201
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Cui T, Man Y, Wang F, Bi S, Lin L, Xie R. Glycoenzyme Tool Development: Principles, Screening Methods, and Recent Advances
†. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tongxiao Cui
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University Nanjing, Jiagsu 210023 China
| | - Yi Man
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University Nanjing, Jiagsu 210023 China
| | - Feifei Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University Nanjing, Jiagsu 210023 China
| | - Shuyang Bi
- State Key Laboratory of Bio‐organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry Shanghai 200032 China
| | - Liang Lin
- State Key Laboratory of Bio‐organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry Shanghai 200032 China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University Nanjing, Jiagsu 210023 China
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202
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Zhong X, D’Antona AM, Scarcelli JJ, Rouse JC. New Opportunities in Glycan Engineering for Therapeutic Proteins. Antibodies (Basel) 2022; 11:5. [PMID: 35076453 PMCID: PMC8788452 DOI: 10.3390/antib11010005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/22/2021] [Accepted: 12/31/2021] [Indexed: 11/17/2022] Open
Abstract
Glycans as sugar polymers are important metabolic, structural, and physiological regulators for cellular and biological functions. They are often classified as critical quality attributes to antibodies and recombinant fusion proteins, given their impacts on the efficacy and safety of biologics drugs. Recent reports on the conjugates of N-acetyl-galactosamine and mannose-6-phosphate for lysosomal degradation, Fab glycans for antibody diversification, as well as sialylation therapeutic modulations and O-linked applications, have been fueling the continued interest in glycoengineering. The current advancements of the human glycome and the development of a comprehensive network in glycosylation pathways have presented new opportunities in designing next-generation therapeutic proteins.
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Affiliation(s)
- Xiaotian Zhong
- BioMedicine Design, Medicinal Sciences, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA 02139, USA;
| | - Aaron M. D’Antona
- BioMedicine Design, Medicinal Sciences, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA 02139, USA;
| | - John J. Scarcelli
- BioProcess R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 1 Burtt Road, Andover, MA 01810, USA;
| | - Jason C. Rouse
- Analytical R&D, Biotherapeutics Pharmaceutical Sciences, Medicinal Sciences, Pfizer Worldwide R&D, 1 Burtt Road, Andover, MA 01810, USA;
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203
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Penning A, Tosoni G, Abiega O, Bielefeld P, Gasperini C, De Pietri Tonelli D, Fitzsimons CP, Salta E. Adult Neural Stem Cell Regulation by Small Non-coding RNAs: Physiological Significance and Pathological Implications. Front Cell Neurosci 2022; 15:781434. [PMID: 35058752 PMCID: PMC8764185 DOI: 10.3389/fncel.2021.781434] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/09/2021] [Indexed: 01/11/2023] Open
Abstract
The adult neurogenic niches are complex multicellular systems, receiving regulatory input from a multitude of intracellular, juxtacrine, and paracrine signals and biological pathways. Within the niches, adult neural stem cells (aNSCs) generate astrocytic and neuronal progeny, with the latter predominating in physiological conditions. The new neurons generated from this neurogenic process are functionally linked to memory, cognition, and mood regulation, while much less is known about the functional contribution of aNSC-derived newborn astrocytes and adult-born oligodendrocytes. Accumulating evidence suggests that the deregulation of aNSCs and their progeny can impact, or can be impacted by, aging and several brain pathologies, including neurodevelopmental and mood disorders, neurodegenerative diseases, and also by insults, such as epileptic seizures, stroke, or traumatic brain injury. Hence, understanding the regulatory underpinnings of aNSC activation, differentiation, and fate commitment could help identify novel therapeutic avenues for a series of pathological conditions. Over the last two decades, small non-coding RNAs (sncRNAs) have emerged as key regulators of NSC fate determination in the adult neurogenic niches. In this review, we synthesize prior knowledge on how sncRNAs, such as microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs), may impact NSC fate determination in the adult brain and we critically assess the functional significance of these events. We discuss the concepts that emerge from these examples and how they could be used to provide a framework for considering aNSC (de)regulation in the pathogenesis and treatment of neurological diseases.
