1
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Austin BK, Firooz A, Valafar H, Blenda AV. An Updated Overview of Existing Cancer Databases and Identified Needs. BIOLOGY 2023; 12:1152. [PMID: 37627037 PMCID: PMC10452211 DOI: 10.3390/biology12081152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Our search of existing cancer databases aimed to assess the current landscape and identify key needs. We analyzed 71 databases, focusing on genomics, proteomics, lipidomics, and glycomics. We found a lack of cancer-related lipidomic and glycomic databases, indicating a need for further development in these areas. Proteomic databases dedicated to cancer research were also limited. To assess overall progress, we included human non-cancer databases in proteomics, lipidomics, and glycomics for comparison. This provided insights into advancements in these fields over the past eight years. We also analyzed other types of cancer databases, such as clinical trial databases and web servers. Evaluating user-friendliness, we used the FAIRness principle to assess findability, accessibility, interoperability, and reusability. This ensured databases were easily accessible and usable. Our search summary highlights significant growth in cancer databases while identifying gaps and needs. These insights are valuable for researchers, clinicians, and database developers, guiding efforts to enhance accessibility, integration, and usability. Addressing these needs will support advancements in cancer research and benefit the wider cancer community.
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Affiliation(s)
- Brittany K. Austin
- Department of Biomedical Sciences, School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA;
| | - Ali Firooz
- Department of Computer Science and Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA;
| | - Homayoun Valafar
- Department of Computer Science and Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA;
| | - Anna V. Blenda
- Department of Biomedical Sciences, School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA;
- Prisma Health Cancer Institute, Prisma Health, Greenville, SC 29605, USA
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2
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Paton B, Suarez M, Herrero P, Canela N. Glycosylation Biomarkers Associated with Age-Related Diseases and Current Methods for Glycan Analysis. Int J Mol Sci 2021; 22:ijms22115788. [PMID: 34071388 PMCID: PMC8198018 DOI: 10.3390/ijms22115788] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
Ageing is a complex process which implies the accumulation of molecular, cellular and organ damage, leading to an increased vulnerability to disease. In Western societies, the increase in the elderly population, which is accompanied by ageing-associated pathologies such as cardiovascular and mental diseases, is becoming an increasing economic and social burden for governments. In order to prevent, treat and determine which subjects are more likely to develop these age-related diseases, predictive biomarkers are required. In this sense, some studies suggest that glycans have a potential role as disease biomarkers, as they modify the functions of proteins and take part in intra- and intercellular biological processes. As the glycome reflects the real-time status of these interactions, its characterisation can provide potential diagnostic and prognostic biomarkers for multifactorial diseases. This review gathers the alterations in protein glycosylation profiles that are associated with ageing and age-related diseases, such as cancer, type 2 diabetes mellitus, metabolic syndrome and several chronic inflammatory diseases. Furthermore, the review includes the available techniques for the determination and characterisation of glycans, such as liquid chromatography, electrophoresis, nuclear magnetic resonance and mass spectrometry.
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Affiliation(s)
- Beatrix Paton
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
| | - Manuel Suarez
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Correspondence: (M.S.); (P.H.)
| | - Pol Herrero
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
- Correspondence: (M.S.); (P.H.)
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
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3
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Chen S, Qin R, Mahal LK. Sweet systems: technologies for glycomic analysis and their integration into systems biology. Crit Rev Biochem Mol Biol 2021; 56:301-320. [PMID: 33820453 DOI: 10.1080/10409238.2021.1908953] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Found in virtually every organism, glycans are essential molecules that play important roles in almost every aspect of biology. The composition of glycome, the repertoire of glycans in an organism or a biological sample, is often found altered in many diseases, including cancer, infectious diseases, metabolic and developmental disorders. Understanding how glycosylation and glycomic changes enriches our knowledge of the mechanisms of disease progression and sheds light on the development of novel therapeutics. However, the inherent diversity of glycan structures imposes challenges on the experimental characterization of glycomes. Advances in high-throughput glycomic technologies enable glycomic analysis in a rapid and comprehensive manner. In this review, we discuss the analytical methods currently used in high-throughput glycomics, including mass spectrometry, liquid chromatography and lectin microarray. Concomitant with the technical advances is the integration of glycomics into systems biology in the recent years. Herein we elaborate on some representative works from this recent trend to underline the important role of glycomics in such integrated approaches to disease.
