) contain large glycan structures called glycosaminoglycans (GAGs) that form crucial ECM components, including perineuronal nets (PNNs), shown to be altered in neuropsychiatric diseases. Thus, there is a growing need for high-throughput methods that combine GAG (glycomics) and PGs (proteomics) analysis to unravel the complete biological picture. The protocol presented here integrates glycomics and proteomics to analyze multiple classes of biomolecules. We use a filter-aided sample preparation (FASP) type serial in-solution digestion of GAG classes, including hyaluronan (HA), chondroitin sulfate (CS), and heparan sulfate (HS), followed by peptides. The GAGs and peptides are then cleaned and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). This protocol is an efficient and economical way of processing tissue or cell lysates to isolate various GAG classes and peptides from the same sample. The method is more efficient (single-pot) than available parallel (multi-pot) release methods, and removal of GAGs facilitates the identification of the proteins with higher peptide-coverage than using conventional-proteomics. Overall, we demonstrate a high-throughput & efficient protocol for mass spectrometry-based glycomic and proteomic analysis (data are available via ProteomeXchange with identifier PXD017513).
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Affiliation(s)
- Manveen K Sethi
- Boston University School of Medicine, Boston University, Department of Biochemistry, Boston, 02118, USA.
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17
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Alonge KM, Logsdon AF, Murphree TA, Banks WA, Keene CD, Edgar JS, Whittington D, Schwartz MW, Guttman M. Quantitative analysis of chondroitin sulfate disaccharides from human and rodent fixed brain tissue by electrospray ionization-tandem mass spectrometry. Glycobiology 2020; 29:847-860. [PMID: 31361007 DOI: 10.1093/glycob/cwz060] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 02/07/2023] Open
Abstract
Chondroitin sulfates (CS) are long, negatively charged, unbranched glycosaminoglycan (GAG) chains attached to CS-proteoglycan (CSPG) core proteins that comprise the glycan component in both loose interstitial extracellular matrices (ECMs) and in rigid, structured perineuronal net (PNN) scaffolds within the brain. As aberrant CS-PNN formations have been linked to a range of pathological states, including Alzheimer's disease (AD) and schizophrenia, the analysis of CS-GAGs in brain tissue at the disaccharide level has great potential to enhance disease diagnosis and prognosis. Two mass-spectrometry (MS)-based approaches were adapted to detect CS disaccharides from minute fixed tissue samples with low picomolar sensitivity and high reproducibility. The first approach employed a straightforward, quantitative direct infusion (DI)-tandem mass spectrometry (MS/MS) technique to determine the percentages of Δ4S- and Δ6S-CS disaccharides within the 4S/6S-CS ratio, while the second used a comprehensive liquid chromatography (LC)-MS/MS technique to determine the relative percentages of Δ0S-, Δ4S-, Δ6S-, Δ4S6S-CS and Δ2S6S-CS disaccharides, with internal validation by full chondroitin lyase activity. The quantitative accuracy of the five primary biologically relevant CS disaccharides was validated using a developmental time course series in fixed rodent brain tissue. We then analyzed the CS disaccharide composition in formalin-fixed human brain tissue, thus providing the first quantitative report of CS sulfation patterns in the human brain. The ability to comprehensively analyze the CS disaccharide composition from fixed brain tissue provides a means with which to identify alterations in the CS-GAG composition in relation to the onset and/or progression of neurological diseases.
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Affiliation(s)
- Kimberly M Alonge
- University of Washington Medicine Diabetes Institute, Department of Medicine, Seattle, WA, USA
| | - Aric F Logsdon
- Department of Geriatric Research Education and Clinical Center (GRECC), Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA.,Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - William A Banks
- Department of Geriatric Research Education and Clinical Center (GRECC), Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA.,Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Division of Neuropathology, Department of Pathology, University of Washington, Seattle, WA, USA
| | - J Scott Edgar
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Dale Whittington
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Michael W Schwartz
- University of Washington Medicine Diabetes Institute, Department of Medicine, Seattle, WA, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
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18
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Tóth G, Vékey K, Sugár S, Kovalszky I, Drahos L, Turiák L. Salt gradient chromatographic separation of chondroitin sulfate disaccharides. J Chromatogr A 2020; 1619:460979. [PMID: 32093904 DOI: 10.1016/j.chroma.2020.460979] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 01/06/2023]
Abstract
In the present study, we describe the development of a fast, 2-step salt gradient for analysis of chondroitin sulfate disaccharides. Using salt gradients, which is somewhat unusual in HILIC-based separations, provides relatively fast chromatography with excellent sensitivity (15 min cycle time, 10-20 fmol/µL detection, 30-50 fmol/µL quantitation limit), and good linearity. The efficiency of the new method is demonstrated by measuring human tissue slices of healthy, cirrhotic, and cancerous liver samples. Preliminary results show major differences among the quantity and sulfation pattern of the various sample types.