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Affiliation(s)
- Amber Penning
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Amsterdam, Netherlands
| | - Giorgia Tosoni
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Amsterdam, Netherlands
| | - Oihane Abiega
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, Netherlands
| | - Pascal Bielefeld
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, Netherlands
| | - Caterina Gasperini
- Neurobiology of miRNAs Lab, Istituto Italiano di Tecnologia, Genova, Italy
| | | | - Carlos P. Fitzsimons
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, Netherlands
| | - Evgenia Salta
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Amsterdam, Netherlands
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204
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Sun R, Kim AMJ, Murray AA, Lim SO. N-Glycosylation Facilitates 4-1BB Membrane Localization by Avoiding Its Multimerization. Cells 2022; 11:cells11010162. [PMID: 35011724 PMCID: PMC8750214 DOI: 10.3390/cells11010162] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/02/2022] [Accepted: 01/03/2022] [Indexed: 01/08/2023] Open
Abstract
Leveraging the T cell immunity against tumors represents a revolutionary type of cancer therapy. 4-1BB is a well-characterized costimulatory immune receptor existing on activated T cells and mediating their proliferation and cytotoxicity under infectious diseases and cancers. Despite the accumulating interest in implementing 4-1BB as a therapeutic target for immune-related disorders, less is known about the pattern of its intracellular behaviors and regulations. It has been previously demonstrated that 4-1BB is heavily modified by N-glycosylation; however, the biological importance of this modification lacks detailed elucidation. Through biochemical, biophysical, and cell-biological approaches, we systematically evaluated the impact of N-glycosylation on the ligand interaction, stability, and localization of 4-1BB. We hereby highlighted that N-glycan functions by preventing the oligomerization of 4-1BB, thus permitting its membrane transportation and fast turn-over. Without N-glycosylation, 4-1BB could be aberrantly accumulated intracellularly and fail to be sufficiently inserted in the membrane. The N-glycosylation-guided intracellular processing of 4-1BB serves as the potential mechanism explicitly modulating the “on” and “off” of 4-1BB through the control of protein abundance. Our study will further solidify the understanding of the biological properties of 4-1BB and facilitate the clinical practice against this promising therapeutic target.
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Affiliation(s)
- Ruoxuan Sun
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (R.S.); (A.M.J.K.); (A.A.M.)
| | - Alyssa Min Jung Kim
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (R.S.); (A.M.J.K.); (A.A.M.)
| | - Allison A. Murray
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (R.S.); (A.M.J.K.); (A.A.M.)
| | - Seung-Oe Lim
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (R.S.); (A.M.J.K.); (A.A.M.)
- Purdue Institute of Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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205
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Rumpret M, von Richthofen HJ, Peperzak V, Meyaard L. Inhibitory pattern recognition receptors. J Exp Med 2022; 219:212908. [PMID: 34905019 PMCID: PMC8674843 DOI: 10.1084/jem.20211463] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/03/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Pathogen- and damage-associated molecular patterns are sensed by the immune system's pattern recognition receptors (PRRs) upon contact with a microbe or damaged tissue. In situations such as contact with commensals or during physiological cell death, the immune system should not respond to these patterns. Hence, immune responses need to be context dependent, but it is not clear how context for molecular pattern recognition is provided. We discuss inhibitory receptors as potential counterparts to activating pattern recognition receptors. We propose a group of inhibitory pattern recognition receptors (iPRRs) that recognize endogenous and microbial patterns associated with danger, homeostasis, or both. We propose that recognition of molecular patterns by iPRRs provides context, helps mediate tolerance to microbes, and helps balance responses to danger signals.
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Affiliation(s)
- Matevž Rumpret
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Helen J von Richthofen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Victor Peperzak
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Linde Meyaard
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
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206
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Alexander RP, Kitchen RR, Tosar JP, Roth M, Mestdagh P, Max KEA, Rozowsky J, Kaczor-Urbanowicz KE, Chang J, Balaj L, Losic B, Van Nostrand EL, LaPlante E, Mateescu B, White BS, Yu R, Milosavljevic A, Stolovitzky G, Spengler RM. Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop. Front Genet 2022; 12:778416. [PMID: 35047007 PMCID: PMC8762274 DOI: 10.3389/fgene.2021.778416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/30/2021] [Indexed: 12/16/2022] Open
Abstract
We now know RNA can survive the harsh environment of biofluids when encapsulated in vesicles or by associating with lipoproteins or RNA binding proteins. These extracellular RNA (exRNA) play a role in intercellular signaling, serve as biomarkers of disease, and form the basis of new strategies for disease treatment. The Extracellular RNA Communication Consortium (ERCC) hosted a two-day online workshop (April 19-20, 2021) on the unique challenges of exRNA data analysis. The goal was to foster an open dialog about best practices and discuss open problems in the field, focusing initially on small exRNA sequencing data. Video recordings of workshop presentations and discussions are available (https://exRNA.org/exRNAdata2021-videos/). There were three target audiences: experimentalists who generate exRNA sequencing data, computational and data scientists who work with those groups to analyze their data, and experimental and data scientists new to the field. Here we summarize issues explored during the workshop, including progress on an effort to develop an exRNA data analysis challenge to engage the community in solving some of these open problems.