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Affiliation(s)
- Shuhui Chen
- Department of Chemistry, New York University, New York City, NY, USA
| | - Rui Qin
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Lara K Mahal
- Department of Chemistry, New York University, New York City, NY, USA.,Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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4
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Shakyawar SK, Pandey S, Harvey DJ, Bousfield G, Guda C. FGDB: Database of follicle stimulating hormone glycans. Comput Struct Biotechnol J 2021; 19:1635-1640. [PMID: 33897975 PMCID: PMC8050109 DOI: 10.1016/j.csbj.2021.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 11/12/2022] Open
Abstract
Glycomics, the study of the entire complement of sugars of an organism has received significant attention in the recent past due to the advances made in high throughput mass spectrometry technologies. These analytical advancements have facilitated the characterization of glycans associated with the follicle-stimulating hormones (FSH), which play a central role in the human reproductive system both in males and females utilizing regulating gonadal (testicular and ovarian) functions. The irregularities in FSH activity are also directly linked with osteoporosis. The glycoanalytical studies have been tremendously helpful in understanding the biological roles of FSH. Subsequently, the increasing number of characterized FSH glycan structures and related glycoform data has thrown a challenge to the glycoinformatics community in terms of data organization, storage and access. Also, a user-friendly platform is needed for providing easy access to the database and performing integrated analysis using a high volume of experimental data to accelerate FSH-focused research. FSH Glycans DataBase (FGDB) serves as a comprehensive and unique repository of structures, features, and related information of glycans associated with FSH. Apart from providing multiple search options, the database also facilitates an integrated user-friendly interface to perform the glycan abundance and comparative analyses using experimental data. The automated integrated pipelines present the possible structures of glycans and variants of FSH based on the input data, and allow the user to perform various analyses. The potential application of FGDB will significantly help both glycoinformaticians as well as wet-lab researchers to stimulate the research in this area. FGDB web access: https://fgdb.unmc.edu/.
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Affiliation(s)
- Sushil K Shakyawar
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Sanjit Pandey
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, United Kingdom
| | - George Bousfield
- Fairmount College of Liberal Arts and Sciences, Wichita State University, KS 67260, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
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5
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Peixoto A, Relvas-Santos M, Azevedo R, Santos LL, Ferreira JA. Protein Glycosylation and Tumor Microenvironment Alterations Driving Cancer Hallmarks. Front Oncol 2019; 9:380. [PMID: 31157165 PMCID: PMC6530332 DOI: 10.3389/fonc.2019.00380] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022] Open
Abstract
Decades of research have disclosed a plethora of alterations in protein glycosylation that decisively impact in all stages of disease and ultimately contribute to more aggressive cell phenotypes. The biosynthesis of cancer-associated glycans and its reflection in the glycoproteome is driven by microenvironmental cues and these events act synergistically toward disease evolution. Such intricate crosstalk provides the molecular foundations for the activation of relevant oncogenic pathways and leads to functional alterations driving invasion and disease dissemination. However, it also provides an important source of relevant glyco(neo)epitopes holding tremendous potential for clinical intervention. Therefore, we highlight the transversal nature of glycans throughout the currently accepted cancer hallmarks, with emphasis on the crosstalk between glycans and the tumor microenvironment stromal components. Focus is also set on the pressing need to include glycans and glycoconjugates in comprehensive panomics models envisaging molecular-based precision medicine capable of improving patient care. We foresee that this may provide the necessary rationale for more comprehensive studies and molecular-based intervention.