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Affiliation(s)
- Gábor Tóth
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2., H-1117 Budapest, Hungary; Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4., H-1111 Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
| | - Simon Sugár
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2., H-1117 Budapest, Hungary; Ph.D. School of Pharmaceutical Sciences, Semmelweis University, Üllői út 26, H-1085, Budapest, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, H-1085, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2., H-1117 Budapest, Hungary.
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20
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Raghunathan R, Sethi MK, Zaia J. On-slide tissue digestion for mass spectrometry based glycomic and proteomic profiling. MethodsX 2019; 6:2329-2347. [PMID: 31660297 PMCID: PMC6807300 DOI: 10.1016/j.mex.2019.09.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022] Open
Abstract
We describe a protocol for glycomic and proteomic profiling that uses serial enzyme digestions from the surface of fresh frozen or fixed tissue slides. The abundances of the extracted glycans and peptides are determined using liquid chromatography-mass spectrometry. In a typical experiment, our method quantifies 14 heparan sulfate disaccharides, 11 chondroitin sulfate disaccharides, 50 N-glycan compositions and approximately 1200 proteins from a 1.8 mm circle, on the surface of a fresh frozen tissue slide from rat brain. Each enzymatic digestion is incubated overnight with direct application of enzyme on the tissue surface. Overall, the sample preparation process for multiple tissue slides takes a day per biomolecule class. This protocol saves time by simultaneous digestion of large N-glycans and small HS disaccharides and subsequent separation using size exclusion chromatography. Compared to wet tissue analysis, this method requires less time by a factor of two. By comparison, MALDI-imaging provides higher spatial resolution of glycans and proteins but lower depth of coverage. MALDI dissociates fragile glycan substituents including sulfates and is not recommended for analysis of glycosaminoglycans (GAGs).
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Affiliation(s)
- Rekha Raghunathan
- Boston University, Molecular and Translational Medicine, Boston, 02118, USA
| | - Manveen K Sethi
- Boston University, Dept. of Biochemistry, Boston, 02118, USA
| | - Joseph Zaia
- Boston University, Molecular and Translational Medicine, Boston, 02118, USA.,Boston University, Dept. of Biochemistry, Boston, 02118, USA
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21
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Turiak L, Kaszás B, Katona K, Lacza Á, Márk L, Vékey K, Drahos L, Tornóczky T. Localized Amyloidosis of the Upper Aerodigestive Tract: Complex Analysis of the Cellular Infiltrate and the Amyloid Mass. Anal Cell Pathol (Amst) 2019; 2019:6165140. [PMID: 31531279 DOI: 10.1155/2019/6165140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/24/2019] [Accepted: 07/24/2019] [Indexed: 12/11/2022] Open
Abstract
Objectives The aim of this study was to analyse the composition of amyloid mass and the plasmacytic infiltrate of localized amyloidosis of the upper aerodigestive tract. Methods Biopsy materials were studied by light microscopy, immunohistochemistry (IHC), and mRNA in situ hybridization (mRNA-ISH). The amyloid mass was also analysed with high-performance liquid chromatography mass spectrometry- (HPLC-MS-) based proteomics. Results Nodular and diffuse forms of amyloid deposition were detected. IHC analysis revealed λ-light chain (LC) in two cases, κ-LC in one case. The remaining two were positive with both. Proteins, well known from other amyloidoses like amyloid A (AA), prealbumin/transthyretin (PA), apolipoprotein A-I (ApoAI), and amyloid P component (APC), and also keratin were found with variable intensities in the cases. HPLC-MS revealed dozens of proteins with both LCs in all the lesions but sometimes with surprisingly small intensities. mRNA-ISH analysis revealed identical λ and κ dominance and only one normal κ/λ cell ratio. Conclusion Cellular infiltrate and protein components in the amyloid showed congruent results in all but one case. The only exception with normal cell ratio and λ-dominant amyloid could be originated from the different protein-secreting activity of plasma cell clones. HPLC-MS analysis explored both LCs in all the amyloid in variable amount, but other proteins with much higher intensities like keratins, apolipoprotein A-IV (ApoAIV), were also detected. Proteins like AA, PA, ApoAI, and APC, previously known about amyloid-forming capability, also appeared. This indicates that localized amyloid in the upper aerodigestive tract is not a homogenous immunoglobulin mass but a mixture of proteins. The sometimes very low light chain intensities might also suggest that not all the localized amyloidosis cases of the upper aerodigestive tract are of convincingly AL type, and the analysis of the cellular infiltrate might indicate that not all are monoclonal.