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Affiliation(s)
| | - Robert R Kitchen
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States
| | - Juan Pablo Tosar
- Pasteur Institute of Montevideo and University of the Republic of Uruguay, Montevideo, Uruguay
| | - Matthew Roth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Pieter Mestdagh
- Center for Medical Genetics, Department of Biomolecular Medicine, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Klaas E. A. Max
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, United States
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | | | - Justin Chang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Bojan Losic
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eric L. Van Nostrand
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Emily LaPlante
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Bogdan Mateescu
- Brain Research Institute, University of Zurich, Zurich, Switzerland
| | | | - Rongshan Yu
- Department of Computer Science, Xiamen University, Aginome Scientific, Ltd., Xiamen, China
| | - Aleksander Milosavljevic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | | | - Ryan M. Spengler
- School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
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207
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Julian JD, Zabotina OA. Xyloglucan Biosynthesis: From Genes to Proteins and Their Functions. FRONTIERS IN PLANT SCIENCE 2022; 13:920494. [PMID: 35720558 PMCID: PMC9201394 DOI: 10.3389/fpls.2022.920494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/13/2022] [Indexed: 05/12/2023]
Abstract
The plant's recalcitrant cell wall is composed of numerous polysaccharides, including cellulose, hemicellulose, and pectin. The most abundant hemicellulose in dicot cell walls is xyloglucan, which consists of a β-(1- > 4) glucan backbone with α-(1- > 6) xylosylation producing an XXGG or XXXG pattern. Xylose residues of xyloglucan are branched further with different patterns of arabinose, fucose, galactose, and acetylation that varies between species. Although xyloglucan research in other species lag behind Arabidopsis thaliana, significant advances have been made into the agriculturally relevant species Oryza sativa and Solanum lycopersicum, which can be considered model organisms for XXGG type xyloglucan. In this review, we will present what is currently known about xyloglucan biosynthesis in A. thaliana, O. sativa, and S. lycopersicum and discuss the recent advances in the characterization of the glycosyltransferases involved in this complex process and their organization in the Golgi.
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Affiliation(s)
- Jordan D Julian
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Olga A Zabotina
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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208
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O’Flaherty R, Opdenakker G, Clausen H, Gerardy-Schahn R, Kieda C, Reis CA, Rudd PM, Sadrieh A, Axford J. OUP accepted manuscript. Glycobiology 2022; 32:458-459. [PMID: 35157774 PMCID: PMC9132246 DOI: 10.1093/glycob/cwac006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Roisin O’Flaherty
- Corresponding author: Department of Chemistry, Maynooth University, Ireland.
| | - Ghislain Opdenakker
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Herestraat 49, Leuven, KU Leuven, BE-3000, Belgium
| | - Henrik Clausen
- Copenhagen Centre for Glycomics, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Rita Gerardy-Schahn
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, 30625, Hannover, Germany
| | - Claudine Kieda
- Centre for Molecular Biophysics, Cell Recognition and Glycobiology, UPR4301-CNRS, rue Charles Sadron, 45071, Orléans, France
| | - Celso A Reis
- Glycobiology in Cancer, i3S – Institute for Research and Innovation in Health, University of Porto, 4200-135, Porto, Portugal
| | - Pauline M Rudd
- UCD School of Medicine, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
- Bioprocessing Technology Institute, 20 Biopolis Way, #06-01 Centros, 138668, Singapore
| | - Azita Sadrieh
- Department of Clinical Rheumatology, St. George's University of London, London, SW17 0QT, UK
| | - John Axford
- Department of Clinical Rheumatology, St. George's University of London, London, SW17 0QT, UK
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209
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Ding WY, Liu HH, Cheng JK, Yao H, Xiang SH, Tan B. Palladium catalyzed decarboxylative β- C-glycosylation of glycals with oxazol-5-(4 H)-ones as acceptors. Org Chem Front 2022. [DOI: 10.1039/d2qo01308h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Palladium catalyzed decarboxylative glycosylation of bicyclic glycals affords a series of C-glycosylated oxazol-5-(4H)-ones with high efficiency and exquisite chemo- and stereoselectivity at the anomeric center under mild reaction conditions.
