1
|
Jiang M, Wang Y, Yu X, He Y, Zheng X, Qin J, Gu Y, Li X, Shi Y, Ma X, Li J, Pu K. An image-based Abplex method for high-throughput GPCRs antibody discovery. Biotechnol J 2024; 19:e2300336. [PMID: 37941478 DOI: 10.1002/biot.202300336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
As the field of antibody therapeutics advances rapidly, membrane proteins, particularly G protein-coupled receptors (GPCRs), have emerged as highly sought-after drug targets. However, the challenges associated with extracting membrane proteins have created a demand for effective antibody screening systems targeting these proteins. In this study, we propose developing an innovative antibody screening strategy (Abplex) based on high-content imaging. This approach leverages intact cells that express target membrane proteins, facilitating the presentation of proteins in their native conformation. Furthermore, it acquires both specific and non-specific binding signals in a single well, thereby bolstering the robustness of the outcomes. The technique involves just one step and can be completed within 50 min, enabling the analysis of a single sample in just one second. The amalgamation of dependable experimental findings, a simplified workflow, reduced hands-on time, and a swift analytical pace positions our method for superior throughput and precision when juxtaposed with traditional techniques such as CbELISA and FACS. Moreover, we introduce the concept of cell barcoding, wherein cells are labeled with different fluorescence spatial patterns. This feature allows for multiplexed detection to meet the needs of various experiments. The characteristics of Abplex promise to expedite GPCR-targeting antibody discovery, advance therapeutics and enable new disease treatments.
Collapse
Affiliation(s)
- Min Jiang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Yuanyuan Wang
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Xinke Yu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) & Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Yiran He
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Xuewen Zheng
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Jingyi Qin
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Yayun Gu
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Xin Li
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Ying Shi
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Xiaochuan Ma
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) & Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Jiong Li
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Kefeng Pu
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| |
Collapse
|
2
|
Quintana JI, Atxabal U, Unione L, Ardá A, Jiménez-Barbero J. Exploring multivalent carbohydrate-protein interactions by NMR. Chem Soc Rev 2023; 52:1591-1613. [PMID: 36753338 PMCID: PMC9987413 DOI: 10.1039/d2cs00983h] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Indexed: 02/09/2023]
Abstract
Nuclear Magnetic Resonance (NMR) has been widely employed to assess diverse features of glycan-protein molecular recognition events. Different types of qualitative and quantitative information at different degrees of resolution and complexity can be extracted from the proper application of the available NMR-techniques. In fact, affinity, structural, kinetic, conformational, and dynamic characteristics of the binding process are available. Nevertheless, except in particular cases, the affinity of lectin-sugar interactions is weak, mostly at the low mM range. This feature is overcome in biological processes by using multivalency, thus augmenting the strength of the binding. However, the application of NMR methods to monitor multivalent lectin-glycan interactions is intrinsically challenging. It is well known that when large macromolecular complexes are formed, the NMR signals disappear from the NMR spectrum, due to the existence of fast transverse relaxation, related to the large size and exchange features. Indeed, at the heart of the molecular recognition event, the associated free-bound chemical exchange process for both partners takes place in a particular timescale. Thus, these factors have to be considered and overcome. In this review article, we have distinguished, in a subjective manner, the existence of multivalent presentations in the glycan or in the lectin. From the glycan perspective, we have also considered whether multiple epitopes of a given ligand are presented in the same linear chain of a saccharide (i.e., poly-LacNAc oligosaccharides) or decorating different arms of a multiantennae scaffold, either natural (as in multiantennae N-glycans) or synthetic (of dendrimer or polymer nature). From the lectin perspective, the presence of an individual binding site at every monomer of a multimeric lectin may also have key consequences for the binding event at different levels of complexity.
Collapse
Affiliation(s)
- Jon I Quintana
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Unai Atxabal
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Luca Unione
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | - Ana Ardá
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
- Department of Organic Chemistry, II Faculty of Science and Technology, EHU-UPV, 48940 Leioa, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain
| |
Collapse
|
3
|
Preliminary Analysis of the Glycolipid Profile in Secondary Brain Tumors. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4293172. [DOI: 10.1155/2022/4293172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 10/17/2022] [Accepted: 11/04/2022] [Indexed: 11/23/2022]
Abstract
Glycosphingolipids (GSLs) play numerous roles in cellular processes, including cell proliferation, apoptosis, inflammation, and cell signaling. Alteration of the GSLs metabolism leads to the accumulation of particular species of GSLs, which can lead to various pathologies, including carcinogenesis and metastasis; in essence, all neoplasms are characterized by the synthesis and aberrant organization of GSLs expressed on the cell surface. Secondary brain tumors make up the majority of intracranial cancers and generally present an unfavorable prognosis. In the present work, a native GSL mixture extracted and purified from a secondary brain tumor with primary pulmonary origin was obtained through extraction and purification and analyzed by MALDI TOF mass spectrometry. Research in the field of lipidomics could offer new data for the understanding of brain tropism and metastatic pathways, by studying the glycolipid molecules involved in the process of metastasis in general and in the production of brain metastases in particular. This could shed new light on the pattern of lipid glycosylation in secondary brain tumors, with a great impact on the effectiveness of cancer therapies, which could be adapted to the specific molecular pattern of the tumor.
Collapse
|
4
|
Marchetti L, Nifosì R, Martelli PL, Da Pozzo E, Cappello V, Banterle F, Trincavelli ML, Martini C, D’Elia M. Quantum computing algorithms: getting closer to critical problems in computational biology. Brief Bioinform 2022; 23:6758194. [PMID: 36220772 PMCID: PMC9677474 DOI: 10.1093/bib/bbac437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022] Open
Abstract
The recent biotechnological progress has allowed life scientists and physicians to access an unprecedented, massive amount of data at all levels (molecular, supramolecular, cellular and so on) of biological complexity. So far, mostly classical computational efforts have been dedicated to the simulation, prediction or de novo design of biomolecules, in order to improve the understanding of their function or to develop novel therapeutics. At a higher level of complexity, the progress of omics disciplines (genomics, transcriptomics, proteomics and metabolomics) has prompted researchers to develop informatics means to describe and annotate new biomolecules identified with a resolution down to the single cell, but also with a high-throughput speed. Machine learning approaches have been implemented to both the modelling studies and the handling of biomedical data. Quantum computing (QC) approaches hold the promise to resolve, speed up or refine the analysis of a wide range of these computational problems. Here, we review and comment on recently developed QC algorithms for biocomputing, with a particular focus on multi-scale modelling and genomic analyses. Indeed, differently from other computational approaches such as protein structure prediction, these problems have been shown to be adequately mapped onto quantum architectures, the main limit for their immediate use being the number of qubits and decoherence effects in the available quantum machines. Possible advantages over the classical counterparts are highlighted, along with a description of some hybrid classical/quantum approaches, which could be the closest to be realistically applied in biocomputation.
Collapse
Affiliation(s)
| | | | - Pier Luigi Martelli
- Corresponding authors: Pier Luigi Martelli. Tel.: +39 0512094005; Fax: +39 0512094005; E-mail: ; Claudia Martini. Tel.: +39 0502219522; Fax: +39 050 2210680; E-mail:
| | - Eleonora Da Pozzo
- University of Pisa, Department of Pharmacy, via Bonanno 6, 56126 Pisa Italy
| | - Valentina Cappello
- Italian Institute of Technology, Center for Materials Interfaces, Viale Rinaldo Piaggio 34, 56025 Pontedera (PI), Italy
| | | | | | - Claudia Martini
- Corresponding authors: Pier Luigi Martelli. Tel.: +39 0512094005; Fax: +39 0512094005; E-mail: ; Claudia Martini. Tel.: +39 0502219522; Fax: +39 050 2210680; E-mail:
| | - Massimo D’Elia
- University of Pisa, Department of Physics, Largo Bruno Pontecorvo 3, 56127, Pisa Italy
- INFN, Sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| |
Collapse
|
5
|
Furukawa K, Ohmi Y, Hamamura K, Kondo Y, Ohkawa Y, Kaneko K, Hashimoto N, Yesmin F, Bhuiyan RH, Tajima O, Furukawa K. Signaling domains of cancer-associated glycolipids. Glycoconj J 2022; 39:145-155. [PMID: 35315508 DOI: 10.1007/s10719-022-10051-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/06/2022] [Accepted: 02/15/2022] [Indexed: 12/16/2022]
Abstract
Immunotherapy of malignant cancers is now becoming one of representative approaches to overcome cancers. To construct strategies for immunotherapy, presence of tumor-specific antigens should be a major promise. A number of cancer specific- or cancer-associated antigens have been reported based on various experimental sets and various animal systems. The most reasonable strategy to define tumor-specific antigens might be "autologous typing" performed by Old's group, proposing three classes of tumor-antigens recognized by host immune systems of cancer patients. Namely, class 1, individual antigens that is present only in the patient's sample analyzed; class 2, shared antigens that can be found only in some group of cancers in some patients, but not in normal cells and tissues; class 3, universal antigens that are present in some cancers but also in normal cells and tissues with different densities. Sen Hakomori reported there were novel carbohydrates in cancers that could not be detected in normal cells mainly by biochemical approaches. Consequently, many of class 2 cancer-specific antigens have been revealed to be carbohydrate antigens, and been used for cancer diagnosis and treatment. Not only as cancer markers, but roles of those cancer-associated carbohydrates have also been recognized as functional molecules in cancer cells. In particular, roles of complex carbohydrates in the regulation of cell signaling on the cell surface microdomains, glycolipid-enriched microdomain (GEM)/rafts have been reported by Hakomori and many other researchers including us. The processes and present status of these studies on cancer-associated glycolipids were summarized.
