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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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2
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Sajid MS, Saleem MN, Jabeen F, Saleem S, Iqbal S, Habib S, Ashiq MN, Ressom HW, Najam-ul-Haq M. Human serum N-glycome profiling via the newly developed asparagine immobilized cellulose/polymer nanohybrid. J Sep Sci 2022; 45:4236-4244. [PMID: 36168850 PMCID: PMC9812403 DOI: 10.1002/jssc.202200179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 01/07/2023]
Abstract
Human serum N-linked glycans expression levels change during the disease progression. The low abundance, structural diversity, and coexisting matrices hinder their detection in mass spectrometry analysis. Considering the hydrophilic nature of N-glycans, cellulose/polymer (1,2-Epoxy-5-hexene) nanohybrid is fabricated with oxirane groups functionalized of asparagine to develop solid phase extraction based hydrophilic interaction liquid chromatography sorbent (cellulose/1,2-Epoxy-5-hexene/asparagine). The morphology, elemental analysis, and surface properties are studied through scanning electron microscopy, energy dispersive X-ray spectroscopy, and Fourier-transform infrared spectroscopy. The large surface area of cellulose/polymer nanohybrid (2.09 × 102 m2 /g) facilitates the high density of asparagine immobilization resulting in better hydrophilic interaction liquid chromatography enrichment under optimized conditions. The enrichment capability of nanohybrid/asparagine is assessed by the N-Linked glycans released from ovalbumin and immunoglobulin G where 23 and 13 N-glycans are detected respectively. The nanohybrid/asparagine shows selectivity of 1:1200 with spiked bovine serum albumin and sensitivity down to 100 attomole. Human serum profiling for N-glycans identifies 52 glycan structures. This new enrichment strategy enriches serum N-linked glycans in the presence of salts, proteins, endogenous serum peptides, and so forth.
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Affiliation(s)
- Muhammad Salman Sajid
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan,Department of Oncology, Genomics and Epigenomics Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Muhammad Nakash Saleem
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Fahmida Jabeen
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan,Corresponding Authors: 1. Prof. Dr. M. Najam-ul-Haq, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan, Tel.: +92 306 7552653, , 2. Dr. Fahmida Jabeen, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan, Tel.: +92 333 4253409,
| | - Shafaq Saleem
- Department of Chemistry, The Women University, Kutchery Campus, L.M.Q. Road, Multan, 66000, Pakistan
| | - Sabeen Iqbal
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | | | - Muhammad Naeem Ashiq
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Habtom W. Ressom
- Department of Oncology, Genomics and Epigenomics Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Muhammad Najam-ul-Haq
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan,Corresponding Authors: 1. Prof. Dr. M. Najam-ul-Haq, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan, Tel.: +92 306 7552653, , 2. Dr. Fahmida Jabeen, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan, Tel.: +92 333 4253409,
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3
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Donohoo KB, Wang J, Goli M, Yu A, Peng W, Hakim MA, Mechref Y. Advances in mass spectrometry-based glycomics-An update covering the period 2017-2021. Electrophoresis 2021; 43:119-142. [PMID: 34505713 DOI: 10.1002/elps.202100199] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022]
Abstract
The wide variety of chemical properties and biological functions found in proteins is attained via post-translational modifications like glycosylation. Covalently bonded to proteins, glycans play a critical role in cell activity. Complex structures with microheterogeneity, the glycan structures that are associated with proteins are difficult to analyze comprehensively. Recent advances in sample preparation methods, separation techniques, and MS have facilitated the quantitation and structural elucidation of glycans. This review focuses on highlighting advances in MS-based techniques for glycomic analysis that occurred over the last 5 years (2017-2021) as an update to the previous review on the subject. The topics of discussion will include progress in glycomic workflow such as glycan release, purification, derivatization, and separation as well as the topics of ionization, tandem MS, and separation techniques that can be coupled with MS. Additionally, bioinformatics tools used for the analysis of glycans will be described.
