1
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Lee J, Yeo I, Kim Y, Shin D, Kim J, Kim Y, Lim YS, Kim Y. Comparison of Fucose-Specific Lectins to Improve Quantitative AFP-L3 Assay for Diagnosing Hepatocellular Carcinoma Using Mass Spectrometry. J Proteome Res 2022; 21:1548-1557. [PMID: 35536554 DOI: 10.1021/acs.jproteome.2c00196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Glycoproteins have many important biological functions. In particular, aberrant glycosylation has been observed in various cancers, such as liver cancer. A well-known glycoprotein biomarker is α-fetoprotein (AFP), a surveillance biomarker for hepatocellular carcinoma (HCC) that contains a glycosylation site at asparagine 251. The low diagnostic sensitivity of AFP led researchers to focus on AFP-L3, which has the same sequence as conventional AFP but contains a fucosylated glycan. AFP-L3 has high affinity for Lens culinaris agglutinin (LCA) lectin, prompting many groups to use it for detecting AFP-L3. However, a few studies have identified more effective lectins for fractionating AFP-L3. In this study, we compared the amounts of enriched AFP-L3 with five fucose-specific lectins─LCA, Lotus tetragonolobus lectin (LTL), Ulex europaeus agglutinin I (UEA I), Aleuria aurantia lectin (AAL), and Aspergillus oryzae lectin (AOL)─to identify better lectins and improve HCC diagnostic assays using mass spectrometry (MS). Our results indicate that LTL was the most effective lectin for capturing AFP-L3 species, yielding approximately 3-fold more AFP-L3 than LCA from the same pool of HCC serum samples. Thus, we recommend the use of LTL for AFP-L3 assays, given its potential to improve the diagnostic sensitivity in patients having limited results by conventional LCA assay. The MS data have been deposited to the PeptideAtlas (PASS01752).
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Affiliation(s)
- Jihyeon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongro-gu, Seoul 03080, Korea
| | - Injoon Yeo
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongro-gu, Seoul 03080, Korea
| | - Yoseop Kim
- Department of Biomedical Engineering, Seoul National University College of Engineering, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Dongyoon Shin
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongro-gu, Seoul 03080, Korea
| | - Jaenyeon Kim
- Department of Biomedical Engineering, Seoul National University College of Engineering, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Yeongshin Kim
- Department of Biomedical Engineering, Seoul National University College of Engineering, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Young-Suk Lim
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro, Songpa-gu, Seoul 05505, Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongro-gu, Seoul 03080, Korea.,Department of Biomedical Engineering, Seoul National University College of Engineering, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
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2
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Kurz E, Chen S, Vucic E, Baptiste G, Loomis C, Agrawal P, Hajdu C, Bar-Sagi D, Mahal LK. Integrated Systems Analysis of the Murine and Human Pancreatic Cancer Glycomes Reveals a Tumor-Promoting Role for ST6GAL1. Mol Cell Proteomics 2021; 20:100160. [PMID: 34634466 PMCID: PMC8604807 DOI: 10.1016/j.mcpro.2021.100160] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in the United States. Glycans, such as carbohydrate antigen 19-9, are biomarkers of PDAC and are emerging as important modulators of cancer phenotypes. Herein, we used a systems-based approach integrating glycomic analysis of the well-established KC mouse, which models early events in transformation, and analysis of samples from human pancreatic cancer patients to identify glycans with potential roles in cancer formation. We observed both common and distinct patterns of glycosylation in pancreatic cancer across species. Common alterations included increased levels of α-2,3-sialic acid and α-2,6-sialic acid, bisecting GlcNAc and poly-N-acetyllactosamine. However, core fucose, which was increased in human PDAC, was not seen in the mouse, indicating that not all human glycomic changes are observed in the KC mouse model. In silico analysis of bulk and single-cell sequencing data identified ST6 beta-galactoside alpha-2,6-sialyltransferase 1, which underlies α-2,6-sialic acid, as overexpressed in human PDAC, concordant with histological data showing higher levels of this enzyme at the earliest stages. To test whether ST6 beta-galactoside alpha-2,6-sialyltransferase 1 promotes pancreatic cancer, we created a novel mouse in which a pancreas-specific genetic deletion of this enzyme overlays the KC mouse model. The analysis of our new model showed delayed cancer formation and a significant reduction in fibrosis. Our results highlight the importance of a strategic systems approach to identifying glycans whose functions can be modeled in mouse, a crucial step in the development of therapeutics targeting glycosylation in pancreatic cancer.
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Affiliation(s)
- Emma Kurz
- Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, USA
| | - Shuhui Chen
- Department of Chemistry, Biomedical Research Institute, New York University, New York, New York, USA
| | - Emily Vucic
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York, USA
| | - Gillian Baptiste
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Cynthia Loomis
- Office of Science and Research, NYU Grossman School of Medicine, New York, New York, USA
| | - Praveen Agrawal
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Cristina Hajdu
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York, USA.
| | - Lara K Mahal
- Department of Chemistry, Biomedical Research Institute, New York University, New York, New York, USA.