Collapse
Affiliation(s)
- Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan. .,Department of Molecular and Cellular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Yuhsuke Ohmi
- Department of Clinical Engineering, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Kazunori Hamamura
- Department of Pharmacology, Aichi Gakuin University School of Dentistry, Nisshin, Japan
| | - Yuji Kondo
- Department of Molecular and Cellular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Institute, Osaka, Japan
| | - Kei Kaneko
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Noboru Hashimoto
- Department of Tissue Regeneration, Tokushima University Graduate School Institute of Biomedical Sciences, Tokushima, Japan
| | - Farhana Yesmin
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Department of Molecular and Cellular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Robiul H Bhuiyan
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Orie Tajima
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| |
Collapse
|
6
|
Glycomic and Glycoproteomic Techniques in Neurodegenerative Disorders and Neurotrauma: Towards Personalized Markers. Cells 2022; 11:cells11030581. [PMID: 35159390 PMCID: PMC8834236 DOI: 10.3390/cells11030581] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022] Open
Abstract
The proteome represents all the proteins expressed by a genome, a cell, a tissue, or an organism at any given time under defined physiological or pathological circumstances. Proteomic analysis has provided unparalleled opportunities for the discovery of expression patterns of proteins in a biological system, yielding precise and inclusive data about the system. Advances in the proteomics field opened the door to wider knowledge of the mechanisms underlying various post-translational modifications (PTMs) of proteins, including glycosylation. As of yet, the role of most of these PTMs remains unidentified. In this state-of-the-art review, we present a synopsis of glycosylation processes and the pathophysiological conditions that might ensue secondary to glycosylation shortcomings. The dynamics of protein glycosylation, a crucial mechanism that allows gene and pathway regulation, is described. We also explain how-at a biomolecular level-mutations in glycosylation-related genes may lead to neuropsychiatric manifestations and neurodegenerative disorders. We then analyze the shortcomings of glycoproteomic studies, putting into perspective their downfalls and the different advanced enrichment techniques that emanated to overcome some of these challenges. Furthermore, we summarize studies tackling the association between glycosylation and neuropsychiatric disorders and explore glycoproteomic changes in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington disease, multiple sclerosis, and amyotrophic lateral sclerosis. We finally conclude with the role of glycomics in the area of traumatic brain injury (TBI) and provide perspectives on the clinical application of glycoproteomics as potential diagnostic tools and their application in personalized medicine.
Collapse
|
7
|
Zagotto G, Bortoli M. Drug Design: Where We Are and Future Prospects. Molecules 2021; 26:7061. [PMID: 34834152 PMCID: PMC8622624 DOI: 10.3390/molecules26227061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 11/24/2022] Open
Abstract
Medicinal chemistry is facing new challenges in approaching precision medicine. Several powerful new tools or improvements of already used tools are now available to medicinal chemists to help in the process of drug discovery, from a hit molecule to a clinically used drug. Among the new tools, the possibility of considering folding intermediates or the catalytic process of a protein as a target for discovering new hits has emerged. In addition, machine learning is a new valuable approach helping medicinal chemists to discover new hits. Other abilities, ranging from the better understanding of the time evolution of biochemical processes to the comprehension of the biological meaning of the data originated from genetic analyses, are on their way to progress further in the drug discovery field toward improved patient care. In this sense, the new approaches to the delivery of drugs targeted to the central nervous system, together with the advancements in understanding the metabolic pathways for a growing number of drugs and relating them to the genetic characteristics of patients, constitute important progress in the field.
Collapse
Affiliation(s)
- Giuseppe Zagotto
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Marco Bortoli
- Institute of Computational Chemistry and Catalysis (IQCC) and Department of Chemistry, Faculty of Sciences, University of Girona, C/M. A. Capmany 69, 17003 Girona, Spain;
| |
Collapse
|
8
|
Zhang P, Ohkawa Y, Yamamoto S, Momota H, Kato A, Kaneko K, Natsume A, Farhana Y, Ohmi Y, Okajima T, Bhuiyan RH, Wakabayashi T, Furukawa K, Furukawa K. St8sia1-deficiency in mice alters tumor environments of gliomas, leading to reduced disease severity. NAGOYA JOURNAL OF MEDICAL SCIENCE 2021; 83:535-549. [PMID: 34552288 PMCID: PMC8438004 DOI: 10.18999/nagjms.83.3.535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/18/2020] [Indexed: 12/29/2022]
Abstract
Ganglioside GD3/GD2 are over-expressed in various neuroectoderm-derived tumors. Previous studies indicated that GD3 is involved in the enhancement of cancer properties such as rapid growth and increased invasiveness. However, little is known about the functions of GD3/GD2 in glioma cells and glioma microenvironments. To clarify the functions of GD3/GD2 in gliomas, we used a mouse glioma model based on the RCAS/Gtv-a system. At first, we compared the gliomas size between wild-type (WT) and GD3 synthase (GD3S) knockout (KO) mice, showing a less malignant histology and slower tumor growth in GD3S-KO mice than in WT mice. Immunohistochemistry of glioma sections from WT and GD3S-KO mice revealed that reactive microglia/macrophages showed different localization patterns between the two genetic types of mice. CD68+ cells were more frequently stained inside glioma tissues of GD3S-KO mice, while they were stained mainly around glioma tissues in WT mice. The number of CD68+ cells markedly increased in tumor tissues of GD3S-KO mice at 2 weeks after injection of transfectant DF-1 cells. Furthermore, CD68+ cells in GD3S(-/-) glioma tissues expressed higher levels of inducible nitric oxide synthase. We observed higher expression levels of pro-inflammatory cytokine genes in primary-cultured glioma cells of WT mice than in GD3S-KO mice. DNA microarray data also revealed differential expression levels of various cytokines and chemokines in glioma tissues between WT and GD3S-KO mice. These results suggest that expression of GD3S allows glioma cells to promote polarization of microglia/macrophages towards M2-like phenotypes by modulating the expression levels of chemokines and cytokines.
Collapse
Affiliation(s)
- Pu Zhang
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuki Ohkawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute
| | - Satoko Yamamoto
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Hiroyuki Momota
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akira Kato
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kei Kaneko
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Atsushi Natsume
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yesmin Farhana
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuhsuke Ohmi
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Tetsuya Okajima
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Robiul H Bhuiyan
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Toshihiko Wakabayashi
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
9
|
Changes in Sphingolipid Profile of Benzo[a]pyrene-Transformed Human Bronchial Epithelial Cells Are Reflected in the Altered Composition of Sphingolipids in Their Exosomes. Int J Mol Sci 2021; 22:ijms22179195. [PMID: 34502101 PMCID: PMC8431443 DOI: 10.3390/ijms22179195] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022] Open
Abstract
Sphingolipids (SLs), glycosphingolipids (GSLs), and eicosanoids are bioactive lipids, which play important roles in the etiology of various diseases, including cancer. However, their content and roles in cancer cells, and in particular in the exosomes derived from tumor cells, remain insufficiently characterized. In this study, we evaluated alterations of SL and GSL levels in transformed cells and their exosomes, using comparative HPLC-MS/MS analysis of parental human bronchial epithelial cells HBEC-12KT and their derivative, benzo[a]pyrene-transformed HBEC-12KT-B1 cells with the acquired mesenchymal phenotype. We examined in parallel SL/GSL contents in the exosomes released from both cell lines. We found significant alterations of the SL/GSL profile in the transformed cell line, which corresponded well with alterations of the SL/GSL profile in exosomes derived from these cells. This suggested that a majority of SLs and GSLs were transported by exosomes in the same relative pattern as in the cells of origin. The only exceptions included decreased contents of sphingosin, sphingosin-1-phosphate, and lactosylceramide in exosomes derived from the transformed cells, as compared with the exosomes derived from the parental cell line. Importantly, we found increased levels of ceramide phosphate, globoside Gb3, and ganglioside GD3 in the exosomes derived from the transformed cells. These positive modulators of epithelial-mesenchymal transition and other pro-carcinogenic processes might thus also contribute to cancer progression in recipient cells. In addition, the transformed HBEC-12KT-B1 cells also produced increased amounts of eicosanoids, in particular prostaglandin E2. Taken together, the exosomes derived from the transformed cells with specifically upregulated SL and GSL species, and increased levels of eicosanoids, might contribute to changes within the cancer microenvironment and in recipient cells, which could in turn participate in cancer development. Future studies should address specific roles of individual SL and GSL species identified in the present study.
Collapse
|
10
|
Ishihara K, Abe M, Fukazawa K, Konno T. Control of Cell-Substrate Binding Related to Cell Proliferation Cycle Status Using a Cytocompatible Phospholipid Polymer Bearing Phenylboronic Acid Groups. Macromol Biosci 2021; 21:e2000341. [PMID: 33502108 DOI: 10.1002/mabi.202000341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/18/2020] [Indexed: 12/19/2022]
Abstract
To provide high-quality cellular raw materials for cell engineering and pharmaceutical engineering, a polymer substrate is prepared for cell separation focusing on the cell proliferation cycle. There are many types of sugar chains on cell membranes, which function as signaling molecules to control interactions with the exterior of the cell; their abundance changes during the cell-proliferation cycle. In this study, a phenylboronic acid group, which has affinity for sugar chains, is introduced into a polymer containing a phosphorylcholine group that does not induce cell activation. On the surface of this polymer, human promyelocytic leukemia cells can adhere. The adhesion rate is increased by pretreating the substrate with an alkaline solution. Moreover, cell adhesion is dependent on the sugar additive in the culture medium. Therefore, cell adhesion is governed by reactions between the sugar chain on the cell membrane and the phenylboronic acid groups on the substrate. It is revealed that the adhesion rate changes depending on the expression level of sugar chains related to the cell-proliferation cycle. Based on this, it may be proposed a cell proliferation cycle-specific separation process using the polymer substrate based on cell adhesion depending on sugar chain density.