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Affiliation(s)
- Kaitlyn B Donohoo
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Md Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
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Lísa M, Řehulková H, Hančová E, Řehulka P. Lipidomic analysis using hydrophilic interaction liquid chromatography microgradient fractionation of total lipid extracts. J Chromatogr A 2021; 1653:462380. [PMID: 34348208 DOI: 10.1016/j.chroma.2021.462380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/07/2021] [Accepted: 06/26/2021] [Indexed: 01/04/2023]
Abstract
Lipidomic samples are complex mixtures of structurally different species of a wide range of concentrations providing challenges in their characterization. In this work, we present a proof of concept for the application of a simple microgradient liquid chromatography device on the detailed analysis of lipid classes. Our lipidomic analysis is based on a lipid class microgradient fractionation of a total lipid extract using an in-house-prepared hydrophilic interaction liquid chromatography microcolumn followed by RP-LC/MS of the collected lipid class fractions. The final fractionation method uses a 40-mm-long microcolumn of 500 μm ID with silica stationary phase obtained from a commercially available chromatographic column and the microgradient of the mobile phase prepared in a microsyringe using methyl tert-butyl ether (MTBE) - methanol - water - ammonium acetate mixtures of various elution strengths. MTBE total lipid extract is directly separated by microgradient elution into lipid classes according to their polarity, which enables the collection of isolated fractions of most lipid classes. The method has been applied to the fractionation of porcine brain extract into nonpolar lipids, hexosylceramides, phosphoethanolamines, phosphocholines, sphingomyelins, and lysophosphocholines classes. Achieved repeatability, recovery, and advanced lipid coverage prove the applicability of the microgradient fractionation of total lipid extract for the comprehensive lipidomic analysis.
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Affiliation(s)
- Miroslav Lísa
- University of Hradec Králové, Faculty of Science, Department of Chemistry, Rokitanského 62, 50003 Hradec Králové, Czech Republic.
| | - Helena Řehulková
- University of Hradec Králové, Faculty of Science, Department of Chemistry, Rokitanského 62, 50003 Hradec Králové, Czech Republic
| | - Eliška Hančová
- University of Hradec Králové, Faculty of Science, Department of Chemistry, Rokitanského 62, 50003 Hradec Králové, Czech Republic
| | - Pavel Řehulka
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Trebešská 1575, 50001 Hradec Králové, Czech Republic
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5
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N-Glycome changes reflecting resistance to platinum-based chemotherapy in ovarian cancer. J Proteomics 2020; 230:103964. [PMID: 32898699 DOI: 10.1016/j.jprot.2020.103964] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022]
Abstract
A number of studies have reported aberrant glycosylation in connection with malignancy. Our investigation further expands on this topic through the examination of N-glycans, which could be associated with the resistance of advanced stage, high-grade non-mucinous ovarian cancer to platinum/taxane based chemotherapy. We used tissue samples of 83 ovarian cancer patients, randomly divided into two independent cohorts (basic and validation). Both groups involved either cases with/without postoperative tumor residue or the cases determined either resistant or sensitive to this chemotherapy. In the validation cohort, preoperative serum samples were also available. N-glycans released from tumors and sera were permethylated and analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The MS analysis yielded a consecutive detection of 68 (tissue) and 63 (serum) N-glycan spectral signals. Eight of these were found to be differentially abundant in tissues of both independent cohorts including the cases with a postoperative cancer residue. One of these glycans was detected as differentially abundant in sera of the validation cohort. No statistically significant differences in intensities due to the same N-glycans were found in the cases without postoperative macroscopic residues in either the basic or validation cohort. From the biochemical point of view, the statistically significant N-glycans correspond to the structures carrying bisecting (terminal) GlcNAc residue and tetra-antennary structures with sialic acid and/or fucose residues. Among them, six tissue N-glycans could be considered potential markers connected with a resistance to chemotherapy in ovarian cancer patients. The prediction of primary resistance to standard chemotherapy may identify the group of patients suitable for alternative treatment strategies. SIGNIFICANCE: Drug resistance has become a major impediment to a successful treatment of patients with advanced ovarian cancer. The glycomic measurements related to cancer are becoming increasingly popular in identification of the key molecules as potential diagnostic and prognostic indicators. Our report deals with identification of differences in N-glycosylation of proteins in tissue and serum samples from the individuals showing sensitivity or resistance to platinum/taxane-based chemotherapy. The detection sensitivity to chemotherapy is vitally important for these patients.