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3
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Nagai-Okatani C, Zou X, Fujita N, Sogabe I, Arakawa K, Nagai M, Angata K, Zhang Y, Aoki-Kinoshita KF, Kuno A. LM-GlycomeAtlas Ver. 2.0: An Integrated Visualization for Lectin Microarray-based Mouse Tissue Glycome Mapping Data with Lectin Histochemistry. J Proteome Res 2021; 20:2069-2075. [PMID: 33657805 DOI: 10.1021/acs.jproteome.0c00907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Laser microdissection-assisted lectin microarray has been used to obtain quantitative and qualitative information on glycans on proteins expressed in microscopic regions of formalin-fixed paraffin-embedded tissue sections. For the effective visualization of this "tissue glycome mapping" data, a novel online tool, LM-GlycomeAtlas (https://glycosmos.org/lm_glycomeatlas/index), was launched in the freely available glycoscience portal, the GlyCosmos Portal (https://glycosmos.org). In LM-GlycomeAtlas Version 1.0, nine tissues from normal mice were used to provide one data set of glycomic profiles. Here we introduce an updated version of LM-GlycomeAtlas, which includes more spatial information. We designed it to deposit multiple data sets of glycomic profiles with high-resolution histological images, which included staining images with multiple lectins on the array. The additionally implemented interfaces allow users to display multiple histological images of interest (e.g., diseased and normal mice), thereby facilitating the evaluation of tissue glycomic profiling and glyco-pathological analysis. Using these updated interfaces, 451 glycomic profiling data and 42 histological images obtained from 14 tissues of normal and diseased mice were successfully visualized. By easy integration with other tools for glycoproteomic data and protein glycosylation machinery, LM-GlycomeAtlas will be one of the most valuable open resources that contribute to both glycoscience and proteomics communities.
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Affiliation(s)
- Chiaki Nagai-Okatani
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Xia Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Noriaki Fujita
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Isami Sogabe
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Kouiti Arakawa
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Misugi Nagai
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Kiyohiko Angata
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kiyoko F Aoki-Kinoshita
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Atsushi Kuno
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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4
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Liu L, Li D, Shu J, Wang L, Zhang F, Zhang C, Yu H, Chen M, Li Z, Guo X. Protein Glycopatterns in Bronchoalveolar Lavage Fluid as Novel Potential Biomarkers for Diagnosis of Lung Cancer. Front Oncol 2021; 10:568433. [PMID: 33520694 PMCID: PMC7840895 DOI: 10.3389/fonc.2020.568433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is one of the most prevalent and life-threatening neoplasias worldwide due to the deficiency of ideal diagnostic biomarkers. Although aberrant glycosylation has been observed in human serum and tissue, little is known about the alterations in bronchoalveolar lavage fluid (BALF) that are extremely associated with lung cancer. In this study, our aim was to systematically investigate and assess the alterations of protein glycopatterns in BALF and possibility as biomarkers for diagnosis of lung cancer. Here, lectin microarrays and blotting analysis were utilized to detect the differential expression of BALF glycoproteins from patients with 80 adenocarcinomas (ADC), 77 squamous carcinomas (SCC), 51 small cell lung cancer (SCLC), and 73 benign pulmonary diseases (BPD). These 281 specimens were then randomly divided into a training cohort and validation cohort for constructing and verifying the diagnostic models based on the glycopattern abundances. Moreover, an independent test was performed with 120 newly collected BALF samples enrolled in the double-blind cohort to further assess the clinical application potential of the diagnostic models. According to the results, there were 15 (e.g., PHA-E, EEL, and BPL) and 14 lectins (e.g., PTL-II, LCA, and SJA) that individually showed significant variations in different types and stages of lung cancer compared to BPD. Notably, the diagnostic models achieved better discriminate power in the validation cohort and exhibited high accuracies of 0.917, 0.864, 0.712, 0.671, and 0.781 in the double-blind cohort for the diagnosis of lung cancer, early stage lung cancer, ADC, SCC, and SCLC, respectively. Taken together, the present study revealed that the abnormally altered protein glycopatterns in BALF are expected to be novel potential biomarkers for the identification and early diagnosis of lung cancer, which will contribute to explain the mechanism of the development of lung cancer from the perspective of glycobiology.
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Affiliation(s)
- Lina Liu
- Department of Clinical Laboratory, Xi’an No. 4 Hospital, Xi’an, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Dan Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, China
| | - Li Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Fan Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, China
| | - Chen Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, China
| | - Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, China
| | - Mingwei Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, China
| | - Xuan Guo
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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5
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Establishment of a 1, 4, 7, 10-tetraazacyclododecane-1,4,7,10-tetraacetic acid mono-N-hydroxysuccinimide ester (DOTA-NHS-ester) based lectin microarray for efficiently detecting serum glycans in gastric cancers. Anal Biochem 2020; 597:113686. [PMID: 32156505 DOI: 10.1016/j.ab.2020.113686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/16/2022]
Abstract
Development of cancers is involved in changes of a variety of glycans. Lectin microarray is one of the most powerful methodologies for investigation of glycan alterations in biological samples with its advantages of high through-put, selectivity and specificity of the technique. However, utilization of lectin microarrays available commercially keeps of great challenges. In this study, we took use of the molecular self-assembled monolayer technique to modify a gold surface with the reagent 1,4,7,10-tetraazacyclododecane- 1,4,7,10-tetraacetic acid mono-N-hydroxysuccinimide ester (DOTA-NHS-ester) in combination with 16-amino-1-hexadecanethiol hydrochloride. Cross-linking effect of DOTA-NHS-ester is brought about via activating three -OH ends to three terminals of succinylimidines, making selective binding of the terminal amino groups in proteins possible. We immobilized ten commercial lectins on the platform and measured changes of serum lectin-matched glycans in patients with gastric cancer. The results demonstrated that this biochip modification platform conferred impressive chemical surface stabilization, sensitivity and geometric images. We observed that all the serum glycans tested in the patients were significantly higher than those in the controls (P < 0.05). The biochip would provide a versatile platform for investigation of potential glycan biomarkers in making tumor diagnosis decision and analyzing escape of tumors from immunity.