Collapse
Affiliation(s)
- Kazuhiko Ishihara
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masashi Abe
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kyoko Fukazawa
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tomohiro Konno
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba-Aramaki, Sendai, Miyagi, 980-8578, Japan
| |
Collapse
|
11
|
Kalmar JG, Garrard KP, Muddiman DC. GlycoHunter: An Open-Source Software for the Detection and Relative Quantification of INLIGHT-Labeled N-Linked Glycans. J Proteome Res 2021; 20:1855-1863. [PMID: 33417767 DOI: 10.1021/acs.jproteome.0c00840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Glycans are responsible for many biological activities; however, their structures are incredibly diverse and complex, often rendering the field of glycomics unsolvable by a single analytical technique. The development of multiple chemical derivatization strategies and bioinformatic software is responsible for some of the greatest analytical gains in the field of glycomics. The INLIGHT strategy is a chemical derivatization technique using hydrazide chemistry to derivatize the reducing end of N-linked glycans and incorporates either a natural (NAT, 12C6) or a stable-isotope label (SIL, 13C6) to carry out relative quantification. Here we present GlycoHunter, a user-friendly software created in MATLAB that enables researchers to accurately and efficiently process MS1 glycomics data where a NAT and SIL pair is generated for relative quantification, including but not limited to, INLIGHT. GlycoHunter accepts the commonly used data file formats imzML and mzXML and effectively identifies all peak pairs associated with NAT- and SIL-labeled N-linked glycans using MS1 data. It also includes the ability to tailor the search parameters and export the results for further analysis using Skyline or Excel.
Collapse
|
12
|
Lam BWS, Yam TYA, Chen CP, Lai MKP, Ong WY, Herr DR. The noncanonical chronicles: Emerging roles of sphingolipid structural variants. Cell Signal 2020; 79:109890. [PMID: 33359087 DOI: 10.1016/j.cellsig.2020.109890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/08/2023]
Abstract
Sphingolipids (SPs) are structurally diverse and represent one of the most quantitatively abundant classes of lipids in mammalian cells. In addition to their structural roles, many SP species are known to be bioactive mediators of essential cellular processes. Historically, studies have focused on SP species that contain the canonical 18‑carbon, mono-unsaturated sphingoid backbone. However, increasingly sensitive analytical technologies, driven by advances in mass spectrometry, have facilitated the identification of previously under-appreciated, molecularly distinct SP species. Many of these less abundant species contain noncanonical backbones. Interestingly, a growing number of studies have identified clinical associations between these noncanonical SPs and disease, suggesting that there is functional significance to the alteration of SP backbone structure. For example, associations have been found between SP chain length and cardiovascular disease, pain, diabetes, and dementia. This review will provide an overview of the processes that are known to regulate noncanonical SP accumulation, describe the clinical correlations reported for these molecules, and review the experimental evidence for the potential functional implications of their dysregulation. It is likely that further scrutiny of noncanonical SPs may provide new insight into pathophysiological processes, serve as useful biomarkers for disease, and lead to the design of novel therapeutic strategies.
Collapse
Affiliation(s)
- Brenda Wan Shing Lam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ting Yu Amelia Yam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Christopher P Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Memory Aging and Cognition Centre, Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mitchell K P Lai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Memory Aging and Cognition Centre, Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Wei-Yi Ong
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Deron R Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biology, San Diego State University, San Diego, CA, USA; American University of Health Sciences, Long Beach, CA, USA.
| |
Collapse
|
13
|
Hajdu T, Váradi T, Rebenku I, Kovács T, Szöllösi J, Nagy P. Comprehensive Model for Epidermal Growth Factor Receptor Ligand Binding Involving Conformational States of the Extracellular and the Kinase Domains. Front Cell Dev Biol 2020; 8:776. [PMID: 32850868 PMCID: PMC7431817 DOI: 10.3389/fcell.2020.00776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/23/2020] [Indexed: 12/03/2022] Open
Abstract
The epidermal growth factor (EGF) receptor (EGFR) undergoes ligand-dependent dimerization to initiate transmembrane signaling. Although crystallographic structures of the extracellular and kinase domains are available, ligand binding has not been quantitatively analyzed taking the influence of both domains into account. Here, we developed a model explicitly accounting for conformational changes of the kinase and extracellular domains, their dimerizations and ligand binding to monomeric and dimeric receptor species. The model was fitted to ligand binding data of suspended cells expressing receptors with active or inactive kinase conformations. Receptor dimers with inactive, symmetric configuration of the kinase domains exhibit positive cooperativity and very weak binding affinity for the first ligand, whereas dimers with active, asymmetric kinase dimers are characterized by negative cooperativity and subnanomolar binding affinity for the first ligand. The homodimerization propensity of EGFR monomers with active kinase domains is ∼100-times higher than that of dimers with inactive kinase domains. Despite this fact, constitutive, ligand-independent dimers are mainly generated from monomers with inactive kinase domains due to the excess of such monomers in the membrane. The experimental finding of increased positive cooperativity at high expression levels of EGFR was recapitulated by the model. Quantitative prediction of ligand binding to different receptor species revealed that EGF binds to receptor monomers and dimers in an expression-level dependent manner without significant recruitment of monomers to dimers upon EGF stimulation below the phase transition temperature of the membrane. Results of the fitting offer unique insight into the workings of the EGFR.
Collapse
Affiliation(s)
- Tímea Hajdu
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tímea Váradi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - István Rebenku
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tamás Kovács
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Szöllösi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| |
Collapse
|
14
|
Rasheduzzaman M, Kulasinghe A, Dolcetti R, Kenny L, Johnson NW, Kolarich D, Punyadeera C. Protein glycosylation in head and neck cancers: From diagnosis to treatment. Biochim Biophys Acta Rev Cancer 2020; 1874:188422. [PMID: 32853734 DOI: 10.1016/j.bbcan.2020.188422] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022]
Abstract
Glycosylation is the most common post-translational modification (PTM) of proteins. Malignant tumour cells frequently undergo an alteration in surface protein glycosylation. This phenomenon is also common in cancers of the head and neck, most of which are squamous cell carcinomas (HNSCC). It affects cell functions, including proliferation, motility and invasiveness, thus increasing the propensity to metastasise. HNSCC represents the sixth most frequent malignancy worldwide. These neoplasms, which arise from the mucous membranes of the various anatomical subsites of the upper aero-digestive tract, are heterogeneous in terms of aetiology and clinico-pathologic features. With current treatments, only about 50% of HNSCC patients survive beyond 5-years. Therefore, there is the pressing need to dissect NHSCC heterogeneity to inform treatment choices. In particular, reliable biomarkers of predictive and prognostic value are eagerly needed. This review describes the current state of the art and bio-pathological meaning of glycosylation signatures associated with HNSCC and explores the possible role of tumour specific glycoproteins as potential biomarkers and attractive therapeutic targets. We have also compiled data relating to altered glycosylation and the nature of glycoproteins as tools for the identification of circulating tumour cells (CTCs) in the new era of liquid biopsy.
Collapse
Affiliation(s)
- Mohammad Rasheduzzaman
- Saliva and Liquid Biopsy Translational Laboratory, The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia; Translational Research Institute, Woolloongabba, QLD, Australia
| | - Arutha Kulasinghe
- Saliva and Liquid Biopsy Translational Laboratory, The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia; Translational Research Institute, Woolloongabba, QLD, Australia
| | - Riccardo Dolcetti
- Translational Research Institute, Woolloongabba, QLD, Australia.; The University of Queensland Diamantina Institute, 37 Kent Street Woolloongabba, QLD 4102, Australia
| | - Liz Kenny
- Department of Radiation Oncology, Cancer Care Services, Royal Brisbane and Women's Hospital, Joyce Tweddell Building, Herston, QLD, 4029, Australia
| | - Newell W Johnson
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; Faculty of Dentistry, Oral and Craniofacial Sciences, King's College, London, United Kingdom
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD, Australia.
| | - Chamindie Punyadeera
- Saliva and Liquid Biopsy Translational Laboratory, The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia; Translational Research Institute, Woolloongabba, QLD, Australia..
| |
Collapse
|
15
|
Zhu H, Wang S, Liu D, Ding L, Chen C, Liu Y, Wu Z, Bollag R, Liu K, Alexander WM, Yin J, Ma C, Li L, Wang PG. Identifying Sialylation Linkages at the Glycopeptide Level by Glycosyltransferase Labeling Assisted Mass Spectrometry (GLAMS). Anal Chem 2020; 92:6297-6303. [PMID: 32271005 PMCID: PMC7750919 DOI: 10.1021/acs.analchem.9b05068] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Precise assignment of sialylation linkages at the glycopeptide level is of importance in bottom-up glycoproteomics and an indispensable step to understand the function of glycoproteins in pathogen-host interactions and cancer progression. Even though some efforts have been dedicated to the discrimination of α2,3/α2,6-sialylated isomers, unambiguous identification of sialoglycopeptide isomers is still needed. Herein, we developed an innovative glycosyltransferase labeling assisted mass spectrometry (GLAMS) strategy. After specific enzymatic labeling, oxonium ions from higher-energy C-trap dissociation (HCD) fragmentation of α2,3-sailoglycopeptides then generate unique reporters to distinctly differentiate those of α2,6-sailoglycopeptide isomers. With this strategy, a total of 1236 linkage-specific sialoglycopeptides were successfully identified from 161 glycoproteins in human serum.