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Using proteomics to identify host cell interaction partners for VgrG and IglJ. Sci Rep 2020; 10:14612. [PMID: 32884055 PMCID: PMC7471685 DOI: 10.1038/s41598-020-71641-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/23/2020] [Indexed: 11/17/2022] Open
Abstract
Francisella tularensis is a highly virulent intracellular bacterium and the causative agent of tularemia. The disease is characterized by the suboptimal innate immune response and consequently by the impaired adaptive immunity. The virulence of this pathogen depends on proteins encoded by a genomic island termed the Francisella Pathogenicity Island (FPI). However, the precise biological roles of most of the FPI-encoded proteins remain to be clarified. In this study, we employed stable isotope labeling by amino acids in cell culture (SILAC) in combination with affinity protein purification coupled with liquid chromatography–mass spectrometry to identify potential protein-effector binding pairs for two FPI virulence effectors IglJ and VgrG. Our results may indicate that while the IglJ protein interactions primarily affect mitochondria, the VgrG interactions affect phagosome and/or autophagosome biogenesis via targeting components of the host’s exocyst complex.
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Long Z, Li M, Dahl J, Guo Z, Li Y, Hao H, Li Y, Li C, Mao Q, Huang T. Determination of glycosylation degree for glycoconjugate vaccines using a solid‐phase extraction combined with liquid chromatography and tandem mass spectrometry method. J Sep Sci 2020; 43:2880-2888. [DOI: 10.1002/jssc.202000075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Zhen Long
- Shimadzu (China) Co. Ltd Beijing P. R. China
| | - Maoguang Li
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech ProductsNational Institutes for Food and Drug Control Beijing P. R. China
| | | | - Zhimou Guo
- Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian P. R. China
| | - Yanan Li
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech ProductsNational Institutes for Food and Drug Control Beijing P. R. China
| | | | - Yueqi Li
- Shimadzu (China) Co. Ltd Beijing P. R. China
| | - Changkun Li
- Shimadzu (China) Co. Ltd Beijing P. R. China
| | - Qiqi Mao
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech ProductsNational Institutes for Food and Drug Control Beijing P. R. China
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Ondrej M, Rehulka P, Rehulkova H, Kupcik R, Tichy A. Fractionation of Enriched Phosphopeptides Using pH/Acetonitrile-Gradient-Reversed-Phase Microcolumn Separation in Combination with LC-MS/MS Analysis. Int J Mol Sci 2020; 21:ijms21113971. [PMID: 32492839 PMCID: PMC7312998 DOI: 10.3390/ijms21113971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
Mass spectrometry (MS) is a powerful and sensitive method often used for the identification of phosphoproteins. However, in phosphoproteomics, there is an identified need to compensate for the low abundance, insufficient ionization, and suppression effects of non-phosphorylated peptides. These may hamper the subsequent liquid chromatography–mass spectrometry/mass spectrometry (LC–MS/MS) analysis, resulting in incomplete phosphoproteome characterization, even when using high-resolution instruments. To overcome these drawbacks, we present here an effective microgradient chromatographic technique that yields specific fractions of enriched phosphopeptides compatible with LC–MS/MS analysis. The purpose of our study was to increase the number of identified phosphopeptides, and thus, the coverage of the sample phosphoproteome using the reproducible and straightforward fractionation method. This protocol includes a phosphopeptide enrichment step followed by the optimized microgradient fractionation of enriched phosphopeptides and final LC–MS/MS analysis of the obtained fractions. The simple fractionation system consists of a gas-tight microsyringe delivering the optimized gradient mobile phase to reversed-phase microcolumn. Our data indicate that combining the phosphopeptide enrichment with the microgradient separation is a promising technique for in-depth phosphoproteomic analysis due to moderate input material requirements and more than 3-fold enhanced protein identification.