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6
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Dang K, Zhang W, Jiang S, Lin X, Qian A. Application of Lectin Microarrays for Biomarker Discovery. ChemistryOpen 2020; 9:285-300. [PMID: 32154049 PMCID: PMC7050261 DOI: 10.1002/open.201900326] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
Many proteins in living organisms are glycosylated. As their glycan patterns exhibit protein-, cell-, and tissue-specific heterogeneity, changes in the glycosylation levels could serve as useful indicators of various pathological and physiological states. Thus, the identification of glycoprotein biomarkers from specific changes in the glycan profiles of glycoproteins is a trending field. Lectin microarrays provide a new glycan analysis platform, which enables rapid and sensitive analysis of complex glycans without requiring the release of glycans from the protein. Recent developments in lectin microarray technology enable high-throughput analysis of glycans in complex biological samples. In this review, we will discuss the basic concepts and recent progress in lectin microarray technology, the application of lectin microarrays in biomarker discovery, and the challenges and future development of this technology. Given the tremendous technical advancements that have been made, lectin microarrays will become an indispensable tool for the discovery of glycoprotein biomarkers.
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Affiliation(s)
- Kai Dang
- Laboratory for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'an710072, ShaanxiChina
| | - Wenjuan Zhang
- Laboratory for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'an710072, ShaanxiChina
| | - Shanfeng Jiang
- Laboratory for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'an710072, ShaanxiChina
| | - Xiao Lin
- Laboratory for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'an710072, ShaanxiChina
| | - Airong Qian
- Laboratory for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life SciencesNorthwestern Polytechnical UniversityXi'an710072, ShaanxiChina
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7
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Yu H, Shu J, Li Z. Lectin microarrays for glycoproteomics: an overview of their use and potential. Expert Rev Proteomics 2020; 17:27-39. [PMID: 31971038 DOI: 10.1080/14789450.2020.1720512] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Glycoproteomics is an important subdiscipline of proteomics, focusing on the role of protein glycosylation in various biological processes. Protein glycosylation is the enzymatic addition of sugars or oligosaccharides to proteins. Altered glycosylation often occurs in the early stages of disease development, for example, certain tumor-associated glycans have been shown to be expressed in precursor lesions of different types of cancer, making them powerful early diagnostic markers. Lectin microarrays have become a powerful tool for both the study of glycosylation and the diagnosis of various diseases including cancer.Areas covered: This review will discuss the most useful features of lectin microarrays, such as their technological advances, their capability for parallel/high-throughput analysis for the important glycopatterns of glycoprotein, and an overview of their use for glycosylation analysis of various complex protein samples, as well as their diagnostic potential in various diseases.Expert opinion: Lectin microarrays have proved to be useful in studying multiple lectin-glycan interactions in a single experiment and, with the advances made in the field, hold a promise of enabling glycopatterns of diseases in a fast and efficient manner. Lectin microarrays will become increasingly powerful early diagnostic tool for a variety of conditions.
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Affiliation(s)
- Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
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8
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Sun S, Hu Y, Ao M, Shah P, Chen J, Yang W, Jia X, Tian Y, Thomas S, Zhang H. N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping. Clin Proteomics 2019; 16:35. [PMID: 31516400 PMCID: PMC6731604 DOI: 10.1186/s12014-019-9254-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. The large-scale characterization of N-linked glycoproteins accomplished by mass spectrometry-based glycoproteomics has provided valuable insights into the interdependence of glycoprotein structure and protein function. However, these studies focused mainly on the analysis of specific sample type, and lack the integration of glycoproteomic data from different tissues, body fluids or cell types. METHODS In this study, we collected the human glycosite-containing peptides identified through their de-glycosylated forms by mass spectrometry from over 100 publications and unpublished datasets generated from our laboratory. A database resource termed N-GlycositeAtlas was created and further used for the distribution analyses of glycoproteins among different human cells, tissues and body fluids. Finally, a web interface of N-GlycositeAtlas was created to maximize the utility and value of the database. RESULTS The N-GlycositeAtlas database contains more than 30,000 glycosite-containing peptides (representing > 14,000 N-glycosylation sites) from more than 7200 N-glycoproteins from different biological sources including human-derived tissues, body fluids and cell lines from over 100 studies. CONCLUSIONS The entire human N-glycoproteome database as well as 22 sub-databases associated with individual tissues or body fluids can be downloaded from the N-GlycositeAtlas website at http://nglycositeatlas.biomarkercenter.org.
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Affiliation(s)
- Shisheng Sun
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
- College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Minghui Ao
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Punit Shah
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Jing Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Xingwang Jia
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Yuan Tian
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Stefani Thomas
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
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Nagai-Okatani C, Aoki-Kinoshita KF, Kakuda S, Nagai M, Hagiwara K, Kiyohara K, Fujita N, Suzuki Y, Sato T, Angata K, Kuno A. LM-GlycomeAtlas Ver. 1.0: A Novel Visualization Tool for Lectin Microarray-Based Glycomic Profiles of Mouse Tissue Sections. Molecules 2019; 24:molecules24162962. [PMID: 31443278 PMCID: PMC6719194 DOI: 10.3390/molecules24162962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/24/2022] Open
Abstract
For the effective discovery of the biological roles and disease-specific alterations concerning protein glycosylation in tissue samples, it is important to know beforehand the quantitative and qualitative variations of glycan structures expressed in various types of cells, sites, and tissues. To this end, we used laser microdissection-assisted lectin microarray (LMA) to establish a simple and reproducible method for high-throughput and in-depth glycomic profiling of formalin-fixed paraffin-embedded tissue sections. Using this “tissue glycome mapping” approach, we present 234 glycomic profiling data obtained from nine tissue sections (pancreas, heart, lung, thymus, gallbladder, stomach, small intestine, colon, and skin) of two 8-week-old male C57BL/6J mice. We provided this LMA-based dataset in the similar interface as that of GlycomeAtlas, a previously developed tool for mass spectrometry-based tissue glycomic profiling, allowing easy comparison of the two types of data. This online tool, called “LM-GlycomeAtlas”, allows users to visualize the LMA-based tissue glycomic profiling data associated with the sample information as an atlas. Since the present dataset allows the comparison of glycomic profiles, it will facilitate the evaluation of site- and tissue-specific glycosylation patterns. Taking advantage of its extensibility, this tool will continue to be updated with the expansion of deposited data.