Collapse
Affiliation(s)
- He Zhu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Shuaishuai Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ding Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Lang Ding
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Congcong Chen
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yunpeng Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Zhigang Wu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Roni Bollag
- Georgia Cancer Center, Augusta University, Augusta, Georgia 30912, United States
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, Georgia 30912, United States
| | - William Max Alexander
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jun Yin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Cheng Ma
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Lei Li
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Peng George Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| |
Collapse
|
16
|
Furukawa K, Ohmi Y, Yesmin F, Tajima O, Kondo Y, Zhang P, Hashimoto N, Ohkawa Y, Bhuiyan RH, Furukawa K. Novel Molecular Mechanisms of Gangliosides in the Nervous System Elucidated by Genetic Engineering. Int J Mol Sci 2020; 21:ijms21061906. [PMID: 32168753 PMCID: PMC7139306 DOI: 10.3390/ijms21061906] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/29/2020] [Accepted: 03/06/2020] [Indexed: 12/13/2022] Open
Abstract
Acidic glycosphingolipids, i.e., gangliosides, are predominantly and consistently expressed in nervous tissues of vertebrates at high levels. Therefore, they are considered to be involved in the development and function of nervous systems. Recent studies involving genetic engineering of glycosyltransferase genes have revealed novel aspects of the roles of gangliosides in the regulation of nervous tissues. In this review, novel findings regarding ganglioside functions and their modes of action elucidated mainly by studies of gene knockout mice are summarized. In particular, the roles of gangliosides in the regulation of lipid rafts to maintain the integrity of nervous systems are reported with a focus on the roles in the regulation of neuro-inflammation and neurodegeneration via complement systems. In addition, recent advances in studies of congenital neurological disorders due to genetic mutations of ganglioside synthase genes and also in the techniques for the analysis of ganglioside functions are introduced.
Collapse
Affiliation(s)
- Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan; (F.Y.); (O.T.); (P.Z.); (R.H.B.); (K.F.)
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan;
- Correspondence: ; Tel./Fax: +81-568-51-9512
| | - Yuhsuke Ohmi
- Department of Medical Technology, Chubu University College of Life and Health Sciences, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan;
| | - Farhana Yesmin
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan; (F.Y.); (O.T.); (P.Z.); (R.H.B.); (K.F.)
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan;
| | - Orie Tajima
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan; (F.Y.); (O.T.); (P.Z.); (R.H.B.); (K.F.)
| | - Yuji Kondo
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan;
| | - Pu Zhang
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan; (F.Y.); (O.T.); (P.Z.); (R.H.B.); (K.F.)
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan;
| | - Noboru Hashimoto
- Department of Tissue Regeneration, Tokushima University Graduate School of Biomedical Sciences, 3-18-5, Kuramoto-cho, Tokushima 770-8504, Japan;
| | - Yuki Ohkawa
- Department of Glycooncology, Osaka International Cancer Institute, Osaka 541-8567, Japan;
| | - Robiul H. Bhuiyan
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan; (F.Y.); (O.T.); (P.Z.); (R.H.B.); (K.F.)
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan; (F.Y.); (O.T.); (P.Z.); (R.H.B.); (K.F.)
| |
Collapse
|
17
|
Takeuchi R, Kambe M, Miyata M, Jeyadevan U, Tajima O, Furukawa K, Furukawa K. TNFα-signal and cAMP-mediated signals oppositely regulate melanoma- associated ganglioside GD3 synthase gene in human melanocytes. Sci Rep 2019; 9:14740. [PMID: 31611597 PMCID: PMC6791844 DOI: 10.1038/s41598-019-51333-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 09/26/2019] [Indexed: 12/17/2022] Open
Abstract
Analyses of expression and regulation of ganglioside synthases in melanocytes are important to understand roles of gangliosides in melanomagenesis. In this study, we analyzed the expression and regulatory mechanisms of glycosyltransferase genes responsible for ganglioside synthesis in normal melanocytes. We reported previously that culture supernatants of UVB-irradiated keratinocytes induced upregulation of ganglioside GD3 synthase gene in melanocytes, and mainly TNFα was responsible for it. Then, we found that elimination of dibutyryl cyclic AMP and IBMX from the medium also resulted in upregulation of the GD3 synthase gene. The addition of α-melanocyte-stimulating hormone which increases cAMP, to the medium led to a significant reduction in the GD3 synthase gene expression level, and a PKA inhibitor enhanced the GD3 synthase gene level. These results suggest that signals mediated via TNFα and cAMP oppositely regulate GD3 synthase gene expression in melanocytes. The results of an IKK inhibitor indicate the possibility that TNFα induces GD3 synthase gene expression via NF-κB signaling in melanocytes. When melanoma cells were treated by these factors, no fluctuation in the GD3 synthase gene expression level was observed, although an IKK inhibitor significantly suppressed it, suggesting that ganglioside synthase genes are regulated in distinct manners between melanocytes and melanomas.
Collapse
Affiliation(s)
- Rika Takeuchi
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Matsumoto 1200, Kasugai, Aichi, 487-8501, Japan
| | - Mariko Kambe
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Matsumoto 1200, Kasugai, Aichi, 487-8501, Japan
| | - Maiko Miyata
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Matsumoto 1200, Kasugai, Aichi, 487-8501, Japan
| | - Upul Jeyadevan
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Matsumoto 1200, Kasugai, Aichi, 487-8501, Japan
| | - Orie Tajima
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Matsumoto 1200, Kasugai, Aichi, 487-8501, Japan
| | - Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Matsumoto 1200, Kasugai, Aichi, 487-8501, Japan
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Matsumoto 1200, Kasugai, Aichi, 487-8501, Japan.
| |
Collapse
|
18
|
Hamamura K, Hamajima K, Yo S, Mishima Y, Furukawa K, Uchikawa M, Kondo Y, Mori H, Kondo H, Tanaka K, Miyazawa K, Goto S, Togari A. Deletion of Gb3 Synthase in Mice Resulted in the Attenuation of Bone Formation via Decrease in Osteoblasts. Int J Mol Sci 2019; 20:ijms20184619. [PMID: 31540393 PMCID: PMC6769804 DOI: 10.3390/ijms20184619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022] Open
Abstract
Glycosphingolipids are known to play a role in developing and maintaining the integrity of various organs and tissues. Among glycosphingolipids, there are several reports on the involvement of gangliosides in bone metabolism. However, there have been no reports on the presence or absence of expression of globo-series glycosphingolipids in osteoblasts and osteoclasts, and the involvement of their glycosphingolipids in bone metabolism. In the present study, we investigated the presence or absence of globo-series glycosphingolipids such as Gb3 (globotriaosylceramide), Gb4 (globoside), and Gb5 (galactosyl globoside) in osteoblasts and osteoclasts, and the effects of genetic deletion of Gb3 synthase, which initiates the synthesis of globo-series glycosphingolipids on bone metabolism. Among Gb3, Gb4, and Gb5, only Gb4 was expressed in osteoblasts. However, these glycosphingolipids were not expressed in pre-osteoclasts and osteoclasts. Three-dimensional micro-computed tomography (3D-μCT) analysis revealed that femoral cancellous bone mass in Gb3 synthase-knockout (Gb3S KO) mice was lower than that in wild type (WT) mice. Calcein double labeling also revealed that bone formation in Gb3S KO mice was significantly lower than that in WT mice. Consistent with these results, the deficiency of Gb3 synthase in mice decreased the number of osteoblasts on the bone surface, and suppressed mRNA levels of osteogenic differentiation markers. On the other hand, osteoclast numbers on the bone surface and mRNA levels of osteoclast differentiation markers in Gb3S KO mice did not differ from WT mice. This study demonstrated that deletion of Gb3 synthase in mice decreases bone mass via attenuation of bone formation.
Collapse
Affiliation(s)
- Kazunori Hamamura
- Department of Pharmacology, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
| | - Kosuke Hamajima
- Department of Pharmacology, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
- Department of Orthodontics, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
| | - Shoyoku Yo
- Department of Pharmacology, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
- Department of Orthodontics, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
| | - Yoshitaka Mishima
- Department of Pharmacology, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
- Department of Orthodontics, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
| | - Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Aichi 487-8501, Japan.
| | - Makoto Uchikawa
- Japanese Red Cross Tokyo Blood Center, Tokyo 162-8639, Japan.
| | - Yuji Kondo
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya 464-8650, Japan.
| | - Hironori Mori
- Department of Pharmacology, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
- Department of Orthodontics, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
| | - Hisataka Kondo
- Department of Pharmacology, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
| | - Kenjiro Tanaka
- Department of Pharmacology, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
| | - Ken Miyazawa
- Department of Orthodontics, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
| | - Shigemi Goto
- Department of Orthodontics, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
| | - Akifumi Togari
- Department of Pharmacology, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
| |
Collapse
|
19
|
Furukawa K, Ohmi Y, Ohkawa Y, Bhuiyan RH, Zhang P, Tajima O, Hashimoto N, Hamamura K, Furukawa K. New era of research on cancer-associated glycosphingolipids. Cancer Sci 2019; 110:1544-1551. [PMID: 30895683 PMCID: PMC6501054 DOI: 10.1111/cas.14005] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/13/2019] [Accepted: 03/19/2019] [Indexed: 12/31/2022] Open
Abstract
Cancer‐associated glycosphingolipids have been used as markers for diagnosis and targets for immunotherapy of malignant tumors. Recent progress in the analysis of their implications in the malignant properties of cancer cells revealed that cancer‐associated glycosphingolipids are not only tumor markers, but also functional molecules regulating various signals introduced by membrane microdomains, lipid rafts. In particular, a novel approach, enzyme‐mediated activation of radical sources combined with mass spectrometry, has enabled us to clarify the mechanisms by which cancer‐associated glycosphingolipids regulate cell signals based on the interaction with membrane molecules and formation of molecular complexes on the cell surface. Novel findings obtained from these approaches are now providing us with insights into the development of new anticancer therapies targeting membrane molecular complexes consisting of cancer‐associated glycolipids and their associated membrane molecules. Thus, a new era of cancer‐associated glycosphingolipids has now begun.