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22
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. Mass Spectrom Rev 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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23
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Turiák L, Ozohanics O, Tóth G, Ács A, Révész Á, Vékey K, Telekes A, Drahos L. High sensitivity proteomics of prostate cancer tissue microarrays to discriminate between healthy and cancerous tissue. J Proteomics 2018; 197:82-91. [PMID: 30439472 DOI: 10.1016/j.jprot.2018.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/28/2018] [Accepted: 11/09/2018] [Indexed: 01/14/2023]
Abstract
Biopsies, in the form of tissue microarrays (TMAs) were studied to identify anomalies indicative of prostate cancer at the proteome level. TMAs offer a valuable source of well-characterized biological material. However, because of the small tissue sample size method development was essential to provide the sensitivity and reliability necessary for the analysis. Surface digestion of TMA cores was followed by peptide extraction and shotgun proteomics analysis. About 5 times better sensitivity was achieved by the optimized surface digestion compared to bulk digestion of the same TMA spot and it allowed the identification of over 500 proteins from individual prostate TMA cores. Label-free quantitation showed that biological variability among all samples was about 3 times larger than the technical reproducibility. We have identified 189 proteins which showed statistically significant changes (t-test p-value <.05) in abundance between healthy and cancerous tissue samples. The proteomic profile changed according to cancer grade, but did not show a correlation with cancer stage. Results of this pilot study were further evaluated using bioinformatics tools, identifying various protein pathways affected by prostate cancer progression indicating the usefulness of studying TMA cores to identify quantitative changes in tissue proteomics. SIGNIFICANCE: Detailed proteomics analysis of TMAs presents a good alternative for tissue analysis. Here we present a novel method, based on tissue surface digestion and nano-LC-MS measurements, which is capable of identifying and quantifying over 500 proteins from a 1.5 mm diameter tissue section. We compared healthy and cancerous prostate tissue samples, and tissues with various grades and stages of cancer. Tissue proteomics clearly distinguished healthy and cancerous samples, furthermore the results correlated well with cancer grade, but not with cancer stage. Over 100 proteins showed statistically significant abundance changes (t-test p-value <.05) between various groups. This was sufficient for a meaningful bioinformatics evaluation; showing e.g. increased abundance of proteins in cancer in the KEGG ribosome pathway, GO mRNA splicing via spliceosome, and chromatin assembly biological processes. The results highlight the feasibility of the developed method for future large-scale tissue proteomics studies using commercially available TMAs.
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Affiliation(s)
- Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary.