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Affiliation(s)
- Chiaki Nagai-Okatani
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan.
| | - Kiyoko F Aoki-Kinoshita
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Shuichi Kakuda
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Misugi Nagai
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Kozue Hagiwara
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Katsue Kiyohara
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Noriaki Fujita
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Yoshinori Suzuki
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Takashi Sato
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Kiyohiko Angata
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Atsushi Kuno
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan.
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10
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Penezić A, Križakova M, Miljuš G, Katrlik J, Nedić O. Diagnostic Potential of Transferrin Glycoforms-A Lectin-Based Protein Microarray Approach. Proteomics Clin Appl 2019; 13:e1800185. [PMID: 31050875 DOI: 10.1002/prca.201800185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/28/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Disease or a specific condition may cause alteration of human transferrin (hTf) glycosylation pattern. A specific analytical platform, lectin-based protein microarray, is designed and optimized for the investigation of hTf glycans, attached to the protein core in their native form. EXPERIMENTAL DESIGN hTf molecules isolated from healthy persons of different age, diabetes mellitus type 2 (T2DM) or colorectal carcinoma (CRC) patients are used for method validation. Reliability of the results is ensured by three criteria for the evaluation of hTf-lectin interactions: i) signal-to-noise ratio above 3, ii) signal intensity above 250 arbitrary units, and iii) hTf concentration ensuring high sensitivity of the assay. RESULTS Six lectins, out of fourteen tested, satisfy the criteria. hTf is spotted at concentration of 50 µg mL-L . When physiological samples (isolated hTf) are analyzed, the highest potential to differentiate between population groups expresses Aleuria aurantia (AAL), Triticum vulgaris (WGA) and Phaseolus vulgaris (PHA-E) lectins. The initial amount of hTf which can be analyzed is very low (75 pg). CONCLUSION AND CLINICAL RELEVANCE Results confirm that a very sensitive, high-throughput lectin-based protein microarray platform can be formulated to detect changes in hTf glycan structures which can be considered as biomarkers of ageing or a disease.
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Affiliation(s)
- Ana Penezić
- Institute for the Application of Nuclear Energy (INEP), Banatska 31b, 11080, Belgrade, Serbia
| | - Martina Križakova
- Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovak Republic
| | - Goran Miljuš
- Institute for the Application of Nuclear Energy (INEP), Banatska 31b, 11080, Belgrade, Serbia
| | - Jaroslav Katrlik
- Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovak Republic
| | - Olgica Nedić
- Institute for the Application of Nuclear Energy (INEP), Banatska 31b, 11080, Belgrade, Serbia
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11
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Dang L, Jia L, Zhi Y, Li P, Zhao T, Zhu B, Lan R, Hu Y, Zhang H, Sun S. Mapping human N-linked glycoproteins and glycosylation sites using mass spectrometry. Trends Analyt Chem 2019; 114:143-150. [PMID: 31831916 PMCID: PMC6907083 DOI: 10.1016/j.trac.2019.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. Over the last decade, large-scale profiling of N-linked glycoproteins and glycosylation sites from biological and clinical samples has been achieved through mass spectrometry-based glycoproteomic approaches. In this paper, we reviewed the human glycoproteomic profiles that have been reported in more than 80 individual studies, and mainly focused on the N-glycoproteins and glycosylation sites identified through their deglycosylated forms of glycosite-containing peptides. According to our analyses, more than 30,000 glycosite-containing peptides and 7,000 human glycoproteins have been identified from five different body fluids, twelve human tissues (or related cell lines), and four special cell types. As the glycoproteomic data is still missing for many organs and tissues, a systematical glycoproteomic analysis of various human tissues and body fluids using a uniform platform is still needed for an integrated map of human N-glycoproteomes.
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Affiliation(s)
- Liuyi Dang
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Li Jia
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Yuan Zhi
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Pengfei Li
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Ting Zhao
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Bojing Zhu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Rongxia Lan
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Shisheng Sun
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
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12
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Nagai-Okatani C, Nagai M, Sato T, Kuno A. An Improved Method for Cell Type-Selective Glycomic Analysis of Tissue Sections Assisted by Fluorescence Laser Microdissection. Int J Mol Sci 2019; 20:ijms20030700. [PMID: 30736315 PMCID: PMC6387264 DOI: 10.3390/ijms20030700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/01/2019] [Accepted: 02/02/2019] [Indexed: 02/07/2023] Open
Abstract
Lectin microarray (LMA) is a highly sensitive technology used to obtain the global glycomic profiles of endogenous glycoproteins in biological samples including formalin-fixed paraffin-embedded tissue sections. Here, we describe an effective method for cell type-selective glycomic profiling of tissue fragments collected by laser microdissection (LMD) under fluorescent histochemical visualization. We optimized each step of histochemical staining and confirmed the reliability and validity of glycomic profiling. Using the optimized procedure, glycomic profiles were obtained with 0.5 mm² of stained thymic sections (5-μm-thick) from 8-week-old C57BL/6J male mice. The glycomic profiles of Ulex europaeus agglutinin-I (UEA-I)-stained medullary regions showed higher UEA-I signals than those of the morphologically determined medulla regions, indicating the utility of this method for UEA-I(+) cell-selective analysis. To further evaluate this method, tissue fragments was serially collected from stained and unstained areas of medullary epithelial cell probes (UEA-I and anti-cytokeratin 5 antibody) and a cortex-staining probe (peanut agglutinin). The medullary regions assigned by the three probes showed significantly different glycomic profiles, highlighting the difference in subpopulation recognition among the three probes, which was consistent with previous reports. In conclusion, our fluorescence LMD-LMA method enabled cell type-selective tissue glycomic analysis of pathological specimens and animal models, especially for glyco-biomarker discovery.