Collapse
Affiliation(s)
- Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuhsuke Ohmi
- Department of Medical Technology, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Yuki Ohkawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Robiul H Bhuiyan
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Pu Zhang
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Orie Tajima
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Noboru Hashimoto
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Anatomy, Faculty of Medical and Dental Sciences, Tokushima University, Tokushima, Japan
| | - Kazunori Hamamura
- Department of Pharmacology, School of Dentistry, Aichi-Gakuin University, Nagoya, Japan
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| |
Collapse
|
20
|
FURUKAWA K, OHMI Y, KONDO Y, BHUIYAN RH, TAJIMA O, ZHANG P, OHKAWA Y, FURUKAWA K. Elucidation of the enigma of glycosphingolipids in the regulation of inflammation and degeneration - Great progress over the last 70 years. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2019; 95:136-149. [PMID: 30853699 PMCID: PMC6541724 DOI: 10.2183/pjab.95.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Since globotetraosylceramide was defined as a major glycosphingolipid in human erythrocytes, various glycolipids have been found in normal cells and diseased organs. However, the implications of their polymorphic structures in the function of individual cells and tissues have not been clarified. Genetic manipulation of glycosphingolipids in cultured cells and experimental animals has enabled us to substantially elucidate their roles. In fact, great progress has been achieved in the last 70 years in revealing that glycolipids are essential in the maintenance of integrity of nervous tissues and other organs. Furthermore, the correct composition of glycosphingolipids has been shown to be critical for the protection against inflammation and degeneration. Here, we summarized historic information and current knowledge about glycosphingolipids, with a focus on their involvement in inflammation and degeneration. This topic is significant for understanding the biological responses to various stresses, because glycosphingolipids play roles in the interaction with various intrinsic and extrinsic factors. These findings are also important for the application of therapeutic interventions of various diseases.
Collapse
Affiliation(s)
- Koichi FURUKAWA
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuhsuke OHMI
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Yuji KONDO
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Robiul H. BHUIYAN
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Orie TAJIMA
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Pu ZHANG
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuki OHKAWA
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Keiko FURUKAWA
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| |
Collapse
|
21
|
Ohmi Y, Kambe M, Ohkawa Y, Hamamura K, Tajima O, Takeuchi R, Furukawa K, Furukawa K. Differential roles of gangliosides in malignant properties of melanomas. PLoS One 2018; 13:e0206881. [PMID: 30462668 PMCID: PMC6248923 DOI: 10.1371/journal.pone.0206881] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/22/2018] [Indexed: 12/18/2022] Open
Abstract
Ganglioside GD3 is widely expressed in human malignant melanomas, and has been reported to be involved in the increased cell proliferation and invasion. In this study, we established GM3-, GM2-, GM1-, GD3-, or GD2-expressing melanoma cell lines by transfecting cDNAs of glyscosyltransferases, and effects of individual gangliosides on the cell phenotypes and signals were examined. The phenotypes of established ganglioside-expressing cells were quite different, i.e. cell growth increased as following order; GD2+, GD3+ > GM1+, GM2+, GM3+ cells. Cell invasion activity increased as GD3+ ≧ GM2+ > GM1+, GM3+, GD2+ cells. Intensity of cell adhesion to collagen I (CL-I) and spreading increased as GD2+ >> GD3+, GM1+ > GM2+, GM3+ cells. In particular, cell adhesion of GD2+ cells was markedly strong. As for cell migration velocity, GD2+ cells were slower than all other cells. The immunocytostaining revealed close localization of gangliosides and F-actin in lamellipodia. Immunoblotting of phosphorylated p130Cas and paxillin by serum treatment reveled that these phosphorylations were more increased in GD3+ cells than in GD2+ or GM3+ cells, while phosphorylation of Akt underwent similarly increased phosphorylation between GD3+ and GD2+ cells compared with GM3+ cells. While GD2 and GD3 enhanced cell growth, GD3 might also contribute in cell invasion. On the other hand, GD2 might contribute in the solid fixation of melanoma cells at metastasized sites. These results suggested that individual gangliosides exert distinct roles in the different aspects of melanomas by differentially regulating cytoskeletons and signaling molecules.
Collapse
Affiliation(s)
- Yuhsuke Ohmi
- Department of Clinical Engineering, Chubu University College of Life and Health Sciences, Kasugai, Aichi, Japan
| | - Mariko Kambe
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Aichi, Japan
| | - Yuki Ohkawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Aichi, Japan
| | - Kazunori Hamamura
- Department of Pharmacology, School of Dentistry, Aichigakuin University, Nagoya, Japan
| | - Orie Tajima
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Aichi, Japan
| | - Rika Takeuchi
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Aichi, Japan
| | - Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Aichi, Japan
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Aichi, Japan
- * E-mail:
| |
Collapse
|
22
|
van Beusekom B, Lütteke T, Joosten RP. Making glycoproteins a little bit sweeter with PDB-REDO. Acta Crystallogr F Struct Biol Commun 2018; 74:463-472. [PMID: 30084395 PMCID: PMC6096482 DOI: 10.1107/s2053230x18004016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/07/2018] [Indexed: 02/04/2023] Open
Abstract
Glycosylation is one of the most common forms of protein post-translational modification, but is also the most complex. Dealing with glycoproteins in structure model building, refinement, validation and PDB deposition is more error-prone than dealing with nonglycosylated proteins owing to limitations of the experimental data and available software tools. Also, experimentalists are typically less experienced in dealing with carbohydrate residues than with amino-acid residues. The results of the reannotation and re-refinement by PDB-REDO of 8114 glycoprotein structure models from the Protein Data Bank are analyzed. The positive aspects of 3620 reannotations and subsequent refinement, as well as the remaining challenges to obtaining consistently high-quality carbohydrate models, are discussed.
Collapse
Affiliation(s)
- Bart van Beusekom
- Division of Biochemistry, Netherlands Cancer Insitute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Frankfurter Strasse 100, 35392 Giessen, Germany
| | - Robbie P. Joosten
- Division of Biochemistry, Netherlands Cancer Insitute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| |
Collapse
|
23
|
Li WW, Yang Y, Dai QG, Lin LL, Xie T, He LL, Tao JL, Shan JJ, Wang SC. Non-invasive urinary metabolomic profiles discriminate biliary atresia from infantile hepatitis syndrome. Metabolomics 2018; 14:90. [PMID: 30830373 DOI: 10.1007/s11306-018-1387-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/14/2018] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Neonatal cholestatic disorders are a group of hepatobiliary diseases occurring in the first 3 months of life. The most common causes of neonatal cholestasis are infantile hepatitis syndrome (IHS) and biliary atresia (BA). The clinical manifestations of the two diseases are too similar to distinguish them. However, early detection is very important in improving the clinical outcome of BA. Currently, a liver biopsy is the only proven and effective method used to differentially diagnose these two similar diseases in the clinic. However, this method is invasive. Therefore, sensitive and non-invasive biomarkers are needed to effectively differentiate between BA and IHS. We hypothesized that urinary metabolomics can produce unique metabolite profiles for BA and IHS. OBJECTIVES The aim of this study was to characterize urinary metabolomic profiles in infants with BA and IHS, and to identify differences among infants with BA, IHS, and normal controls (NC). METHODS Urine samples along with patient characteristics were obtained from 25 BA, 38 IHS, and 38 NC infants. A non-targeted gas chromatography-mass spectrometry (GC-MS) metabolomics method was used in conjunction with orthogonal partial least squares discriminant analysis (OPLS-DA) to explore the metabolomic profiles of BA, IHS, and NC infants. RESULTS In total, 41 differentially expressed metabolites between BA vs. NC, IHS vs. NC, and BA vs. IHS were identified. N-acetyl-D-mannosamine and alpha-aminoadipic acid were found to be highly accurate at distinguishing between BA and IHS. CONCLUSIONS BA and IHS infants have specific urinary metabolomic profiles. The results of our study underscore the clinical potential of metabolomic profiling to uncover metabolic changes that could be used to discriminate BA from IHS.
Collapse
Affiliation(s)
- Wei-Wei Li
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yan Yang
- TCM Department, Beijing Children's Hospital Affiliated to Capital Medical University, Beijing, China
| | - Qi-Gang Dai
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Li-Li Lin
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tong Xie
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China
| | - Li-Li He
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jia-Lei Tao
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Jun Shan
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Shou-Chuan Wang
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| |
Collapse
|
24
|
Dewald JH, Cavdarli S, Steenackers A, Delannoy CP, Mortuaire M, Spriet C, Noël M, Groux-Degroote S, Delannoy P. TNF differentially regulates ganglioside biosynthesis and expression in breast cancer cell lines. PLoS One 2018; 13:e0196369. [PMID: 29698439 PMCID: PMC5919650 DOI: 10.1371/journal.pone.0196369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/11/2018] [Indexed: 12/26/2022] Open
Abstract
Gangliosides are glycosphingolipids concentrated in glycolipid-enriched membrane microdomains. Mainly restricted to the nervous system in healthy adult, complex gangliosides such as GD3 and GD2 have been shown to be involved in aggressiveness and metastasis of neuro-ectoderm derived tumors such as melanoma and neuroblastoma. GD3 synthase (GD3S), the key enzyme that controls the biosynthesis of complex gangliosides, was shown to be over-expressed in Estrogen Receptor (ER)-negative breast cancer tumors, and associated with a decreased overall survival of patients. We previously demonstrated that GD3S expression in ER-negative breast cancer cells induced a proliferative phenotype and an increased tumor growth. In addition, our results clearly indicate that Tumor Necrosis Factor (TNF) induced GD3S over-expression in breast cancer cells via NFκB pathway. In this study, we analyzed the effect of TNF on ganglioside biosynthesis and expression in breast cancer cells from different molecular subtypes. We showed that TNF up-regulated the expression of GD3S in MCF-7 and Hs578T cells, whereas no change was observed for MDA-MB-231. We also showed that TNF induced an increased expression of complex gangliosides at the cell surface of a small proportion of MCF-7 cells. These results demonstrate that TNF differentially regulates gangliosides expression in breast cancer cell lines and establish a possible link between inflammation at the tumor site environment, expression of complex gangliosides and tumor development.