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Affiliation(s)
- Wei-Yi Ding
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Huan-Huan Liu
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jun Kee Cheng
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hui Yao
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, 443002, China
| | - Shao-Hua Xiang
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Bin Tan
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
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210
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Van Damme EJM. 35 years in plant lectin research: a journey from basic science to applications in agriculture and medicine. Glycoconj J 2022; 39:83-97. [PMID: 34427812 PMCID: PMC8383723 DOI: 10.1007/s10719-021-10015-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 06/30/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023]
Abstract
Plants contain an extended group of lectins differing from each other in their molecular structures, biochemical properties and carbohydrate-binding specificities. The heterogeneous group of plant lectins can be classified in several families based on the primary structure of the lectin domain. All proteins composed of one or more lectin domains, or having a domain architecture including one or more lectin domains in combination with other protein domains can be defined as lectins. Plant lectins reside in different cell compartments, and depending on their location will encounter a large variety carbohydrate structures, allowing them to be involved in multiple biological functions. Over the years lectins have been studied intensively for their carbohydrate-binding properties and biological activities, which also resulted in diverse applications. The present overview on plant lectins especially focuses on the structural and functional characteristics of plant lectins and their applications for crop improvement, glycobiology and biomedical research.
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Affiliation(s)
- Els J. M. Van Damme
- Laboratory of Glycobiology and Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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211
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Lachke SA. RNA-binding proteins and post-transcriptional regulation in lens biology and cataract: Mediating spatiotemporal expression of key factors that control the cell cycle, transcription, cytoskeleton and transparency. Exp Eye Res 2022; 214:108889. [PMID: 34906599 PMCID: PMC8792301 DOI: 10.1016/j.exer.2021.108889] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023]
Abstract
Development of the ocular lens - a transparent tissue capable of sustaining frequent shape changes for optimal focusing power - pushes the boundaries of what cells can achieve using the molecular toolkit encoded by their genomes. The mammalian lens contains broadly two types of cells, the anteriorly located monolayer of epithelial cells which, at the equatorial region of the lens, initiate differentiation into fiber cells that contribute to the bulk of the tissue. This differentiation program involves massive upregulation of select fiber cell-expressed RNAs and their subsequent translation into high amounts of proteins, such as crystallins. But intriguingly, fiber cells achieve this while also simultaneously undergoing significant morphological changes such as elongation - involving about 1000-fold length-wise increase - and migration, which requires modulation of cytoskeletal and cell adhesion factors. Adding further to the challenges, these molecular and cellular events have to be coordinated as fiber cells progress toward loss of their nuclei and organelles, which irreversibly compromises their potential for harnessing genetically hardwired information. A long-standing question is how processes downstream of signaling and transcription, which may also participate in feedback regulation, contribute toward orchestrating these cellular differentiation events in the lens. It is now becoming clear from findings over the past decade that post-transcriptional gene expression regulatory mechanisms are critical in controlling cellular proteomes and coordinating key processes in lens development and fiber cell differentiation. Indeed, RNA-binding proteins (RBPs) such as Caprin2, Celf1, Rbm24 and Tdrd7 have now been described in mediating post-transcriptional control over key factors (e.g. Actn2, Cdkn1a (p21Cip1), Cdkn1b (p27Kip1), various crystallins, Dnase2b, Hspb1, Pax6, Prox1, Sox2) that are variously involved in cell cycle, transcription, cytoskeleton maintenance and differentiation in the lens. Furthermore, deficiencies of these RBPs have been shown to result in various eye and lens defects and/or cataract. Because fiber cell differentiation in the lens occurs throughout life, the underlying regulatory mechanisms operational in development are expected to also be recruited for the maintenance of transparency in aged lenses. Indeed, in support of this, TDRD7 and CAPRIN2 loci have been linked to age-related cataract in humans. Here, I will review the role of key RBPs in the lens and their importance in understanding the pathology of lens defects. I will discuss advances in RBP-based gene expression control, in general, and the important challenges that need to be addressed in the lens to define the mechanisms that determine the epithelial and fiber cell proteome. Finally, I will also discuss in detail several key future directions including the application of bioinformatics approaches such as iSyTE to study RBP-based post-transcriptional gene expression control in the aging lens and in the context of age-related cataract.