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Affiliation(s)
- Chiaki Nagai-Okatani
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan.
| | - Misugi Nagai
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan.
| | - Takashi Sato
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan.
| | - Atsushi Kuno
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan.
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13
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Pearson AJ, Gallagher ES. Overview of Characterizing Cancer Glycans with Lectin-Based Analytical Methods. Methods Mol Biol 2019; 1928:389-408. [PMID: 30725466 DOI: 10.1007/978-1-4939-9027-6_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Glycosylation is a post-translational modification that is often altered in disease development and progression, including cancer. In cancerous patients, the abnormal expression of glycosylation enzymes leads to aberrant glycosylation, which has been linked to malignant tissues. Due to aberrant glycosylation, the presence of specific glycans can be used as biomarkers for identifying the type and stage of cancer. Glycan structures are heterogeneous, with different protein glycoforms having different functional activities. Lectins are an important tool in glycan analysis due to their specificity in binding to unique glycan linkages and monosaccharide units, which allows for the identification of unique glycan structural properties. In this review, we will discuss the use of lectins in microarrays and chromatography for characterizing glycan structures.
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Affiliation(s)
- Amanda J Pearson
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
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14
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Narimatsu H, Kaji H, Vakhrushev SY, Clausen H, Zhang H, Noro E, Togayachi A, Nagai-Okatani C, Kuno A, Zou X, Cheng L, Tao SC, Sun Y. Current Technologies for Complex Glycoproteomics and Their Applications to Biology/Disease-Driven Glycoproteomics. J Proteome Res 2018; 17:4097-4112. [PMID: 30359034 DOI: 10.1021/acs.jproteome.8b00515] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glycoproteomics is an important recent advance in the field of glycoscience. In glycomics, glycan structures are comprehensively analyzed after glycans are released from glycoproteins. However, a major limitation of glycomics is the lack of insight into glycoprotein functions. The Biology/Disease-driven Human Proteome Project has a particular focus on biological and medical applications. Glycoproteomics technologies aimed at obtaining a comprehensive understanding of intact glycoproteins, i.e., the kind of glycan structures that are attached to particular amino acids and proteins, have been developed. This Review focuses on the recent progress of the technologies and their applications. First, the methods for large-scale identification of both N- and O-glycosylated proteins are summarized. Next, the progress of analytical methods for intact glycopeptides is outlined. MS/MS-based methods were developed for improving the sensitivity and speed of the mass spectrometer, in parallel with the software for complex spectrum assignment. In addition, a unique approach to identify intact glycopeptides using MS1-based accurate masses is introduced. Finally, as an advance of glycomics, two approaches to provide the spatial distribution of glycans in cells are described, i.e., MS imaging and lectin microarray. These methods allow rapid glycomic profiling of different types of biological samples and thus facilitate glycoproteomics.
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Affiliation(s)
- Hisashi Narimatsu
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Hiroyuki Kaji
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics , University of Copenhagen , Blegdamsvej 3 , Copenhagen 2200 , Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics , University of Copenhagen , Blegdamsvej 3 , Copenhagen 2200 , Denmark
| | - Hui Zhang
- Center for Biomarker Discovery and Translation , Johns Hopkins University , 400 North Broadway , Baltimore , Maryland 21205 , United States
| | - Erika Noro
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Akira Togayachi
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Chiaki Nagai-Okatani
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Atsushi Kuno
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Xia Zou
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan.,Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Li Cheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Yangyang Sun
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
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15
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Waniwan JT, Chen YJ, Capangpangan R, Weng SH, Chen YJ. Glycoproteomic Alterations in Drug-Resistant Nonsmall Cell Lung Cancer Cells Revealed by Lectin Magnetic Nanoprobe-Based Mass Spectrometry. J Proteome Res 2018; 17:3761-3773. [PMID: 30261726 DOI: 10.1021/acs.jproteome.8b00433] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the functional role of glycosylation-mediated pathogenesis requires deep characterization of glycoproteome, which remains extremely challenging due to the inherently complex nature of glycoproteins. We demonstrate the utility of lectin-magnetic nanoprobe (MNP@lectin) coupled to Orbitrap HCD-CID-MS/MS for complementary glycotope-specific enrichment and site-specific glycosylation analysis of the glycoproteome. By three nanoprobes, MNP@ConA, MNP@AAL, and MNP@SNA, our results revealed the first large-scale glycoproteome of nonsmall cell lung cancer (NSCLC) with 2290 and 2767 nonredundant glycopeptides confidently identified (Byonic score ≥100) in EGFR-TKI-sensitive PC9 and -resistant PC9-IR cells, respectively, especially with more fucosylated and sialylated glycopeptides in PC9-IR cells. The complementary enrichment was demonstrated with only five glycopeptides commonly enriched in three MNP@lectins. Glycotope specificity of 79 and 62% for enrichment was achieved using MNP@AAL and MNP@SNA, respectively. Label-free quantitation revealed predominant fucosylation in PC9-IR cells, suggesting its potential role associated with NSCLC resistance. Moreover, without immunoprecipitation, this multilectin nanoprobe allows the sensitive identification of 51 glycopeptides from 10 of 12 reported sites from onco-protein EGFR. Our results not only demonstrated a sensitive approach to study the vastly under-represented N-glycoprotome but also may pave the way for a glycoproteomic atlas to further explore the site-specific function of glycoproteins associated with drug resistance in NSCLC.