| | - Oliver Ozohanics
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary; Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - András Ács
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary; Semmelweis University, Ph.D. School of Pharmaceutical Sciences, Üllői út 26, H-1085 Budapest, Hungary
| | - Ágnes Révész
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - András Telekes
- Div. Sect. of Geriatrics, 2nd Department of Internal Medicine, Semmelweis University, Halmi utca 20-22, H-1115 Budapest, Hungary; Dept. of Oncology, St Lazarus County Hospital, Füleki út 54-56, H-1117, Salgótarján, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
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24
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Raghunathan R, Polinski NK, Klein JA, Hogan JD, Shao C, Khatri K, Leon D, McComb ME, Manfredsson FP, Sortwell CE, Zaia J. Glycomic and Proteomic Changes in Aging Brain Nigrostriatal Pathway. Mol Cell Proteomics 2018; 17:1778-1787. [PMID: 29915149 DOI: 10.1074/mcp.ra118.000680] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 06/12/2018] [Indexed: 12/19/2022] Open
Abstract
Parkinson's disease (PD) is a neurological disorder characterized by the progressive loss of functional dopaminergic neurons in the nigrostriatal pathway in the brain. Although current treatments provide only symptomatic relief, gene therapy has the potential to slow or halt the degeneration of nigrostriatal dopamine neurons in PD patients. Adeno-associated viruses (AAV) are vectors of choice in gene therapy because of their well-characterized safety and efficacy profiles; however, although gene therapy has been successful in preclinical models of the disease, clinical trials in humans have failed to demonstrate efficacy. Significantly, all primary AAV receptors of the virus are glycans. We thus hypothesize that age related changes in glycan receptors of heparan sulfate (HS) proteoglycans (receptor for rAAV2), and/or N-glycans with terminal galactose (receptor for rAAV9) results in poor adeno-associated virus binding in either the striatum or substantia nigra, or both, affecting transduction and gene delivery. To test our hypothesis we analyzed the striatum and substantia nigra for changes in HS, N-glycans and proteomic signatures in young versus aged rat brain striatum and substantia nigra. We observed different brain region-specific HS disaccharide profiles in aged compared with young adult rats for brain region-specific profiles in striatum versus substantia nigra. We observed brain region- and age-specific N-glycan compositional profiles with respect to the terminal galactose units that serve as receptors for AAV9. We also observed brain region-specific changes in protein expression in the aging nigrostriatal pathway. These studies provide insight into age- and brain region-specific changes in glycan receptors and proteome that will inform design of improved viral vectors for Parkinson Disease (PD) gene therapy.
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Affiliation(s)
- Rekha Raghunathan
- From the ‡Department of Molecular and Translational Medicine, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, Boston, Massachusetts
| | - Nicole K Polinski
- ‖Department of Translational Science and Molecular Medicine, Michigan State University
| | - Joshua A Klein
- ¶Bioinformatics Program, Boston University, Boston, Massachusetts
| | - John D Hogan
- ¶Bioinformatics Program, Boston University, Boston, Massachusetts
| | - Chun Shao
- §Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, Boston, Massachusetts
| | - Kshitij Khatri
- §Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, Boston, Massachusetts
| | - Deborah Leon
- §Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, Boston, Massachusetts
| | - Mark E McComb
- §Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, Boston, Massachusetts
| | - Fredric P Manfredsson
- ‖Department of Translational Science and Molecular Medicine, Michigan State University
| | - Caryl E Sortwell
- ‖Department of Translational Science and Molecular Medicine, Michigan State University
| | - Joseph Zaia
- From the ‡Department of Molecular and Translational Medicine, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, Boston, Massachusetts; .,§Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, Boston, Massachusetts.,¶Bioinformatics Program, Boston University, Boston, Massachusetts
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25
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Turiák L, Tóth G, Ozohanics O, Révész Á, Ács A, Vékey K, Zaia J, Drahos L. Sensitive method for glycosaminoglycan analysis of tissue sections. J Chromatogr A 2018; 1544:41-8. [PMID: 29506752 DOI: 10.1016/j.chroma.2018.02.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/28/2022]
Abstract
A simple, isocratic HPLC method based on HILIC-WAX separation, has been developed for analyzing sulfated disaccharides of glycosaminoglycans (GAGs). To our best knowledge, this is the first successful attempt using this special phase in nano-HPLC-MS analysis. Mass spectrometry was based on negative ionization, improving both sensitivity and specificity. Detection limit for most sulfated disaccharides were approximately 1 fmol; quantitation limits 10 fmol. The method was applied for glycosaminoglycan profiling of tissue samples, using surface digestion protocols. This novel combination provides sufficient sensitivity for GAG disaccharide analysis, which was first performed using prostate cancer tissue microarrays. Preliminary results show that GAG analysis may be useful for identifying cancer related changes in small amounts of tissue samples (ca. 10 μg).