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Affiliation(s)
- Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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212
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Mahara G, Tian C, Xu X, Zhu J. Breakthrough of glycobiology in the 21st century. Front Immunol 2022; 13:1071360. [PMID: 36685548 PMCID: PMC9850147 DOI: 10.3389/fimmu.2022.1071360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/01/2022] [Indexed: 01/07/2023] Open
Abstract
As modern medicine began to emerge at the turn of the 20th century, glycan-based therapies advanced. DNA- and protein-centered therapies became widely available. The research and development of structurally defined carbohydrates have led to new tools and methods that have sparked interest in the therapeutic applications of glycans. One of the latest omics disciplines to emerge in the contemporary post-genomics age is glycomics. In addition, to providing hope for patients and people with different health conditions through a deeper understanding of the mechanisms of common complex diseases, this new specialty in system sciences has much to offer to communities involved in the development of diagnostics and therapeutics in medicine and life sciences.This review focuses on recent developments that have pushed glycan-based therapies into the spotlight in medicine and the technologies powering these initiatives, which we can take as the most significant success of the 21st century.
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Affiliation(s)
- Gehendra Mahara
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Cuihong Tian
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Center for Precision Health, Edith Cowan University, Perth, WA, Australia
| | - Xiaojia Xu
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Center for Precision Health, Edith Cowan University, Perth, WA, Australia
- Department of Infection Control, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Jinxiu Zhu
- Institute of Clinical Electrocardiography, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Longgang Maternity and Child Institute of Shantou University Medical College, Shenzhen, Guangdong, China
- *Correspondence: Jinxiu Zhu,
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213
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Han K, Wang F, Yue Y, Tan X, Tian M, Miao Y, Zhao S, Dong W, Yu M. Glycomics reveal that ST6GAL1-mediated sialylation regulates uterine lumen closure during implantation. Cell Prolif 2021; 55:e13169. [PMID: 34957619 PMCID: PMC8780930 DOI: 10.1111/cpr.13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 11/28/2022] Open
Abstract
Objectives Implantation failure is a major cause of prenatal mortality. The uterine lumen closure contributes to embryo adhesion to the uterus, but its underlying mechanisms are largely unknown. Our previous study has reported that endometrial fold extension can lead to uterine lumen closure in pigs. The objective of this study was to reveal molecular mechanisms of the uterine lumen closure by characterizing the molecular basis of the endometrial fold extension during implantation in pigs. Materials and methods Uterine and endometrium tissues during implantation were collected in pigs. MALDI‐TOF MS was used to characterize the N‐glycomic profiles. Histochemistry, siRNA transfection, Western blotting, lectin immumoprecipitation, mass spectrometry and assays of wounding healing and cell aggregation were performed to investigate the molecular basis. Results We observed that uterine luminal epithelium (LE) migrated collectively during endometrial fold extension. For the first time, we identified a large number of N‐glycan compositions from endometrium during implantation using MALDI‐TOF MS. Notably, the α2,6‐linked sialic acid and ST6GAL1 were highly expressed in uterine LE when the endometrial folds extended greatly. Subsequently, the role of ST6GAL1‐mediated 2,6‐sialylation in collective epithelial migration was demonstrated. Finally, we found that ST6GAL1‐mediated α2,6‐sialylation of E‐cadherin may participate in collective migration of uterine LE. Conclusions The study reveals a mechanism of uterine lumen closure by identifying that ST6GAL1‐mediated α2,6‐sialylation of cell adhesion molecules contributes to endometrial fold extension through regulating collective migration of uterine LE.
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Affiliation(s)
- Kun Han
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Feiyu Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yulu Yue
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xihong Tan
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Miao Tian
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yiliang Miao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weijie Dong
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Mei Yu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
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214
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Richards SJ, Gibson MI. Toward Glycomaterials with Selectivity as Well as Affinity. JACS AU 2021; 1:2089-2099. [PMID: 34984416 PMCID: PMC8717392 DOI: 10.1021/jacsau.1c00352] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Indexed: 05/08/2023]
Abstract
Multivalent glycosylated materials (polymers, surfaces, and particles) often show high affinity toward carbohydrate binding proteins (e.g., lectins) due to the nonlinear enhancement from the cluster glycoside effect. This affinity gain has potential in applications from diagnostics, biosensors, and targeted delivery to anti-infectives and in an understanding of basic glycobiology. This perspective highlights the question of selectivity, which is less often addressed due to the reductionist nature of glycomaterials and the promiscuity of many lectins. The use of macromolecular features, including architecture, heterogeneous ligand display, and the installation of non-natural glycans, to address this challenge is discussed, and examples of selectivity gains are given.
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Affiliation(s)
| | - Matthew I. Gibson
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Medical School, University of Warwick, Coventry CV4 7AL, U.K.