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Affiliation(s)
- Martin Ondrej
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
| | - Pavel Rehulka
- Department of Molecular Biology and Pathology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic;
| | - Helena Rehulkova
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
| | - Rudolf Kupcik
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, 532 10 Pardubice, Czech Republic;
| | - Ales Tichy
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
- Correspondence: ; Tel.: +420-973-253-216
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9
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Mass spectrometry-based qualitative and quantitative N-glycomics: An update of 2017-2018. Anal Chim Acta 2019; 1091:1-22. [PMID: 31679562 DOI: 10.1016/j.aca.2019.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 12/14/2022]
Abstract
N-glycosylation is one of the most frequently occurring protein post-translational modifications (PTMs) with broad cellular, physiological and pathological relevance. Mass spectrometry-based N-glycomics has become the state-of-the-art instrumental analytical pipeline for sensitive, high-throughput and comprehensive characterization of N-glycans and N-glycomes. Improvement and new development of methods in N-glycan release, enrichment, derivatization, isotopic labeling, separation, ionization, MS, tandem MS and informatics accompany side-by-side wider and deeper application. This review provides a comprehensive update of mass spectrometry-based qualitative and quantitative N-glycomics in the years of 2017-2018.
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Xin M, Vechtova P, Shaliutina-Kolesova A, Fussy Z, Loginov D, Dzyuba B, Linhart O, Boryshpolets S, Rodina M, Li P, Loginova Y, Sterba J. Transferrin Identification in Sterlet ( Acipenser ruthenus) Reproductive System. Animals (Basel) 2019; 9:ani9100753. [PMID: 31575042 PMCID: PMC6826671 DOI: 10.3390/ani9100753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 01/06/2023] Open
Abstract
Transferrins are a superfamily of iron-binding proteins and are recognized as multifunctional proteins. In the present study, transcriptomic and proteomic methods were used to identify transferrins in the reproductive organs and sperm of out-of-spawning and spermiating sterlet (Acipenser ruthenus) males. The results showed that seven transferrin transcripts were identified in the transcriptome of sterlet, and these transcripts were qualified as two different transferrin genes, serotransferrin and melanotransferrin, with several isoforms present for serotransferrin. The relative abundance of serotransferrin isoforms was higher in the kidneys and Wolffian ducts in the spermiating males compared to out-of-spawning males. In addition, transferrin was immunodetected in sterlet seminal plasma, but not in sterlet spermatozoa extract. Mass spectrometry identification of transferrin in seminal plasma but not in spermatozoa corroborates immunodetection. The identification of transferrin in the reproductive organs and seminal plasma of sterlet in this study provides the potential function of transferrin during sturgeon male reproduction.
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Affiliation(s)
- Miaomiao Xin
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
- Sino-Czech Joint Laboratory of Fish Conservation and Biotechnology: Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Pavlina Vechtova
- Institute of Chemistry, Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.
- Biology Centre of Academy of Sciences of the Czech Republic, Institute of Parasitology, Branisovska 31, 37005 Ceske Budejovice, Czech Republic.
| | - Anna Shaliutina-Kolesova
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Zoltan Fussy
- Institute of Chemistry, Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.
| | - Dmitry Loginov
- Institute of Chemistry, Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.
- Biology Centre of Academy of Sciences of the Czech Republic, Institute of Parasitology, Branisovska 31, 37005 Ceske Budejovice, Czech Republic.
| | - Borys Dzyuba
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Otomar Linhart
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Serhii Boryshpolets
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Marek Rodina
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Ping Li
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
- Marine College, Shandong University (Weihai), Weihai 264209, Shandong, China.
| | - Yana Loginova
- Institute of Chemistry, Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.
| | - Jan Sterba
- Institute of Chemistry, Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.
- Biology Centre of Academy of Sciences of the Czech Republic, Institute of Parasitology, Branisovska 31, 37005 Ceske Budejovice, Czech Republic.
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Kupcik R, Macak JM, Rehulkova H, Sopha H, Fabrik I, Anitha VC, Klimentova J, Murasova P, Bilkova Z, Rehulka P. Amorphous TiO 2 Nanotubes as a Platform for Highly Selective Phosphopeptide Enrichment. ACS OMEGA 2019; 4:12156-12166. [PMID: 31460330 PMCID: PMC6682070 DOI: 10.1021/acsomega.9b00571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Abstract
This work reports highly selective phosphopeptide enrichment using amorphous TiO2 nanotubes (TiO2NTs) and the same material decorated with superparamagnetic Fe3O4 nanoparticles (TiO2NTs@Fe3O4NPs). TiO2NTs and TiO2NTs@Fe3O4NPs materials were applied for phosphopeptide enrichment both from a simple peptide mixture (tryptic digest of bovine serum albumin and α-casein) and from a complex peptide mixture (tryptic digest of Jurkat T cell lysate). The obtained enrichment efficiency and selectivity for phosphopeptides of TiO2NTs and TiO2NTs@Fe3O4NPs were increased to 28.7 and 25.3%, respectively, as compared to those of the well-established TiO2 microspheres. The enrichment protocol was extended for a second elution step facilitating the identification of additional phosphopeptides. It further turned out that both types of amorphous TiO2 nanotubes provide qualitatively new physicochemical features that are clearly advantageous for highly selective phosphopeptide enrichment. This has been confirmed experimentally resulting in substantial reduction of non-phosphorylated peptides in the enriched samples. In addition, TiO2NTs@Fe3O4NPs combine high selectivity and ease of handling due to the superparamagnetic character of the material. The presented materials and performances are further promising for applications toward a whole range of other types of biomolecules to be treated in a similar fashion.