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26
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Abstract
The glycosaminoglycan hyaluronan (HA) is a key component of the microenvironment surrounding cells. In healthy tissues, HA molecules have extremely high molecular mass and consequently large hydrodynamic volumes. Tethered to the cell surface by clustered receptor proteins, HA molecules crowd each other, as well as other macromolecular species. This leads to severe nonideality in physical properties of the biomatrix, because steric exclusion leads to an increase in effective concentration of the macromolecules. The excluded volume depends on both polymer concentration and hydrodynamic volume/molecular mass. The biomechanical properties of the extracellular matrix, tissue hydration, receptor clustering, and receptor-ligand interactions are strongly affected by the presence of HA and by its molecular mass. In inflammation, reactive oxygen and nitrogen species fragment the HA chains. Depending on the rate of chain degradation relative to the rates of new synthesis and removal of damaged chains, short fragments of the HA molecules can be present at significant levels. Not only are the physical properties of the extracellular matrix affected, but the HA fragments decluster their primary receptors and act as endogenous danger signals. Bioanalytical methods to isolate and quantify HA fragments have been developed to determine profiles of HA content and size in healthy and diseased biological fluids and tissues. These methods have potential use in medical diagnostic tests. Therapeutic agents that modulate signaling by HA fragments show promise in wound healing and tissue repair without fibrosis.
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Affiliation(s)
- Mary K Cowman
- Tandon School of Engineering, New York University, New York, NY, United States
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27
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Abrahams JL, Campbell MP, Packer NH. Building a PGC-LC-MS N-glycan retention library and elution mapping resource. Glycoconj J 2017; 35:15-29. [PMID: 28905148 DOI: 10.1007/s10719-017-9793-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/10/2017] [Accepted: 08/18/2017] [Indexed: 11/27/2022]
Abstract
Porous graphitised carbon-liquid chromatography (PGC-LC) has been proven to be a powerful technique for the analysis and characterisation of complex mixtures of isomeric and isobaric glycan structures. Here we evaluate the elution behaviour of N-glycans on PGC-LC and thereby provide the potential of using chromatographic separation properties, together with mass spectrometry (MS) fragmentation, to determine glycan structure assignments more easily. We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. Over 100 glycan structures were determined by MS/MS, and together with targeted exoglycosidase digestions, created a N-glycan PGC retention library covering a full spectrum of biologically significant N-glycans from pauci mannose to sialylated tetra-antennary classes. The resultant PGC retention library ( http://www.glycostore.org/showPgc ) incorporates retention times and supporting fragmentation spectra including exoglycosidase digestion products, and provides detailed knowledge on the elution properties of N-glycans by PGC-LC. Consequently, this platform should serve as a valuable resource for facilitating the detailed analysis of the glycosylation of both purified recombinant, and complex mixtures of, glycoproteins using established workflows.
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Affiliation(s)
- Jodie L Abrahams
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia
| | - Matthew P Campbell
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia.
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia.
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28
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Chen H, Deng Z, Huang C, Wu H, Zhao X, Li Y. Mass spectrometric profiling reveals association of N-glycan patterns with epithelial ovarian cancer progression. Tumour Biol 2017; 39:1010428317716249. [DOI: 10.1177/1010428317716249] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aberrant changes of N-glycan modifications on proteins have been linked to various diseases including different cancers, suggesting possible avenue for exploring their etiologies based on N-glycomic analysis. Changes in N-glycan patterns during epithelial ovarian cancer development have so far been investigated mainly using serum, plasma, ascites, and cell lines. However, changes in patterns of N-glycans in tumor tissues during epithelial ovarian cancer progression have remained largely undefined. To investigate whether changes in N-glycan patterns correlate with oncogenesis and progression of epithelial ovarian cancer, we profiled N-glycans from formalin-fixed paraffin-embedded tissue slides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and quantitatively compared among different pathological grades of epithelial ovarian cancer and healthy controls. Our results show that among the 80 compositions of N-glycan detected, expression levels of high-mannose type were higher in epithelial ovarian cancer samples than that observed in healthy controls, accompanied by reduced levels of hybrid-type glycans. By applying receiver operating characteristic analysis, we show that a combined panel composed of four high-mannose and three fucosylated neutral complex N-glycans allows for good discrimination of epithelial ovarian cancer from healthy controls. Furthermore, using a statistical analysis of variance assay, we found that different N-glycan patterns, including 2 high-mannose-type, 2 fucosylated and sialylated complex structures, and 10 fucosylated neutral complex N-glycans, exhibited specific changes in N-glycan abundance across epithelial ovarian cancer grades. Together, our results provide strong evidence that N-glycomic changes are a strong indicator for epithelial ovarian cancer pathological grades and should provide avenues to identify novel biomarkers for epithelial ovarian cancer diagnosis and monitoring.