Collapse
Affiliation(s)
- Justine H. Dewald
- University of Lille, Structural and Functional Glycobiology Unit, UMR CNRS 8576, Lille, France
| | - Sumeyye Cavdarli
- University of Lille, Structural and Functional Glycobiology Unit, UMR CNRS 8576, Lille, France
| | - Agata Steenackers
- University of Lille, Structural and Functional Glycobiology Unit, UMR CNRS 8576, Lille, France
| | - Clément P. Delannoy
- University of Lille, Structural and Functional Glycobiology Unit, UMR CNRS 8576, Lille, France
| | - Marlène Mortuaire
- University of Lille, Structural and Functional Glycobiology Unit, UMR CNRS 8576, Lille, France
| | - Corentin Spriet
- University of Lille, Bio Imaging Center Lille, Lille, France
| | - Maxence Noël
- University of Lille, Structural and Functional Glycobiology Unit, UMR CNRS 8576, Lille, France
| | - Sophie Groux-Degroote
- University of Lille, Structural and Functional Glycobiology Unit, UMR CNRS 8576, Lille, France
| | - Philippe Delannoy
- University of Lille, Structural and Functional Glycobiology Unit, UMR CNRS 8576, Lille, France
- * E-mail:
| |
Collapse
|
25
|
Gangliosides in Inflammation and Neurodegeneration. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 156:265-287. [PMID: 29747817 DOI: 10.1016/bs.pmbts.2018.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Gangliosides play roles in the regulation of cell signaling that are mediated via membrane microdomains, lipid rafts. In this review, functions of gangliosides in the maintenance of nervous systems with a focus on regulation of inflammation and neurodegeneration are addressed. During analyses of various ganglioside-lacking mutant mice, we demonstrated that nervous tissues exhibited inflammatory reactions and subsequent neurodegeneration. Among inflammation-related genes, factors of the complement system showed up-regulation with aging. Analyses of architectures and compositions of lipid rafts in nervous tissues from these mutant mice revealed that dysfunctions of complement regulatory proteins based on disrupted lipid rafts were main factors to induce the inflammatory reactions resulting in neurodegeneration. Ganglioside changes in development and senescence, and implication of them in the integrity of cell membranes and cellular phenotypes in physiological and pathological conditions including Alzheimer disease have been summarized. Novel directions to further analyze mechanisms for ganglioside functions in membrane microdomains have been also addressed.
Collapse
|
26
|
Rouhanifard SH, Lopez Aguilar A, Meng L, Moremen KW, Wu P. Engineered Glycocalyx Regulates Stem Cell Proliferation in Murine Crypt Organoids. Cell Chem Biol 2018; 25:439-446.e5. [PMID: 29429899 DOI: 10.1016/j.chembiol.2018.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/30/2017] [Accepted: 01/09/2018] [Indexed: 12/17/2022]
Abstract
At the base of the intestinal crypt, long-lived Lgr5+ stem cells are intercalated by Paneth cells that provide essential niche signals for stem cell maintenance. This unique epithelial anatomy makes the intestinal crypt one of the most accessible models for the study of adult stem cell biology. The glycosylation patterns of this compartment are poorly characterized, and the impact of glycans on stem cell differentiation remains largely unexplored. We find that Paneth cells, but not Lgr5+ stem cells, express abundant terminal N-acetyllactosamine (LacNAc). Employing an enzymatic method to edit glycans in cultured crypt organoids, we assess the functional role of LacNAc in the intestinal crypt. We discover that blocking access to LacNAc on Paneth cells leads to hyperproliferation of the neighboring Lgr5+ stem cells, which is accompanied by the downregulation of genes that are known as negative regulators of proliferation.
Collapse
Affiliation(s)
- Sara H Rouhanifard
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Aime Lopez Aguilar
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lu Meng
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Peng Wu
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
27
|
Groux-Degroote S, Rodríguez-Walker M, Dewald JH, Daniotti JL, Delannoy P. Gangliosides in Cancer Cell Signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 156:197-227. [DOI: 10.1016/bs.pmbts.2017.10.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
28
|
In Vivo Synthesis of Polyhydroxylated Compounds from a “Hidden Reservoir” of Toxic Aldehyde Species. ChemCatChem 2017. [DOI: 10.1002/cctc.201700469] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
29
|
Role of Cytokine-Induced Glycosylation Changes in Regulating Cell Interactions and Cell Signaling in Inflammatory Diseases and Cancer. Cells 2016; 5:cells5040043. [PMID: 27916834 PMCID: PMC5187527 DOI: 10.3390/cells5040043] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/23/2016] [Accepted: 11/24/2016] [Indexed: 12/17/2022] Open
Abstract
Glycosylation is one of the most important modifications of proteins and lipids, and cell surface glycoconjugates are thought to play important roles in a variety of biological functions including cell-cell and cell-substrate interactions, bacterial adhesion, cell immunogenicity and cell signaling. Alterations of glycosylation are observed in number of diseases such as cancer and chronic inflammation. In that context, pro-inflammatory cytokines have been shown to modulate cell surface glycosylation by regulating the expression of glycosyltransferases involved in the biosynthesis of carbohydrate chains. These changes in cell surface glycosylation are also known to regulate cell signaling and could contribute to disease pathogenesis. This review summarizes our current knowledge of the glycosylation changes induced by pro-inflammatory cytokines, with a particular focus on cancer and cystic fibrosis, and their consequences on cell interactions and signaling.
Collapse
|
30
|
Ji S, Tokizane K, Ohkawa Y, Ohmi Y, Banno R, Okajima T, Kiyama H, Furukawa K, Furukawa K. Increased a-series gangliosides positively regulate leptin/Ob receptor-mediated signals in hypothalamus of GD3 synthase-deficient mice. Biochem Biophys Res Commun 2016; 479:453-460. [DOI: 10.1016/j.bbrc.2016.09.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/15/2016] [Indexed: 12/14/2022]
|
31
|
Diethylaminoethyl Sepharose (DEAE-Sepharose) microcolumn for enrichment of glycopeptides. Anal Bioanal Chem 2016; 409:511-518. [DOI: 10.1007/s00216-016-9937-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 08/30/2016] [Accepted: 09/08/2016] [Indexed: 12/13/2022]
|
32
|
Binnington B, Nguyen L, Kamani M, Hossain D, Marks DL, Budani M, Lingwood CA. Inhibition of Rab prenylation by statins induces cellular glycosphingolipid remodeling. Glycobiology 2016; 26:166-80. [PMID: 26405105 PMCID: PMC4691287 DOI: 10.1093/glycob/cwv084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 09/11/2015] [Accepted: 09/14/2015] [Indexed: 12/17/2022] Open
Abstract
Statins, which specifically inhibit HMG Co-A reductase, the rate-limiting step of cholesterol biosynthesis, are widely prescribed to reduce serum cholesterol and cardiac risk, but many other effects are seen. We now show an effect of these drugs to induce profound changes in the step-wise synthesis of glycosphingolipids (GSLs) in the Golgi. Glucosylceramide (GlcCer) was increased several-fold in all cell lines tested, demonstrating a widespread effect. Additionally, de novo or elevated lactotriaosylceramide (Lc3Cer; GlcNAcβ1-3Galβ1-4GlcCer) synthesis was observed in 70%. Western blot showed that GlcCer synthase (GCS) was elevated by statins, and GCS and Lc3Cer synthase (Lc3S) activities were increased; however, transcript was elevated for Lc3S only. Supplementation with the isoprenoid precursor, geranylgeranyl pyrophosphate (GGPP), a downstream product of HMG Co-A reductase, reversed statin-induced glycosyltransferase and GSL elevation. The Rab geranylgeranyl transferase inhibitor 3-PEHPC, but not specific inhibitors of farnesyl transferase, or geranylgeranyl transferase I, was sufficient to replicate statin-induced GlcCer and Lc3Cer synthesis, supporting a Rab prenylation-dependent mechanism. While total cholesterol was unaffected, the trans-Golgi network (TGN) cholesterol pool was dissipated and medial Golgi GCS partially relocated by statins. GSL-dependent vesicular retrograde transport of Verotoxin and cholera toxin to the Golgi/endoplasmic reticulum were blocked after statin or 3-PEHPC treatment, suggesting aberrant, prenylation-dependent vesicular traffic as a basis of glycosyltransferase increase and GSL remodeling. These in vitro studies indicate a previously unreported link between Rab prenylation and regulation of GCS activity and GlcCer metabolism.
Collapse
Affiliation(s)
- Beth Binnington
- Research Institute, Program in Molecular Structure and Function, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 1X8, Canada
| | - Long Nguyen
- Research Institute, Program in Molecular Structure and Function, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 1X8, Canada
| | - Mustafa Kamani
- Research Institute, Program in Molecular Structure and Function, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 1X8, Canada Department of Biochemistry
| | - Delowar Hossain
- Research Institute, Program in Molecular Structure and Function, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 1X8, Canada
| | - David L Marks
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
| | - Monique Budani
- Research Institute, Program in Molecular Structure and Function, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 1X8, Canada Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Clifford A Lingwood
- Research Institute, Program in Molecular Structure and Function, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 1X8, Canada Department of Biochemistry Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
33
|
Hecht ES, Scholl EH, Walker SH, Taylor AD, Cliby WA, Motsinger-Reif AA, Muddiman DC. Relative Quantification and Higher-Order Modeling of the Plasma Glycan Cancer Burden Ratio in Ovarian Cancer Case-Control Samples. J Proteome Res 2015; 14:4394-401. [PMID: 26347193 DOI: 10.1021/acs.jproteome.5b00703] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
An early-stage, population-wide biomarker for ovarian cancer (OVC) is essential to reverse its high mortality rate. Aberrant glycosylation by OVC has been reported, but studies have yet to identify an N-glycan with sufficiently high specificity. We curated a human biorepository of 82 case-control plasma samples, with 27%, 12%, 46%, and 15% falling across stages I-IV, respectively. For relative quantitation, glycans were analyzed by the individuality normalization when labeling with glycan hydrazide tags (INLIGHT) strategy for enhanced electrospray ionization, MS/MS analysis. Sixty-three glycan cancer burden ratios (GBRs), defined as the log10 ratio of the case-control extracted ion chromatogram abundances, were calculated above the limit of detection. The final GBR models, built using stepwise forward regression, included three significant terms: OVC stage, normalized mean GBR, and tag chemical purity; glycan class, fucosylation, or sialylation were not significant variables. After Bonferroni correction, seven N-glycans were identified as significant (p < 0.05), and after false discovery rate correction, an additional four glycans were determined to be significant (p < 0.05), with one borderline (p = 0.05). For all N-glycans, the vectors of the effects from stages II-IV were sequentially reversed, suggesting potential biological changes in OVC morphology or in host response.