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Affiliation(s)
- Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal.,Tumour and Microenvironment Interactions Group, INEB-Institute for Biomedical Engineering, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
| | - Rita Azevedo
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Department of Surgical Oncology, Portuguese Institute of Oncology, Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center, Porto, Portugal
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6
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Glycoproteomics and Glycomics in the Biomedical Area Special Issue. Proteomics Clin Appl 2019; 12:e1800122. [PMID: 30203442 DOI: 10.1002/prca.201800122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Indexed: 11/10/2022]
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7
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Ma Q, Adua E, Boyce MC, Li X, Ji G, Wang W. IMass Time: The Future, in Future! ACTA ACUST UNITED AC 2018; 22:679-695. [DOI: 10.1089/omi.2018.0162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qingwei Ma
- Bioyong (Beijing) Technology Co., Ltd., Beijing, China
| | - Eric Adua
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Mary C. Boyce
- School of Science, Edith Cowan University, Joondalup, Australia
| | - Xingang Li
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Guang Ji
- China-Canada Centre of Research for Digestive Diseases, University of Ottawa, Ottawa, Canada
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
- School of Public Health, Taishan Medical University, Taian, China
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8
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Le HT, Park KH, Jung W, Park HS, Kim TW. Combination of Microwave-Assisted Girard Derivatization with Ionic Liquid Matrix for Sensitive MALDI-TOF MS Analysis of Human Serum N-Glycans. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2018; 2018:7832987. [PMID: 30420937 PMCID: PMC6215560 DOI: 10.1155/2018/7832987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/18/2018] [Indexed: 06/09/2023]
Abstract
We developed a new method for MALDI-TOF MS detection of N-glycans derived from human serum. The synergistic combination of microwave-assisted Girard T derivatization, solid-phase extraction desalting, and an ionic liquid matrix (2, 5-dihydroxybenzoic acid/aniline) (GT-SPE-DHB/An) allowed of more sensitive N-glycans detection than a conventional ionic liquid matrix in MALDI-TOF MS. The superior sensitivity of our method was confirmed by the number of assigned N-glycans in 900-2,000 m/z range. Using our GT-SPE-DHB/An method, we were successfully able to assign 31 glycans. However, with the established method, i.e., DHB/An method, only 15 glycans were assigned. To the best of our knowledge, this GT-SPE-DHB/An method is the first to combine cationic derivatization of N-glycan and ionic liquid matrix for N-glycan analysis in MALDI-TOF MS.
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Affiliation(s)
- Hoa Thi Le
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Kyu H. Park
- R&D Center, ASTA Inc., Suwon 16229, Republic of Korea
| | - Woong Jung
- Department of Emergency Medicine, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | | | - Tae Woo Kim
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin 17104, Republic of Korea
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9
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine , Leiden University Medical Center , 2333 ZA Leiden , The Netherlands
| | - Gege Xu
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Qiongyu Li
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elisha Goonatilleke
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Carlito B Lebrilla
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States.,Department of Biochemistry and Molecular Medicine , University of California, Davis , Davis , California 95616 , United States.,Foods for Health Institute , University of California, Davis , Davis , California 95616 , United States
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10
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Kailemia MJ, Xu G, Wong M, Li Q, Goonatilleke E, Leon F, Lebrilla CB. Recent Advances in the Mass Spectrometry Methods for Glycomics and Cancer. Anal Chem 2018; 90:208-224. [PMID: 29049885 PMCID: PMC6200424 DOI: 10.1021/acs.analchem.7b04202] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Muchena J. Kailemia
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- These authors contributed equally to this work
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- These authors contributed equally to this work
| | - Maurice Wong
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Frank Leon
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
- Foods for Health Institute, University of California, Davis, CA 95616, USA
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11
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Yang S, Clark D, Liu Y, Li S, Zhang H. High-throughput analysis of N-glycans using AutoTip via glycoprotein immobilization. Sci Rep 2017; 7:10216. [PMID: 28860471 PMCID: PMC5578957 DOI: 10.1038/s41598-017-10487-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/11/2017] [Indexed: 12/15/2022] Open
Abstract
Analysis of a large number of samples requires an efficient, rapid and reproducible method. Automation is an ideal approach for high-throughput sample preparation. Multi-plexing sample preparation via a 96-well plate format becomes popular in recent years; however, those methods lack specificity and require several cleanup steps via chromatography purification. To overcome these drawbacks, a chemoenzymatic method has been developed utilizing protein conjugation on solid-phase. Previously, sample preparation was successfully performed in a snap-cap spin-column (SCSC) format. However, sample preparation using SCSC is time-consuming and lacks reproducibility. In this work, we integrated the chemoenzymatic technique in a pipette tip (AutoTip) that was operated by an automated liquid handler. We established a multi-step protocol involving protein immobilization, sialic acid modification, and N-glycan release. We first optimized our automated protocol using bovine fetuin as a standard glycoprotein, and then assessed the reproducibility of the AutoTip using isobaric tags for relative N-linked glycan quantification. We then applied this methodology to profile N-glycans from 58 prostate cancer patient urine samples, revealing increased sialyation on urinary N-glycans derived from prostate cancer patients. Our results indicated AutoTip has applications for high-throughput sample preparation for studying the N-linked glycans.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA.