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Affiliation(s)
- Huanhuan Chen
- Key Laboratory of Marine Drugs, Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Zaian Deng
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chuncui Huang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hongmei Wu
- GuangDong Bio-Healtech Advanced Co., Ltd, Foshan, China
| | - Xia Zhao
- Key Laboratory of Marine Drugs, Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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29
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Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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30
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Shajahan A, Heiss C, Ishihara M, Azadi P. Glycomic and glycoproteomic analysis of glycoproteins-a tutorial. Anal Bioanal Chem 2017; 409:4483-4505. [PMID: 28585084 PMCID: PMC5498624 DOI: 10.1007/s00216-017-0406-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 01/18/2023]
Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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31
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Donczo B, Szarka M, Tovari J, Ostoros G, Csanky E, Guttman A. Molecular glycopathology by capillary electrophoresis: Analysis of the N-glycome of formalin-fixed paraffin-embedded mouse tissue samples. Electrophoresis 2017; 38:1602-1608. [PMID: 28334446 DOI: 10.1002/elps.201600558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/18/2017] [Accepted: 02/19/2017] [Indexed: 12/17/2022]
Abstract
Capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection was used to analyze endoglycosidase released and fluorophore-labeled N-glycans from formalin-fixed paraffin-embedded (FFPE) mouse tissue samples of lung, brain, heart, spleen, liver, kidney and intestine. The FFPE samples were first deparaffinized followed by solubilization and glycoprotein retrieval. PNGase F mediated release of the N-linked oligosaccharides was followed by labeling with aminopyrene trisulfonate. After CE-LIF glycoprofiling of the FFPE mouse tissues, the N-glycan pool of the lung specimen was subject to further investigation by exoglycosidase array based carbohydrate sequencing. Structural assignment of the oligosaccharides was accomplished by the help of the GUcal software and the associated database, based on the mobility shifts after treatments with the corresponding exoglycosidase reaction mixtures. Sixteen major N-linked carbohydrate structures were sequenced from the mouse lung FFPE tissue glycome and identified, as high mannose (3) neutral biantennary (3) sialylated monoantennary (1) and sialylated bianennary (9) oligosaccharides. Two of these latter ones also possessed alpha(1-3) linked galactose residues.
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Affiliation(s)
- Boglarka Donczo
- Horváth Csaba Laboratory of Bioseparation Sciences, University of Debrecen, Hungary
| | - Mate Szarka
- Horváth Csaba Laboratory of Bioseparation Sciences, University of Debrecen, Hungary
| | | | | | | | - Andras Guttman
- Horváth Csaba Laboratory of Bioseparation Sciences, University of Debrecen, Hungary.,MTA-PE Translational Glycomics Group, University of Pannonia, Veszprem, Hungary
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32
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Rizzo DG, Prentice BM, Moore JL, Norris JL, Caprioli RM. Enhanced Spatially Resolved Proteomics Using On-Tissue Hydrogel-Mediated Protein Digestion. Anal Chem 2017; 89:2948-2955. [DOI: 10.1021/acs.analchem.6b04395] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David G. Rizzo
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Boone M. Prentice
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jessica L. Moore
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jeremy L. Norris
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M. Caprioli
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
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33
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Hinneburg H, Korać P, Schirmeister F, Gasparov S, Seeberger PH, Zoldoš V, Kolarich D. Unlocking Cancer Glycomes from Histopathological Formalin-fixed and Paraffin-embedded (FFPE) Tissue Microdissections. Mol Cell Proteomics 2017; 16:524-536. [PMID: 28122943 DOI: 10.1074/mcp.m116.062414] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 01/22/2017] [Indexed: 12/22/2022] Open
Abstract
N- and O-glycans are attractive clinical biomarkers as glycosylation changes in response to diseases. The limited availability of defined clinical specimens impedes glyco-biomarker identification and validation in large patient cohorts. Formalin-fixed paraffin-embedded (FFPE) clinical specimens are the common form of sample preservation in clinical pathology, but qualitative and quantitative N- and O-glycomics of such samples has not been feasible to date. Here, we report a highly sensitive and glycan isomer selective method for simultaneous N- and O-glycomics from histopathological slides. As few as 2000 cells isolated from FFPE tissue sections by laser capture microdissection were sufficient for in-depth histopathology-glycomics using porous graphitized carbon nanoLC ESI-MS/MS. N- and O-glycan profiles were similar between unstained and hematoxylin and eosin stained FFPE samples but differed slightly compared with fresh tissue. This method provides the key to unlock glyco-biomarker information from FFPE histopathological tissues archived in pathology laboratories worldwide.