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215
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Tesovnik T, Jenko Bizjan B, Šket R, Debeljak M, Battelino T, Kovač J. Technological Approaches in the Analysis of Extracellular Vesicle Nucleotide Sequences. Front Bioeng Biotechnol 2021; 9:787551. [PMID: 35004647 PMCID: PMC8733665 DOI: 10.3389/fbioe.2021.787551] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Together with metabolites, proteins, and lipid components, the EV cargo consists of DNA and RNA nucleotide sequence species, which are part of the intracellular communication network regulating specific cellular processes and provoking distinct target cell responses. The extracellular vesicle (EV) nucleotide sequence cargo molecules are often investigated in association with a particular pathology and may provide an insight into the physiological and pathological processes in hard-to-access organs and tissues. The diversity and biological function of EV nucleotide sequences are distinct regarding EV subgroups and differ in tissue- and cell-released EVs. EV DNA is present mainly in apoptotic bodies, while there are different species of EV RNAs in all subgroups of EVs. A limited sample volume of unique human liquid biopsy provides a small amount of EVs with limited isolated DNA and RNA, which can be a challenging factor for EV nucleotide sequence analysis, while the additional difficulty is technical variability of molecular nucleotide detection. Every EV study is challenged with its first step of the EV isolation procedure, which determines the EV's purity, yield, and diameter range and has an impact on the EV's downstream analysis with a significant impact on the final result. The gold standard EV isolation procedure with ultracentrifugation provides a low output and not highly pure isolated EVs, while modern techniques increase EV's yield and purity. Different EV DNA and RNA detection techniques include the PCR procedure for nucleotide sequence replication of the molecules of interest, which can undergo a small-input EV DNA or RNA material. The nucleotide sequence detection approaches with their advantages and disadvantages should be considered to appropriately address the study problem and to extract specific EV nucleotide sequence information with the detection using qPCR or next-generation sequencing. Advanced next-generation sequencing techniques allow the detection of total EV genomic or transcriptomic data even at the single-molecule resolution and thus, offering a sensitive and accurate EV DNA or RNA biomarker detection. Additionally, with the processes where the EV genomic or transcriptomic data profiles are compared to identify characteristic EV differences in specific conditions, novel biomarkers could be discovered. Therefore, a suitable differential expression analysis is crucial to define the EV DNA or RNA differences between conditions under investigation. Further bioinformatics analysis can predict molecular cell targets and identify targeted and affected cellular pathways. The prediction target tools with functional studies are essential to help specify the role of the investigated EV-targeted nucleotide sequences in health and disease and support further development of EV-related therapeutics. This review will discuss the biological diversity of human liquid biopsy-obtained EV nucleotide sequences DNA and RNA species reported as potential biomarkers in health and disease and methodological principles of their detection, from human liquid biopsy EV isolation, EV nucleotide sequence extraction, techniques for their detection, and their cell target prediction.
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Affiliation(s)
- Tine Tesovnik
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Barbara Jenko Bizjan
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Robert Šket
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Maruša Debeljak
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
- Faculty of Medicine, Chair of Paediatrics, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Kovač
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
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216
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Isakova A, Neff N, Quake SR. Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states. Proc Natl Acad Sci U S A 2021; 118:e2113568118. [PMID: 34911763 PMCID: PMC8713755 DOI: 10.1073/pnas.2113568118] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2021] [Indexed: 12/22/2022] Open
Abstract
The ability to interrogate total RNA content of single cells would enable better mapping of the transcriptional logic behind emerging cell types and states. However, current single-cell RNA-sequencing (RNA-seq) methods are unable to simultaneously monitor all forms of RNA transcripts at the single-cell level, and thus deliver only a partial snapshot of the cellular RNAome. Here we describe Smart-seq-total, a method capable of assaying a broad spectrum of coding and noncoding RNA from a single cell. Smart-seq-total does not require splitting the RNA content of a cell and allows the incorporation of unique molecular identifiers into short and long RNA molecules for absolute quantification. It outperforms current poly(A)-independent total RNA-seq protocols by capturing transcripts of a broad size range, thus enabling simultaneous analysis of protein-coding, long-noncoding, microRNA, and other noncoding RNA transcripts from single cells. We used Smart-seq-total to analyze the total RNAome of human primary fibroblasts, HEK293T, and MCF7 cells, as well as that of induced murine embryonic stem cells differentiated into embryoid bodies. By analyzing the coexpression patterns of both noncoding RNA and mRNA from the same cell, we were able to discover new roles of noncoding RNA throughout essential processes, such as cell cycle and lineage commitment during embryonic development. Moreover, we show that independent classes of short-noncoding RNA can be used to determine cell-type identity.