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Affiliation(s)
- Rudolf Kupcik
- Department
of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532
10 Pardubice, Czech Republic
| | - Jan M. Macak
- Center
of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice, Nam. Cs. Legii 565, 530 02 Pardubice, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Helena Rehulkova
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
| | - Hanna Sopha
- Center
of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice, Nam. Cs. Legii 565, 530 02 Pardubice, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Ivo Fabrik
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
| | - V. C. Anitha
- Center
of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice, Nam. Cs. Legii 565, 530 02 Pardubice, Czech Republic
| | - Jana Klimentova
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
| | - Pavla Murasova
- Department
of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532
10 Pardubice, Czech Republic
| | - Zuzana Bilkova
- Department
of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532
10 Pardubice, Czech Republic
| | - Pavel Rehulka
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
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Loginov DS, Loginova YF, Dycka F, Böttinger K, Vechtova P, Sterba J. Tissue-specific signatures in tick cell line MS profiles. Parasit Vectors 2019; 12:212. [PMID: 31060584 PMCID: PMC6503378 DOI: 10.1186/s13071-019-3460-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/27/2019] [Indexed: 11/10/2022] Open
Abstract
Background The availability of tick in vitro cell culture systems has facilitated many aspects of tick research, including proteomics. However, certain cell lines have shown a tissue-specific response to infection. Thus, a more thorough characterization of tick cell lines is necessary. Proteomic comparative studies of various tick cell lines will contribute to more efficient application of tick cell lines as model systems for investigation of host-vector-pathogen interactions. Results Three cell lines obtained from a hard tick, Ixodes ricinus, and two from I. scapularis were investigated. A cell mass spectrometry approach (MALDI-TOF MS) was applied, as well as classical proteomic workflows. Using PCA, tick cell line MS profiles were grouped into three clusters comprising IRE/CTVM19 and ISE18, IRE11 and IRE/CTVM20, and ISE6 cell lines. Two other approaches confirmed the results of PCA: in-solution digestion followed by nanoLC-ESI-Q-TOF MS/MS and 2D electrophoresis. The comparison of MS spectra of the cell lines and I. ricinus tick organs revealed 29 shared peaks. Of these, five were specific for ovaries, three each for gut and salivary glands, and one for Malpighian tubules. For the first time, characteristic peaks in MS profiles of tick cell lines were assigned to proteins identified in acidic extracts of corresponding cell lines. Conclusions Several organ-specific MS signals were revealed in the profiles of tick cell lines. Electronic supplementary material The online version of this article (10.1186/s13071-019-3460-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dmitry S Loginov
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic. .,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic.