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Affiliation(s)
- Hannes Hinneburg
- From the ‡Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany.,§Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, 14195 Berlin, Germany
| | - Petra Korać
- ¶Faculty of Science, Department of Biology, Division of Molecular Biology, University of Zagreb, Zagreb, Croatia
| | - Falko Schirmeister
- From the ‡Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany.,§Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, 14195 Berlin, Germany
| | - Slavko Gasparov
- ‖Institute for Pathology and Cytology, University Hospital Merkur, Zagreb, Croatia.,**Department of Pathology, Medical School Zagreb, University of Zagreb, Zagreb, Croatia
| | - Peter H Seeberger
- From the ‡Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany.,§Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, 14195 Berlin, Germany
| | - Vlatka Zoldoš
- ¶Faculty of Science, Department of Biology, Division of Molecular Biology, University of Zagreb, Zagreb, Croatia
| | - Daniel Kolarich
- From the ‡Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany;
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34
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Affiliation(s)
- Stefan Gaunitz
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Gabe Nagy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicola L. B. Pohl
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Regional Center for Applied Molecular Oncology, Masaryk Memorial Oncological Institute, 656 53 Brno, Czech Republic
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35
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Abstract
The availability of well-defined samples in sufficient numbers represents a major bottleneck for any biomarker related research. The utilization of preserved, archived and clinically well-described samples therefore holds a great potential to bridge this gap. This chapter describes a universal workflow for the comprehensive characterization of N- and O-glycans released from whole formalin-fixed, paraffin-embedded tissue sections, including an option for further partitioning using laser microdissection of specific tissue areas/cell populations. Glycoproteins are extracted and subsequently immobilized onto a PVDF membrane prior enzymatic release of N-glycans. Following N-glycan retrieval O-glycans are released using reductive β-elimination from the same sample spot, significantly reducing the required amount of starting material. Released and reduced glycan structures are characterized using porous graphitized carbon liquid chromatography online coupled to an electrospray ionization-ion trap mass spectrometer. This technique provides information on the relative abundances of individual glycans along with detailed structural information, including isomer differentiation and functional epitope characterization of N- and O-glycans obtained from minimal amounts of tissue down to a few thousand cells.
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Affiliation(s)
- Hannes Hinneburg
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Falko Schirmeister
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Petra Korać
- Faculty of Science, Department of Biology, Division of Molecular Biology, University of Zagreb, Zagreb, Croatia
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany.
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36
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Angel PM, Mehta A, Norris-Caneda K, Drake RR. MALDI Imaging Mass Spectrometry of N-glycans and Tryptic Peptides from the Same Formalin-Fixed, Paraffin-Embedded Tissue Section. Methods Mol Biol 2018; 1788:225-41. [PMID: 29058228 DOI: 10.1007/7651_2017_81] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a unique and well developed tool for probing the protein content of formalin-fixed, paraffin-embedded tissue (FFPE). Integral to this approach is the application of trypsin, and more recently peptide N-glycosidase F, to release tryptic peptides or N-glycans from tissue and report localization of distinct species. This is typically done on serial or adjacent tissue sections, and there is an emerging need to understand the colocalized protein population linked to the exact same regions of N-glycans. Here we describe an approach where N-glycans are first imaged from a tissue section followed by reprocessing of the same tissue section for tryptic peptide MALDI IMS. Strategies for colocalizing peptides to target N-glycans or N-glycan regions are described.