Collapse
Affiliation(s)
| | | | | | | | - William A Cliby
- Division of Gynecologic Surgery, Mayo Clinic , Rochester, Minnesota 55905, United States
| | | | | |
Collapse
|
34
|
Szekrenyi A, Garrabou X, Parella T, Joglar J, Bujons J, Clapés P. Asymmetric assembly of aldose carbohydrates from formaldehyde and glycolaldehyde by tandem biocatalytic aldol reactions. Nat Chem 2015; 7:724-9. [DOI: 10.1038/nchem.2321] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 07/08/2015] [Indexed: 01/11/2023]
|
35
|
Gene Signature of Human Oral Mucosa Fibroblasts: Comparison with Dermal Fibroblasts and Induced Pluripotent Stem Cells. BIOMED RESEARCH INTERNATIONAL 2015; 2015:121575. [PMID: 26339586 PMCID: PMC4538314 DOI: 10.1155/2015/121575] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/03/2015] [Accepted: 04/10/2015] [Indexed: 01/27/2023]
Abstract
Oral mucosa is a useful material for regeneration therapy with the advantages of its accessibility and versatility regardless of age and gender. However, little is known about the molecular characteristics of oral mucosa. Here we report the first comparative profiles of the gene signatures of human oral mucosa fibroblasts (hOFs), human dermal fibroblasts (hDFs), and hOF-derived induced pluripotent stem cells (hOF-iPSCs), linking these with biological roles by functional annotation and pathway analyses. As a common feature of fibroblasts, both hOFs and hDFs expressed glycolipid metabolism-related genes at higher levels compared with hOF-iPSCs. Distinct characteristics of hOFs compared with hDFs included a high expression of glycoprotein genes, involved in signaling, extracellular matrix, membrane, and receptor proteins, besides a low expression of HOX genes, the hDFs-markers. The results of the pathway analyses indicated that tissue-reconstructive, proliferative, and signaling pathways are active, whereas senescence-related genes in p53 pathway are inactive in hOFs. Furthermore, more than half of hOF-specific genes were similarly expressed to those of hOF-iPSC genes and might be controlled by WNT signaling. Our findings demonstrated that hOFs have unique cellular characteristics in specificity and plasticity. These data may provide useful insight into application of oral fibroblasts for direct reprograming.
Collapse
|
36
|
Ohkawa Y, Momota H, Kato A, Hashimoto N, Tsuda Y, Kotani N, Honke K, Suzumura A, Furukawa K, Ohmi Y, Natsume A, Wakabayashi T, Furukawa K. Ganglioside GD3 Enhances Invasiveness of Gliomas by Forming a Complex with Platelet-derived Growth Factor Receptor α and Yes Kinase. J Biol Chem 2015; 290:16043-58. [PMID: 25940087 DOI: 10.1074/jbc.m114.635755] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Indexed: 11/06/2022] Open
Abstract
There have been a few studies on the ganglioside expression in human glioma tissues. However, the role of these gangliosides such as GD3 and GD2 has not been well understood. In this study we employed a genetically engineered mouse model of glioma to clarify the functions of GD3 in gliomas. Forced expression of platelet-derived growth factor B in cultured astrocytes derived from p53-deficient mice resulted in the expression of GD3 and GD2. GD3-positive astrocytes exhibited increased cell growth and invasion activities along with elevated phosphorylation of Akt and Yes kinase. By enzyme-mediated activation of radical sources reaction and mass spectrometry, we identified PDGF receptor α (PDGFRα) as a GD3-associated molecule. GD3-positive astrocytes showed a significant amount of PDGFRα in glycolipid-enriched microdomains/rafts compared with GD3-negative cells. Src kinase family Yes was co-precipitated with PDGFRα, and its pivotal role in the increased cell invasion of GD3-positive astrocytes was demonstrated by silencing with anti-Yes siRNA. Direct association between PDGFRα and GD3 was also shown, suggesting that GD3 forms ternary complex with PDGFRα and Yes. The fact that GD3, PDGFRα, and activated Yes were colocalized in lamellipodia and the edge of tumors in cultured cells and glioma tissues, respectively, suggests that GD3 induced by platelet-derived growth factor B enhances PDGF signals in glycolipid-enriched microdomain/rafts, leading to the promotion of malignant phenotypes such as cell proliferation and invasion in gliomas.
Collapse
Affiliation(s)
- Yuki Ohkawa
- From the Department of Biochemistry II, the Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan, the Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | - Hiroyuki Momota
- the Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan
| | - Akira Kato
- the Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan
| | | | | | - Norihiro Kotani
- the Department of Biochemistry, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Koichi Honke
- the Department of Biochemistry, Kochi University Medical School, Kohasu, Okou-cho, Nankoku, Kochi 783-8505, Japan
| | - Akio Suzumura
- the Department of Neuroimmunology, Research Institute of Environmental Medicine, Nagoya University, Furou-cho, Chikusa-ku, Nagoya 464-8601, Japan, and
| | - Keiko Furukawa
- From the Department of Biochemistry II, the Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | | | - Atsushi Natsume
- the Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan
| | - Toshihiko Wakabayashi
- the Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan
| | - Koichi Furukawa
- From the Department of Biochemistry II, the Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| |
Collapse
|
37
|
Regulatory function of glycosphingolipids in the inflammation and degeneration. Arch Biochem Biophys 2015; 571:58-65. [PMID: 25688919 DOI: 10.1016/j.abb.2015.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/19/2015] [Accepted: 02/09/2015] [Indexed: 12/26/2022]
Abstract
Recent progress in the biological sciences has revealed that a number of extrinsic and intrinsic environmental factors may cause chronic inflammation. When these insults are persistent or intermittently repeated, regardless of extrinsic or intrinsic origins, homeostasis of our bodies would be disturbed and undergo long-term impact. These situations might give rise to chronic inflammation, leading to various diseases as results of accumulative effects of various inflammatory reactions. Complex carbohydrates expressed mainly on the cell surface have been demonstrated to play roles in fine-tuning of various biological processes to maintain homeostasis of cells, organs and our bodies. When abnormal physicochemical insults and harmful pathogens invade, the fine-tuning including modification of the glycosylation patterns is continuously exerted. Therefore, defects in the proper response with proper glycosylation lead to chronic inflammation and subsequent deterioration of individual tissues and organs. Genetic depletion of sialic acid-containing glycolipids, gangliosides resulted in the inflammation of CNS and neurodegeneration. Lactosylceramide was also reported to mediate neuroinflammation, leading to chronic inflammatory diseases. Defects of globoseries glycolipids resulted in the increased sensitivity to LPS toxicity. Thus, possibilities that manipulation of synthesis and expression of glycosphingolipids may be applicable for the disease control are now proposed.
Collapse
|
38
|
Xu X, Ng SM, Hassouna E, Warrington A, Oh SH, Rodriguez M. Human-derived natural antibodies: biomarkers and potential therapeutics. FUTURE NEUROLOGY 2015; 10:25-39. [PMID: 25678860 DOI: 10.2217/fnl.14.62] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The immune system generates antibodies and antigen-specific T-cells as basic elements of the immune networks that differentiate self from non-self in a finely tuned manner. The antigen-specific nature of immune responses ensures that normal immune activation contains non-self when tolerating self. Here we review the B-1 subset of lymphocytes which produce self-reactive antibodies. By analyzing the IgM class of natural antibodies that recognize antigens from the nervous system, we emphasize that natural antibodies are biomarkers of how the immune system monitors the host. The immune response activated against self can be detrimental when triggered in an autoimmune genetic background. In contrast, tuning immune activity with natural antibodies is a potential therapeutic strategy.
Collapse
Affiliation(s)
- Xiaohua Xu
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Sher May Ng
- School of Clinical Medicine, University Of Cambridge, Hills Rd, Cambridge CB2 0SP, UK
| | - Eamonn Hassouna
- Department of General Medicine, Charles University Hradec Kralove Faculty, Prague, Czech Republic
| | - Arthur Warrington
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Sang-Hyun Oh
- Laboratory of Nanostructures & Biosensing, Department of Electrical & Computer Engineering, University of Minnesota, Minneapolis, MN 55455, USA ; Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Moses Rodriguez
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA ; Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| |
Collapse
|
39
|
Zhu Z, Su X, Go EP, Desaire H. New glycoproteomics software, GlycoPep Evaluator, generates decoy glycopeptides de novo and enables accurate false discovery rate analysis for small data sets. Anal Chem 2014; 86:9212-9. [PMID: 25137014 PMCID: PMC4165450 DOI: 10.1021/ac502176n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Glycoproteins
are biologically significant large molecules that
participate in numerous cellular activities. In order to obtain site-specific
protein glycosylation information, intact glycopeptides, with the
glycan attached to the peptide sequence, are characterized by tandem
mass spectrometry (MS/MS) methods such as collision-induced dissociation
(CID) and electron transfer dissociation (ETD). While several emerging
automated tools are developed, no consensus is present in the field
about the best way to determine the reliability of the tools and/or
provide the false discovery rate (FDR). A common approach to calculate
FDRs for glycopeptide analysis, adopted from the target-decoy strategy
in proteomics, employs a decoy database that is created based on the
target protein sequence database. Nonetheless, this approach is not
optimal in measuring the confidence of N-linked glycopeptide
matches, because the glycopeptide data set is considerably smaller
compared to that of peptides, and the requirement of a consensus sequence
for N-glycosylation further limits the number of
possible decoy glycopeptides tested in a database search. To address
the need to accurately determine FDRs for automated glycopeptide assignments,
we developed GlycoPep Evaluator (GPE), a tool that helps to measure
FDRs in identifying glycopeptides without using a decoy database.