| | - Yana F Loginova
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic.,Orekhovich Institute of Biomedical Chemistry, Pogodinskaja str. 10, Moscow, 119191, Russia
| | - Filip Dycka
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic
| | - Katharina Böttinger
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic
| | - Pavlina Vechtova
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic
| | - Jan Sterba
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 1760, 37005, Ceske Budejovice, Czech Republic
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Combined Transcriptome and Proteome Analysis of Immortalized Human Keratinocytes Expressing Human Papillomavirus 16 (HPV16) Oncogenes Reveals Novel Key Factors and Networks in HPV-Induced Carcinogenesis. mSphere 2019; 4:4/2/e00129-19. [PMID: 30918060 PMCID: PMC6437273 DOI: 10.1128/msphere.00129-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human papillomavirus (HPV)-associated cancers still remain a big health problem, especially in developing countries, despite the availability of prophylactic vaccines. Although HPV oncogenes have been intensively investigated for decades, a study applying recent advances in RNA-Seq and quantitative proteomic approaches to a precancerous model system with well-defined HPV oncogene expression alongside HPV-negative parental cells has been missing until now. Here, combined omics analyses reveal global changes caused by the viral oncogenes in a less biased way and allow the identification of novel factors and key cellular networks potentially promoting malignant transformation. In addition, this system also provides a basis for mechanistic research on novel key factors regulated by HPV oncogenes, especially those that are confirmed in vivo in cervical cancer as well as in head and neck cancer patient samples from TCGA data sets. Although the role of high-risk human papillomaviruses (hrHPVs) as etiological agents in cancer development has been intensively studied during the last decades, there is still the necessity of understanding the impact of the HPV E6 and E7 oncogenes on host cells, ultimately leading to malignant transformation. Here, we used newly established immortalized human keratinocytes with a well-defined HPV16 E6E7 expression cassette to get a more complete and less biased overview of global changes induced by HPV16 by employing transcriptome sequencing (RNA-Seq) and stable isotope labeling by amino acids in cell culture (SILAC). This is the first study combining transcriptome and proteome data to characterize the impact of HPV oncogenes in human keratinocytes in comparison with their virus-negative counterparts. To enhance the informative value and accuracy of the RNA-Seq data, four different bioinformatic workflows were used. We identified potential novel upstream regulators (e.g., CNOT7, SPDEF, MITF, and PAX5) controlling distinct clusters of genes within the HPV-host cell network as well as distinct factors (e.g., CPPED1, LCP1, and TAGLN) with essential functions in cancer. Validated results in this study were compared to data sets from The Cancer Genome Atlas (TCGA), demonstrating that several identified factors were also differentially expressed in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) and HPV-positive head and neck squamous cell carcinomas (HNSCs). This highly integrative approach allows the identification of novel HPV-induced cellular changes that are also reflected in cancer patients, providing a promising omics data set for future studies in both basic and translational research. IMPORTANCE Human papillomavirus (HPV)-associated cancers still remain a big health problem, especially in developing countries, despite the availability of prophylactic vaccines. Although HPV oncogenes have been intensively investigated for decades, a study applying recent advances in RNA-Seq and quantitative proteomic approaches to a precancerous model system with well-defined HPV oncogene expression alongside HPV-negative parental cells has been missing until now. Here, combined omics analyses reveal global changes caused by the viral oncogenes in a less biased way and allow the identification of novel factors and key cellular networks potentially promoting malignant transformation. In addition, this system also provides a basis for mechanistic research on novel key factors regulated by HPV oncogenes, especially those that are confirmed in vivo in cervical cancer as well as in head and neck cancer patient samples from TCGA data sets.
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Benktander JD, Gizaw ST, Gaunitz S, Novotny MV. Analytical Scheme Leading to Integrated High-Sensitivity Profiling of Glycosphingolipids Together with N- and O-Glycans from One Sample. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1125-1137. [PMID: 29744812 PMCID: PMC6226365 DOI: 10.1007/s13361-018-1933-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 05/15/2023]
Abstract
Glycoconjugates are directly or indirectly involved in many biological processes. Due to their complex structures, the structural elucidation of glycans and the exploration of their role in biological systems have been challenging. Glycan pools generated through release from glycoprotein or glycolipid mixtures can often be very complex. For the sake of procedural simplicity, many glycan profiling studies choose to concentrate on a single class of glycoconjugates. In this paper, we demonstrate it feasible to cover glycosphingolipids, N-glycans, and O-glycans isolated from the same sample. Small volumes of human blood serum and ascites fluid as well as small mouse brain tissue samples are sufficient to profile sequentially glycans from all three classes of glycoconjugates and even positively identify some mixture components through MALDI-MS and LC-ESI-MS. The results show that comprehensive glycan profiles can be obtained from the equivalent of 500-μg protein starting material or possibly less. These methodological improvements can help accelerating future glycomic comprehensive studies, especially for precious clinical samples. Graphical Abstract Outline of glycan profiling procedures.
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Affiliation(s)
- John D Benktander
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Solomon T Gizaw
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Stefan Gaunitz
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Milos V Novotny
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA.
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