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Banazadeh A, Veillon L, Wooding KM, Zabet-Moghaddam M, Mechref Y. Recent advances in mass spectrometric analysis of glycoproteins. Electrophoresis 2016; 38:162-189. [PMID: 27757981 DOI: 10.1002/elps.201600357] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 12/13/2022]
Abstract
Glycosylation is one of the most common posttranslational modifications of proteins that plays essential roles in various biological processes, including protein folding, host-pathogen interaction, immune response, and inflammation and aberrant protein glycosylation is a well-known event in various disease states including cancer. As a result, it is critical to develop rapid and sensitive methods for the analysis of abnormal glycoproteins associated with diseases. Mass spectrometry (MS) in conjunction with different separation methods, such as capillary electrophoresis (CE), ion mobility (IM), and high performance liquid chromatography (HPLC) has become a popular tool for glycoprotein analysis, providing highly informative fragments for structural identification of glycoproteins. This review provides an overview of the developments and accomplishments in the field of glycomics and glycoproteomics reported between 2014 and 2016.
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Affiliation(s)
- Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Lucas Veillon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Kerry M Wooding
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.,Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
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Donczo B, Szigeti M, Ostoros G, Gacs A, Tovari J, Guttman A. N-Glycosylation analysis of formalin fixed paraffin embedded samples by capillary electrophoresis. Electrophoresis 2015; 37:2292-6. [DOI: 10.1002/elps.201500446] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 11/06/2015] [Accepted: 11/07/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Boglarka Donczo
- Horváth Csaba Laboratory of Bioseparation Sciences; University of Debrecen; Debrecen Hungary
| | - Marton Szigeti
- Horváth Csaba Laboratory of Bioseparation Sciences; University of Debrecen; Debrecen Hungary
- MTA-PE Translational Glycomics Group; Pannon University; Veszprem Hungary
| | - Gyorgyi Ostoros
- MTA-PE Translational Glycomics Group; Pannon University; Veszprem Hungary
- National Institute of Oncology; Department of Experimental Pharmacology; Budapest Hungary
| | - Alexandra Gacs
- National Institute of Oncology; Department of Experimental Pharmacology; Budapest Hungary
| | - Jozsef Tovari
- National Institute of Oncology; Department of Experimental Pharmacology; Budapest Hungary
| | - Andras Guttman
- Horváth Csaba Laboratory of Bioseparation Sciences; University of Debrecen; Debrecen Hungary
- MTA-PE Translational Glycomics Group; Pannon University; Veszprem Hungary
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Abstract
This manuscript describes the enrichment and mass spectrometric analysis of intact glycopeptides from mouse liver, which yielded site-specific N- and O-glycosylation data for ∼ 130 proteins. Incorporation of different sialic acid variants in both N- and O-linked glycans was observed, and the importance of using both collisional activation and electron transfer dissociation for glycopeptide analysis was illustrated. The N-glycan structures of predicted lysosomal, endoplasmic reticulum (ER), secreted and transmembrane proteins were compared. The data suggest that protein N-glycosylation differs depending on cellular location. The glycosylation patterns of several mouse liver and mouse brain glycopeptides were compared. Tissue-specific differences in glycosylation were observed between sites within the same protein: Some sites displayed a similar spectrum of glycan structures in both tissues, whereas for others no overlap was observed. We present comparative brain/liver glycosylation data on 50 N-glycosylation sites from 34 proteins and 13 O-glycosylation sites from seven proteins.
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Affiliation(s)
- Katalin F Medzihradszky
- From the ‡Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, 600 16th Street Genentech Hall, N474A, Box 2240, San Francisco, California 94158-2517
| | - Krista Kaasik
- From the ‡Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, 600 16th Street Genentech Hall, N474A, Box 2240, San Francisco, California 94158-2517
| | - Robert J Chalkley
- From the ‡Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, 600 16th Street Genentech Hall, N474A, Box 2240, San Francisco, California 94158-2517
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