| | - David Clark
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Yang Liu
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
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12
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Thaysen-Andersen M, Packer NH, Schulz BL. Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease. Mol Cell Proteomics 2016; 15:1773-90. [PMID: 26929216 PMCID: PMC5083109 DOI: 10.1074/mcp.o115.057638] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/09/2016] [Indexed: 12/21/2022] Open
Abstract
The glycoproteome remains severely understudied because of significant analytical challenges associated with glycoproteomics, the system-wide analysis of intact glycopeptides. This review introduces important structural aspects of protein N-glycosylation and summarizes the latest technological developments and applications in LC-MS/MS-based qualitative and quantitative N-glycoproteomics. These maturing technologies provide unique structural insights into the N-glycoproteome and its synthesis and regulation by complementing existing methods in glycoscience. Modern glycoproteomics is now sufficiently mature to initiate efforts to capture the molecular complexity displayed by the N-glycoproteome, opening exciting opportunities to increase our understanding of the functional roles of protein N-glycosylation in human health and disease.
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Affiliation(s)
- Morten Thaysen-Andersen
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia;
| | - Nicolle H Packer
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Benjamin L Schulz
- §School of Chemistry & Molecular Biosciences, St Lucia, The University of Queensland, Brisbane, QLD, Australia
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13
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Kumar A, Baycin-Hizal D, Shiloach J, Bowen MA, Betenbaugh MJ. Coupling enrichment methods with proteomics for understanding and treating disease. Proteomics Clin Appl 2015; 9:33-47. [PMID: 25523641 DOI: 10.1002/prca.201400097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/12/2014] [Accepted: 12/15/2014] [Indexed: 12/17/2022]
Abstract
Owing to recent advances in proteomics analytical methods and bioinformatics capabilities there is a growing trend toward using these capabilities for the development of drugs to treat human disease, including target and drug evaluation, understanding mechanisms of drug action, and biomarker discovery. Currently, the genetic sequences of many major organisms are available, which have helped greatly in characterizing proteomes in model animal systems and humans. Through proteomics, global profiles of different disease states can be characterized (e.g. changes in types and relative levels as well as changes in PTMs such as glycosylation or phosphorylation). Although intracellular proteomics can provide a broad overview of physiology of cells and tissues, it has been difficult to quantify the low abundance proteins which can be important for understanding the diseased states and treatment progression. For this reason, there is increasing interest in coupling comparative proteomics methods with subcellular fractionation and enrichment techniques for membranes, nucleus, phosphoproteome, glycoproteome as well as low abundance serum proteins. In this review, we will provide examples of where the utilization of different proteomics-coupled enrichment techniques has aided target and biomarker discovery, understanding the drug targeting mechanism, and mAb discovery. Taken together, these improvements will help to provide a better understanding of the pathophysiology of various diseases including cancer, autoimmunity, inflammation, cardiovascular disease, and neurological conditions, and in the design and development of better medicines for treating these afflictions.