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Affiliation(s)
- Juanilita T Waniwan
- Department of Chemistry , National Taiwan University , Taipei 115 , Taiwan.,Chemical Biology and Molecular Biophysics , Taiwan International Graduate Program , Taipei 115 , Taiwan.,Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
| | - Rey Capangpangan
- Caraga State University , Butuan City 8600 , Philippines.,Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
| | - Shao-Hsing Weng
- Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan.,Genome and Systems Biology Degree Program , National Taiwan University , Taipei 115 , Taiwan
| | - Yu-Ju Chen
- Department of Chemistry , National Taiwan University , Taipei 115 , Taiwan.,Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
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16
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Togayachi A, Tomioka A, Fujita M, Sukegawa M, Noro E, Takakura D, Miyazaki M, Shikanai T, Narimatsu H, Kaji H. Identification of Poly-N-Acetyllactosamine-Carrying Glycoproteins from HL-60 Human Promyelocytic Leukemia Cells Using a Site-Specific Glycome Analysis Method, Glyco-RIDGE. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1138-1152. [PMID: 29675740 PMCID: PMC6004004 DOI: 10.1007/s13361-018-1938-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 05/15/2023]
Abstract
To elucidate the relationship between the protein function and the diversity and heterogeneity of glycans conjugated to the protein, glycosylation sites, glycan variation, and glycan proportions at each site of the glycoprotein must be analyzed. Glycopeptide-based structural analysis technology using mass spectrometry has been developed; however, complicated analyses of complex spectra obtained by multistage fragmentation are necessary, and sensitivity and throughput of the analyses are low. Therefore, we developed a liquid chromatography/mass spectrometry (MS)-based glycopeptide analysis method to reveal the site-specific glycome (Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile, Glyco-RIDGE). This method used accurate masses and retention times of glycopeptides, without requiring MS2, and could be applied to complex mixtures. To increase the number of identified peptide, fractionation of sample glycopeptides for reduction of sample complexity is required. Therefore, in this study, glycopeptides were fractionated into four fractions by hydrophilic interaction chromatography, and each fraction was analyzed using the Glyco-RIDGE method. As a result, many glycopeptides having long glycans were enriched in the highest hydrophilic fraction. Based on the monosaccharide composition, these glycans were thought to be poly-N-acetyllactosamine (polylactosamine [pLN]), and 31 pLN-carrier proteins were identified in HL-60 cells. Gene ontology enrichment analysis revealed that pLN carriers included many molecules related to signal transduction, receptors, and cell adhesion. Thus, these findings provided important insights into the analysis of the glycoproteome using our novel Glyco-RIDGE method. Graphical Abstract ᅟ.
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Affiliation(s)
- Akira Togayachi
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Azusa Tomioka
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Mika Fujita
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Masako Sukegawa
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Erika Noro
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Daisuke Takakura
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Michiyo Miyazaki
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Toshihide Shikanai
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Hisashi Narimatsu
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
| | - Hiroyuki Kaji
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
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17
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Differential N-glycan patterns identified in lung adenocarcinoma by N-glycan profiling of formalin-fixed paraffin-embedded (FFPE) tissue sections. J Proteomics 2018; 172:1-10. [DOI: 10.1016/j.jprot.2017.11.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/08/2017] [Accepted: 11/15/2017] [Indexed: 12/15/2022]
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18
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Togayachi A, Iwaki J, Kaji H, Matsuzaki H, Kuno A, Hirao Y, Nomura M, Noguchi M, Ikehara Y, Narimatsu H. Glycobiomarker, Fucosylated Short-Form Secretogranin III Levels Are Increased in Serum of Patients with Small Cell Lung Carcinoma. J Proteome Res 2017; 16:4495-4505. [DOI: 10.1021/acs.jproteome.7b00484] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | | | | | | | | | | | - Masaharu Nomura
- Department
of Surgery, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
| | - Masayuki Noguchi
- Department
of Pathology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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19
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Poiroux G, Barre A, van Damme EJM, Benoist H, Rougé P. Plant Lectins Targeting O-Glycans at the Cell Surface as Tools for Cancer Diagnosis, Prognosis and Therapy. Int J Mol Sci 2017; 18:ijms18061232. [PMID: 28598369 PMCID: PMC5486055 DOI: 10.3390/ijms18061232] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 12/30/2022] Open
Abstract
Aberrant O-glycans expressed at the surface of cancer cells consist of membrane-tethered glycoproteins (T and Tn antigens) and glycolipids (Lewis a, Lewis x and Forssman antigens). All of these O-glycans have been identified as glyco-markers of interest for the diagnosis and the prognosis of cancer diseases. These epitopes are specifically detected using T/Tn-specific lectins isolated from various plants such as jacalin from Artocarpus integrifola, and fungi such as the Agaricus bisporus lectin. These lectins accommodate T/Tn antigens at the monosaccharide-binding site; residues located in the surrounding extended binding-site of the lectins often participate in the binding of more extended epitopes. Depending on the shape and size of the extended carbohydrate-binding site, their fine sugar-binding specificity towards complex O-glycans readily differs from one lectin to another, resulting in a great diversity in their sugar-recognition capacity. T/Tn-specific lectins have been extensively used for the histochemical detection of cancer cells in biopsies and for the follow up of the cancer progression and evolution. T/Tn-specific lectins also induce a caspase-dependent apoptosis in cancer cells, often associated with a more or less severe inhibition of proliferation. Moreover, they provide another potential source of molecules adapted to the building of photosensitizer-conjugates allowing a specific targeting to cancer cells, for the photodynamic treatment of tumors.