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Affiliation(s)
- Alina Isakova
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305;
- Chan Zuckerberg Biohub, San Francisco, CA 94158
- Department of Applied Physics, Stanford University, Stanford, CA 94305
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217
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Guo L, Liang Y, Li H, Zheng H, Yang Z, Chen Y, Zhao X, Li J, Li B, Shi H, Sun M, Liu L. Epigenetic glycosylation of SARS-CoV-2 impact viral infection through DC&L-SIGN receptors. iScience 2021; 24:103426. [PMID: 34786539 PMCID: PMC8582233 DOI: 10.1016/j.isci.2021.103426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/06/2021] [Accepted: 11/08/2021] [Indexed: 01/06/2023] Open
Abstract
Glycosylation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein mediates viral entry and immune escape. While glycan site is determined by viral genetic code, glycosylation is completely dependent on host cell post-translational modification. Here, by producing SARS-CoV-2 virions from various host cell lines, viruses of different origins with diverse spike protein glycan patterns were revealed. Binding affinities to C-type lectin receptors (CLRs) DC&L-SIGN differed in the different glycan pattern virions. Although none of the CLRs supported viral productive infection, viral trans&cis-infection mediated by the CLRs were substantially changed among the different virions. Specifically, trans&cis-infection of virions with a high-mannose structure (Man5GlcNAc2) at the N1098 glycan site of the spike postfusion trimer were markedly enhanced. Considering L-SIGN co-expression with ACE2 on respiratory tract cells, our work underlines viral epigenetic glycosylation in authentic viral infection and highlights the attachment co-receptor role of DC&L-SIGN in SARS-CoV-2 infection and prevention. DC&L-SIGN are SARS-CoV-2 attachment co-receptor Viral spike (S) glycoprotein undergoes epigenetic modification during infection Epigenetic glycosylation affects viral in-cis&-trans infections through DC&L-SIGN High-mannose glycan at 1098 site of postfusion S trimer is vital for viral infection
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Affiliation(s)
- Lei Guo
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Medical Center for Pediatric Diseases, Yunnan Institute of Pediatrics, Kunming Children's Hospital, Kunming, China
| | - Yan Liang
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Heng Li
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Huiwen Zheng
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Zening Yang
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yanli Chen
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xin Zhao
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jing Li
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Binxiang Li
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haijing Shi
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ming Sun
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Longding Liu
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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218
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van Houtum EJH, Büll C, Cornelissen LAM, Adema GJ. Siglec Signaling in the Tumor Microenvironment. Front Immunol 2021; 12:790317. [PMID: 34966391 PMCID: PMC8710542 DOI: 10.3389/fimmu.2021.790317] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/23/2021] [Indexed: 12/16/2022] Open
Abstract
Sialic acid-binding immunoglobulin-like lectins (Siglecs) are a family of receptors that recognize sialoglycans - sialic acid containing glycans that are abundantly present on cell membranes. Siglecs are expressed on most immune cells and can modulate their activity and function. The majority of Siglecs contains immune inhibitory motifs comparable to the immune checkpoint receptor PD-1. In the tumor microenvironment (TME), signaling through the Siglec-sialoglycan axis appears to be enhanced through multiple mechanisms favoring tumor immune evasion similar to the PD-1/PD-L1 signaling pathway. Siglec expression on tumor-infiltrating immune cells appears increased in the immune suppressive microenvironment. At the same time, enhanced Siglec ligand expression has been reported for several tumor types as a result of aberrant glycosylation, glycan modifications, and the increased expression of sialoglycans on proteins and lipids. Siglec signaling has been identified as important regulator of anti-tumor immunity in the TME, but the key factors contributing to Siglec activation by tumor-associated sialoglycans are diverse and poorly defined. Among others, Siglec activation and signaling are co-determined by their expression levels, cell surface distribution, and their binding preferences for cis- and trans-ligands in the TME. Siglec binding preference are co-determined by the nature of the proteins/lipids to which the sialoglycans are attached and the multivalency of the interaction. Here, we review the current understanding and emerging conditions and factors involved in Siglec signaling in the TME and identify current knowledge gaps that exist in the field.