GPE generates decoy glycopeptides de novo for every target glycopeptide,
in a 1:20 target-to-decoy ratio. The decoys, along with target glycopeptides,
are scored against the ETD data, from which FDRs can be calculated
accurately based on the number of decoy matches and the ratio of the
number of targets to decoys, for small data sets. GPE is freely accessible
for download and can work with any search engine that interprets ETD
data of N-linked glycopeptides. The software is provided
at https://desairegroup.ku.edu/research.
Collapse
Affiliation(s)
- Zhikai Zhu
- Department of Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
| | | | | | | |
Collapse
|
40
|
Pantazaka E, Papadimitriou E. Chondroitin sulfate-cell membrane effectors as regulators of growth factor-mediated vascular and cancer cell migration. Biochim Biophys Acta Gen Subj 2014; 1840:2643-50. [DOI: 10.1016/j.bbagen.2014.01.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 01/02/2014] [Accepted: 01/03/2014] [Indexed: 12/18/2022]
|
41
|
Ruiz-May E, Hucko S, Howe KJ, Zhang S, Sherwood RW, Thannhauser TW, Rose JKC. A comparative study of lectin affinity based plant N-glycoproteome profiling using tomato fruit as a model. Mol Cell Proteomics 2014; 13:566-79. [PMID: 24198434 PMCID: PMC3916654 DOI: 10.1074/mcp.m113.028969] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 10/20/2013] [Indexed: 12/22/2022] Open
Abstract
Lectin affinity chromatography (LAC) can provide a valuable front-end enrichment strategy for the study of N-glycoproteins and has been used to characterize a broad range eukaryotic N-glycoproteomes. Moreover, studies with mammalian systems have suggested that the use of multiple lectins with different affinities can be particularly effective. A multi-lectin approach has also been reported to provide a significant benefit for the analysis of plant N-glycoproteins; however, it has yet to be determined whether certain lectins, or combinations of lectins are optimal for plant N-glycoproteome profiling; or whether specific lectins show preferential association with particular N-glycosylation sites or N-glycan structures. We describe here a comparative study of three mannose-binding lectins, concanavalin A, snowdrop lectin, and lentil lectin, to profile the N-glycoproteome of mature green stage tomato (Solanum lycopersicum) fruit pericarp. Through coupling lectin affinity chromatography with a shotgun proteomics strategy, we identified 448 putative N-glycoproteins, whereas a parallel lectin affinity chromatography plus hydrophilic interaction chromatography analysis revealed 318 putative N-glycosylation sites on 230 N-glycoproteins, of which 100 overlapped with the shotgun analysis, as well as 17 N-glycan structures. The use of multiple lectins substantially increased N-glycoproteome coverage and although there were no discernible differences in the structures of N-glycans, or the charge, isoelectric point (pI) or hydrophobicity of the glycopeptides that differentially bound to each lectin, differences were observed in the amino acid frequency at the -1 and +1 subsites of the N-glycosylation sites. We also demonstrated an alternative and complementary in planta recombinant expression strategy, followed by affinity MS analysis, to identify the putative N-glycan structures of glycoproteins whose abundance is too low to be readily determined by a shotgun approach, and/or combined with deglycosylation for predicted deamidated sites, using a xyloglucan-specific endoglucanase inhibitor protein as an example.
Collapse
Affiliation(s)
- Eliel Ruiz-May
- From the ‡Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Simon Hucko
- §USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - Kevin J. Howe
- §USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - Sheng Zhang
- ¶Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Ithaca, New York 14853
| | - Robert W. Sherwood
- ¶Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Ithaca, New York 14853
| | | | - Jocelyn K. C. Rose
- From the ‡Department of Plant Biology, Cornell University, Ithaca, New York 14853
| |
Collapse
|
42
|
Iminosugars: Therapeutic Applications and Synthetic Considerations. TOPICS IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1007/7355_2014_50] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
|
43
|
Furukawa K, Kambe M, Miyata M, Ohkawa Y, Tajima O, Furukawa K. Ganglioside GD3 induces convergence and synergism of adhesion and hepatocyte growth factor/Met signals in melanomas. Cancer Sci 2013; 105:52-63. [PMID: 24372645 PMCID: PMC4317880 DOI: 10.1111/cas.12310] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/15/2013] [Accepted: 10/24/2013] [Indexed: 12/11/2022] Open
Abstract
Ganglioside GD3 is highly expressed in human melanomas and enhances malignant properties of melanomas, such as cell proliferation and invasion activity. In this study, we analyzed the effects of GD3 expression on cell signals triggered by hepatocyte growth factor (HGF)/Met interaction and by adhesion to collagen type I (CL-I). Although stimulation of melanoma N1 cells (GD3+ and GD3−) with either HGF or adhesion to CL-I did not show marked differences in the phosphorylation levels of Akt at Ser473 and Thr308 between two types of cells, simultaneous treatment resulted in definite and markedly increased activation of Akt in GD3+ cells. Similar increases were also shown in Erk1/2 phosphorylation levels with the costimulation in GD3+ cells. When resistance to induced apoptosis by H2O2 was examined, only GD3+ cells treated with both HGF and adhesion to CL-I showed clearly low percentages of dead cells compared with GD3− cells or GD3+ cells treated with either one of the stimulants. Cell growth measured by 5-ethynyl-2‘ deoxyuridine uptake also showed synergistic effects in GD3+ cells. These results suggested that GD3 plays a crucial role in the convergence of multiple signals, leading to the synergistic effects of those signals on malignant properties of melanomas.
Collapse
Affiliation(s)
- Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan; Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | | | | | | | | |
Collapse
|
44
|
Zhu Z, Hua D, Clark DF, Go EP, Desaire H. GlycoPep Detector: a tool for assigning mass spectrometry data of N-linked glycopeptides on the basis of their electron transfer dissociation spectra. Anal Chem 2013; 85:5023-32. [PMID: 23510108 DOI: 10.1021/ac400287n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Electron transfer dissociation (ETD) is commonly used in fragmenting N-linked glycopeptides in their mass spectral analyses to complement collision-induced dissociation (CID) experiments. The glycan remains intact through ETD, while the peptide backbone is cleaved, providing the sequence of amino acids for a glycopeptide. Nonetheless, data analysis is a major bottleneck to high-throughput glycopeptide identification based on ETD data, due to the complexity and diversity of ETD mass spectra compared to CID counterparts. GlycoPep Detector (GPD) is a web-based tool to address this challenge. It filters out noise peaks that interfere with glycopeptide sequencing, correlates input glycopeptide compositions with the ETD spectra, and assigns a score for each candidate. By considering multiple ion series (c-, z-, and y-ions) and scoring them separately, the software gives more weighting to the ion series that matches peaks of high intensity in the spectra. This feature enables the correct glycopeptide to receive a high score while keeping scores of incorrect compositions low. GPD has been utilized to interpret data collected on six model glycoproteins (RNase B, avidin, fetuin, asialofetuin, transferrin, and AGP) as well as a clade C HIV envelope glycoprotein, C.97ZA012 gp140ΔCFI. In every assignment made by GPD, the correct glycopeptide composition earns a score that is about 2-fold higher than other incorrect glycopeptide candidates (decoys). The software can be accessed at http://glycopro.chem.ku.edu/ZZKHome.php .
Collapse
Affiliation(s)
- Zhikai Zhu
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | | | | | | | | |
Collapse
|
45
|
Furukawa K, Hamamura K, Ohkawa Y, Ohmi Y, Furukawa K. Disialyl gangliosides enhance tumor phenotypes with differential modalities. Glycoconj J 2012; 29:579-84. [PMID: 22763744 DOI: 10.1007/s10719-012-9423-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 06/20/2012] [Accepted: 06/21/2012] [Indexed: 01/22/2023]
Abstract
Sialic acid-containing glycosphingolipids, gangliosides are highly expressed in human cancer cells and regulate cell signals transduced via membrane microdomains. Generally, disialyl gangliosides enhance tumor phenotypes, while monosialyl gangliosides suppress them. In particular, gangliosides GD3 and GD2 are highly expressed in melanomas and small cell lung cancer cells, and their expression cause increased cell growth and invasion. In osteosarcomas, expression of GD3 and GD2 also enhanced cell invasion and motility, and caused increased phosphorylation of focal adhesion kinase and paxillin. In addition to focal adhesion kinase, Lyn kinase was also activated by GD3/GD2 expression, leading to the phosphorylation of paxillin. In contrast with melanoma cells, osteosarcomas showed reduced cell adhesion with increased phosphorylation of paxillin. Thus, increased expression of GD3/GD2 caused enhanced activation of signaling molecules, leading to distinct phenotypes between melanomas and osteosarcomas, i.e. increased and decreased adhesion activity. Thus, whole features of glycolipid-enriched microdomain/rafts formed in the individual cancer types seem to determine the main signaling pathway and biological outcome.
Collapse
Affiliation(s)
- Koichi Furukawa
- Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya, Japan,
| | | | | | | | | |
Collapse
|