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Affiliation(s)
- Guillaume Poiroux
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche, Centre de Recherche en Cancérologie de Toulouse, 31037 Toulouse, France.
| | - Annick Barre
- Unité Mixte de Recherche, 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, 35 Chemin des Maraîchers Université Paul Sabatier, 31062 Toulouse, France.
| | - Els J M van Damme
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium.
| | - Hervé Benoist
- Unité Mixte de Recherche, 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, 35 Chemin des Maraîchers Université Paul Sabatier, 31062 Toulouse, France.
| | - Pierre Rougé
- Unité Mixte de Recherche, 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, 35 Chemin des Maraîchers Université Paul Sabatier, 31062 Toulouse, France.
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20
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Tozawa-Ono A, Kubota M, Honma C, Nakagawa Y, Yokomichi N, Yoshioka N, Tsuda C, Ohara T, Koizumi H, Suzuki N. Glycan profiling using formalin-fixed, paraffin-embedded tissues: Hippeastrum hybrid lectin is a sensitive biomarker for squamous cell carcinoma of the uterine cervix. J Obstet Gynaecol Res 2017; 43:1326-1334. [DOI: 10.1111/jog.13359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/06/2017] [Accepted: 03/20/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Akiko Tozawa-Ono
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Manabu Kubota
- Department of Pathology; St. Marianna University School of Medicine; Miyamae, Kawasaki Japan
| | - Chika Honma
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Yuko Nakagawa
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Noriyuki Yokomichi
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Norihito Yoshioka
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Chiharu Tsuda
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Tatsuru Ohara
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Hirotaka Koizumi
- Department of Pathology; St. Marianna University School of Medicine; Miyamae, Kawasaki Japan
| | - Nao Suzuki
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
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21
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Toyoda M, Kaji H, Sawaki H, Togayachi A, Angata T, Narimatsu H, Kameyama A. Identification and characterization of sulfated glycoproteins from small cell lung carcinoma cells assisted by management of molecular charges. Glycoconj J 2016; 33:917-926. [PMID: 27318476 DOI: 10.1007/s10719-016-9700-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/03/2016] [Accepted: 06/05/2016] [Indexed: 01/17/2023]
Abstract
Proteins carrying sulfated glycans (i.e., sulfated glycoproteins) are known to be associated with diseases, such as cancer, cystic fibrosis, and osteoarthritis. Sulfated glycoproteins, however, have not been isolated or characterized from complex biological samples due to lack of appropriate tools for their enrichment. Here, we describe a method to identify and characterize sulfated glycoproteins that are involved in chemical modifications to control the molecular charge of the peptides. In this method, acetohydrazidation of carboxyl groups was performed to accentuate the negative charge of the sulfate group, and Girard's T modification of aspartic acid was performed to assist in protein identification by MS tagging. Using this approach, we identified and characterized the sulfated glycoproteins: Golgi membrane protein 1, insulin-like growth factor binding protein-like 1, and amyloid beta precursor-like protein 1 from H2171 cells, a small cell lung carcinoma cell line. These sulfated glycoproteins carry a complex-type N-glycan with a core fucose and 4'-O-sulfated LacdiNAc as the major glycan.
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Affiliation(s)
- Masaaki Toyoda
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
| | - Hiroyuki Kaji
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
| | - Hiromichi Sawaki
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
| | - Akira Togayachi
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
| | - Takashi Angata
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
| | - Hisashi Narimatsu
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
| | - Akihiko Kameyama
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan.
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22
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Syed P, Gidwani K, Kekki H, Leivo J, Pettersson K, Lamminmäki U. Role of lectin microarrays in cancer diagnosis. Proteomics 2016; 16:1257-65. [PMID: 26841254 DOI: 10.1002/pmic.201500404] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 12/22/2022]
Abstract
The majority of cell differentiation associated tumor markers reported to date are either glycoproteins or glycolipids. Despite there being a large number of glycoproteins reported as candidate markers for various cancers, only a handful are approved by the US Food and Drug Administration. Lectins, which bind to the glycan part of the glycoproteins, can be exploited to identify aberrant glycosylation patterns, which in turn would help in enhancing the specificity of cancer diagnosis. Although conventional techniques such as HPLC and MS have been instrumental in performing the glycomic analyses, these techniques lack multiplexity. Lectin microarrays have proved to be useful in studying multiple lectin-glycan interactions in a single experiment and, with the advances made in the field, hold a promise of enabling glycomic profiling of cancers in a fast and efficient manner.
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Affiliation(s)
- Parvez Syed
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
| | - Kamlesh Gidwani
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
| | - Henna Kekki
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
| | - Janne Leivo
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
| | - Kim Pettersson
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
| | - Urpo Lamminmäki
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
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23
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Narimatsu H. Development of M2BPGi: a novel fibrosis serum glyco-biomarker for chronic hepatitis/cirrhosis diagnostics. Expert Rev Proteomics 2015; 12:683-93. [PMID: 26394846 DOI: 10.1586/14789450.2015.1084874] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many proteins in the living body are glycoproteins, which present glycans linked on their surface. Glycan structures reflect the degree of cell differentiation or canceration and are cell specific. These characteristics are advantageous in the development of various disease biomarkers. Glycoprotein-based biomarkers (glyco-biomarkers) are developed by utilizing the specific changes in the glycan structure on a glycoprotein secreted from the diseased cells of interest. Therefore, quantification of the altered glycan structures is the key to developing a new glyco-biomarker. Glycoscience is a relatively new area of molecular science, and recent advancement of glycotechnologies is remarkable. In the author's institute, new glycoscience technologies have been designed to be efficiently utilized for the development of new diagnostic agents. This paper introduces a strategy for glyco-biomarker development, which was successfully applied in the development of Wisteria floribunda agglutinin-positive Mac-2 binding protein M2BPGi, a liver fibrosis marker now commercially available for clinical use.