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Affiliation(s)
- Amit Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Antibody Discovery and Protein Engineering, MedImmune LLC, One MedImmune Way, Gaithersburg, MD, USA; Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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14
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High-Throughput Analysis and Automation for Glycomics Studies. Chromatographia 2014; 78:321-333. [PMID: 25814696 PMCID: PMC4363487 DOI: 10.1007/s10337-014-2803-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/17/2014] [Accepted: 10/17/2014] [Indexed: 11/12/2022]
Abstract
This review covers advances in analytical technologies for high-throughput (HTP) glycomics. Our focus is on structural studies of glycoprotein glycosylation to support biopharmaceutical realization and the discovery of glycan biomarkers for human disease. For biopharmaceuticals, there is increasing use of glycomics in Quality by Design studies to help optimize glycan profiles of drugs with a view to improving their clinical performance. Glycomics is also used in comparability studies to ensure consistency of glycosylation both throughout product development and between biosimilars and innovator drugs. In clinical studies there is as well an expanding interest in the use of glycomics—for example in Genome Wide Association Studies—to follow changes in glycosylation patterns of biological tissues and fluids with the progress of certain diseases. These include cancers, neurodegenerative disorders and inflammatory conditions. Despite rising activity in this field, there are significant challenges in performing large scale glycomics studies. The requirement is accurate identification and quantitation of individual glycan structures. However, glycoconjugate samples are often very complex and heterogeneous and contain many diverse branched glycan structures. In this article we cover HTP sample preparation and derivatization methods, sample purification, robotization, optimized glycan profiling by UHPLC, MS and multiplexed CE, as well as hyphenated techniques and automated data analysis tools. Throughout, we summarize the advantages and challenges with each of these technologies. The issues considered include reliability of the methods for glycan identification and quantitation, sample throughput, labor intensity, and affordability for large sample numbers.
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15
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Brockhausen I. Crossroads between Bacterial and Mammalian Glycosyltransferases. Front Immunol 2014; 5:492. [PMID: 25368613 PMCID: PMC4202792 DOI: 10.3389/fimmu.2014.00492] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/23/2014] [Indexed: 11/26/2022] Open
Abstract
Bacterial glycosyltransferases (GT) often synthesize the same glycan linkages as mammalian GT; yet, they usually have very little sequence identity. Nevertheless, enzymatic properties, folding, substrate specificities, and catalytic mechanisms of these enzyme proteins may have significant similarity. Thus, bacterial GT can be utilized for the enzymatic synthesis of both bacterial and mammalian types of complex glycan structures. A comparison is made here between mammalian and bacterial enzymes that synthesize epitopes found in mammalian glycoproteins, and those found in the O antigens of Gram-negative bacteria. These epitopes include Thomsen–Friedenreich (TF or T) antigen, blood group O, A, and B, type 1 and 2 chains, Lewis antigens, sialylated and fucosylated structures, and polysialic acids. Many different approaches can be taken to investigate the substrate binding and catalytic mechanisms of GT, including crystal structure analyses, mutations, comparison of amino acid sequences, NMR, and mass spectrometry. Knowledge of the protein structures and functions helps to design GT for specific glycan synthesis and to develop inhibitors. The goals are to develop new strategies to reduce bacterial virulence and to synthesize vaccines and other biologically active glycan structures.
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Affiliation(s)
- Inka Brockhausen
- Department of Medicine, Queen's University , Kingston, ON , Canada ; Department of Biomedical and Molecular Sciences, Queen's University , Kingston, ON , Canada
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Direct analysis of hCGβcf glycosylation in normal and aberrant pregnancy by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Int J Mol Sci 2014; 15:10067-82. [PMID: 24905406 PMCID: PMC4100140 DOI: 10.3390/ijms150610067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 05/20/2014] [Accepted: 05/21/2014] [Indexed: 11/18/2022] Open
Abstract
The analysis of human chorionic gonadotropin (hCG) in clinical chemistry laboratories by specific immunoassay is well established. However, changes in glycosylation are not as easily assayed and yet alterations in hCG glycosylation is associated with abnormal pregnancy. hCGβ-core fragment (hCGβcf) was isolated from the urine of women, pregnant with normal, molar and hyperemesis gravidarum pregnancies. Each sample was subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) analysis following dithiothreitol (DTT) reduction and fingerprint spectra of peptide hCGβ 6–40 were analyzed. Samples were variably glycosylated, where most structures were small, core and largely mono-antennary. Larger single bi-antennary and mixtures of larger mono-antennary and bi-antennary moieties were also observed in some samples. Larger glycoforms were more abundant in the abnormal pregnancies and tri-antennary carbohydrate moieties were only observed in the samples from molar and hyperemesis gravidarum pregnancies. Given that such spectral profiling differences may be characteristic, development of small sample preparation for mass spectral analysis of hCG may lead to a simpler and faster approach to glycostructural analysis and potentially a novel clinical diagnostic test.
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