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Affiliation(s)
- Hisashi Narimatsu
- a Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
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24
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Ambasta RK, Jha SK, Kumar D, Sharma R, Jha NK, Kumar P. Comparative study of anti-angiogenic activities of luteolin, lectin and lupeol biomolecules. J Transl Med 2015; 13:307. [PMID: 26385094 PMCID: PMC4575424 DOI: 10.1186/s12967-015-0665-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/08/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Angiogenesis is a hallmark feature in the initiation, progression and growth of tumour. There are various factors for promotion of angiogenesis on one hand and on the other hand, biomolecules have been reported to inhibit cancer through anti-angiogenesis mechanism. Biomolecules, for instance, luteolin, lectin and lupeol are known to suppress cancer. This study aims to compare and evaluate the biomolecule(s) like luteolin, lupeol and lectin on CAM assay and HT-29 cell culture to understand the efficacy of these drugs. METHOD The biomolecules have been administered on CAM assay, HT-29 cell culture, cell migration assay. Furthermore, bioinformatics analysis of the identified targets of these biomolecules have been performed. RESULT Luteolin has been found to be better in inhibiting angiogenesis on CAM assay in comparison to lupeol and lectin. In line with this study when biomolecules was administered on cell migration assay via scratch assay method. We provided evidence that Luteolin was again found to be better in inhibiting HT-29 cell migration. In order to identify the target sites of luteolin for inhibition, we used software analysis for identifying the best molecular targets of luteolin. Using software analysis best target protein molecule of these biomolecules have been identified. VEGF was found to be one of the target of luteolin. Studies have found several critical point mutation in VEGF A, B and C. Hence docking analysis of all biomolecules with VEGFR have been performed. Multiple allignment result have shown that the receptors are conserved at the docking site. CONCLUSION Therefore, it can be concluded that luteolin is not only comparatively better in inhibiting blood vessel in CAM assay, HT-29 cell proliferation and cell migration assay rather the domain of VEGFR is conserved to be targeted by luteolin, lupeol and lectin.
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Affiliation(s)
- Rashmi K Ambasta
- Department of Biotechnology, Delhi Technological University (Former Delhi College of Engineering), Delhi, India. .,School of Biosciences and Technology, Vellore Institute of Technology, University (VITU), Vellore, India.
| | - Saurabh Kumar Jha
- Department of Biotechnology, Delhi Technological University (Former Delhi College of Engineering), Delhi, India. .,School of Biosciences and Technology, Vellore Institute of Technology, University (VITU), Vellore, India.
| | - Dhiraj Kumar
- Department of Biotechnology, Delhi Technological University (Former Delhi College of Engineering), Delhi, India.
| | - Renu Sharma
- Department of Biotechnology, Delhi Technological University (Former Delhi College of Engineering), Delhi, India.
| | - Niraj Kumar Jha
- Department of Biotechnology, Delhi Technological University (Former Delhi College of Engineering), Delhi, India. .,School of Biosciences and Technology, Vellore Institute of Technology, University (VITU), Vellore, India.
| | - Pravir Kumar
- Department of Biotechnology, Delhi Technological University (Former Delhi College of Engineering), Delhi, India. .,School of Biosciences and Technology, Vellore Institute of Technology, University (VITU), Vellore, India. .,Neurology Department, Adjunct Faculty, Tufts University School of Medicine, Boston, MA, USA.
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25
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Dan X, Liu W, Ng TB. Development and Applications of Lectins as Biological Tools in Biomedical Research. Med Res Rev 2015; 36:221-47. [PMID: 26290041 DOI: 10.1002/med.21363] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/15/2015] [Accepted: 07/16/2015] [Indexed: 01/08/2023]
Abstract
As a new and burgeoning area following genomics and proteomics, glycomics has become a hot issue due to its pivotal roles in many physiological and pathological processes. Glycans are much more complicated than genes or proteins since glycans are highly branched and dynamic. Antibodies and lectins are the two major molecular tools applied for glycan profiling. Though the study of antibodies and lectins started at almost the same time in 1880s, lectins gained much less attention than the antibodies until recent decades when the importance and difficulties of glycomics were realized. The present review summarizes the discovery history of lectins and their biological functions with a special emphasis on their various applications as biological tools. Both older techniques that had been developed in the last century and new technologies developed in recent years, especially lectin microarrays and lectin-based biosensors, are included in this account.
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Affiliation(s)
- Xiuli Dan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wenlong Liu
- Department of Orthopaedics & Traumatology, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Tzi Bun Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
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26
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Thongboonkerd V, LaBaer J, Domont GB. Recent Advances of Proteomics Applied to Human Diseases. J Proteome Res 2014; 13:4493-6. [DOI: 10.1021/pr501038g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Visith Thongboonkerd
- Medical Proteomics Unit,
Office for Research and Development, Faculty of Medicine Siriraj Hospital,
and Center for Research in Complex Systems Science, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Joshua LaBaer
- Virginia G. Piper Center
for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287-6401, United States
| | - Gilberto B. Domont
- Proteomics Unit, Institute
of Chemistry, Federal University of Rio de Janeiro (UFRJ), Avenida
Athos da Silveira Ramos, Rio de Janeiro, 21941-909 RJ, Brazil
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