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Affiliation(s)
- Eline J. H. van Houtum
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Büll
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, Netherlands
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lenneke A. M. Cornelissen
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Gosse J. Adema
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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219
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Lusky OS, Meir M, Goldbourt A. Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR. BIOPHYSICAL REPORTS 2021; 1:100027. [PMID: 36425459 PMCID: PMC9680805 DOI: 10.1016/j.bpr.2021.100027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/23/2021] [Indexed: 05/14/2023]
Abstract
RNA is a polymer with pivotal functions in many biological processes. RNA structure determination is thus a vital step toward understanding its function. The secondary structure of RNA is stabilized by hydrogen bonds formed between nucleotide basepairs, and it defines the positions and shapes of functional stem-loops, internal loops, bulges, and other functional and structural elements. In this work, we present a methodology for studying large intact RNA biomolecules using homonuclear 15N solid-state NMR spectroscopy. We show that proton-driven spin-diffusion experiments with long mixing times, up to 16 s, improved by the incorporation of multiple rotor-synchronous 1H inversion pulses (termed radio-frequency dipolar recoupling pulses), reveal key hydrogen-bond contacts. In the full-length RNA isolated from MS2 phage, we observed strong and dominant contributions of guanine-cytosine Watson-Crick basepairs, and beyond these common interactions, we observe a significant contribution of the guanine-uracil wobble basepairs. Moreover, we can differentiate basepaired and non-basepaired nitrogen atoms. Using the improved technique facilitates characterization of hydrogen-bond types in intact large-scale RNA using solid-state NMR. It can be highly useful to guide secondary structure prediction techniques and possibly structure determination methods.
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Affiliation(s)
| | - Moran Meir
- School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Faculty of Exact Sciences
- Corresponding author
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220
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Marcelo F, Nativi C, Russo L, Silipo A, Velasco-Torrijos T. Editorial: Glyco-Tools to Crack Unsolved Biomedical Needs. Front Chem 2021; 9:789839. [PMID: 34869237 PMCID: PMC8638825 DOI: 10.3389/fchem.2021.789839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Filipa Marcelo
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry / Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Cristina Nativi
- Department of Chemistry, University of Florence, Sesto Fiorentino (FI), Italy
| | - Laura Russo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Alba Silipo
- Department of Chemical Sciences, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Naples, Italy
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221
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How pervasive are post-translational and -transcriptional modifications? Trends Cell Biol 2021; 32:475-478. [PMID: 34863586 DOI: 10.1016/j.tcb.2021.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/06/2021] [Accepted: 11/10/2021] [Indexed: 12/19/2022]
Abstract
Cells use post-translational and post-transcription modifications as crucial mechanisms to maintain homeostasis and regulate gene transcription. Recent discoveries demonstrate that these modifications are more pervasive and important than scientists previously posited. Here, we discuss their importance and provide insight to stimulate new research into these modifications.
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222
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Keane JT, Posey AD. Chimeric Antigen Receptors Expand the Repertoire of Antigenic Macromolecules for Cellular Immunity. Cells 2021; 10:cells10123356. [PMID: 34943864 PMCID: PMC8699116 DOI: 10.3390/cells10123356] [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: 11/01/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 12/16/2022] Open
Abstract
T-cell therapies have made significant improvements in cancer treatment over the last decade. One cellular therapy utilizing T-cells involves the use of a chimeric MHC-independent antigen-recognition receptor, typically referred to as a chimeric antigen receptor (CAR). CAR molecules, while mostly limited to the recognition of antigens on the surface of tumor cells, can also be utilized to exploit the diverse repertoire of macromolecules targetable by antibodies, which are incorporated into the CAR design. Leaning into this expansion of target macromolecules will enhance the diversity of antigens T-cells can target and may improve the tumor-specificity of CAR T-cell therapy. This review explores the types of macromolecules targetable by T-cells through endogenous and synthetic antigen-specific receptors.
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Affiliation(s)
- John T. Keane
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Avery D. Posey
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA 19104, USA
- Correspondence:
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223
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Esmail S, Manolson MF. Advances in understanding N-glycosylation structure, function, and regulation in health and disease. Eur J Cell Biol 2021; 100:151186. [PMID: 34839178 DOI: 10.1016/j.ejcb.2021.151186] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/14/2021] [Accepted: 11/18/2021] [Indexed: 01/17/2023] Open
Abstract
N-linked glycosylation is a post-translational modification crucial for membrane protein folding, stability and other cellular functions. Alteration of membrane protein N-glycans is implicated in wide range of pathological conditions including cancer metastasis, chronic inflammatory diseases, and viral pathogenesis. Even though the roles of N-glycans have been studied extensively, our knowledge of their mechanisms remains unclear due to the lack of detailed structural analysis of the N-glycome. Mapping the N-glycome landscape will open new avenues to explore disease mechanisms and identify novel therapeutic targets. This review discusses the diverse structure of N-linked glycans, the function and regulation of N-glycosylation in health and disease, and ends with a focus on recent approaches to target N-glycans in rheumatoid arthritis and cancer metastasis.
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Affiliation(s)
- Sally Esmail
- Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada.
| | - Morris F Manolson
- Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
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224
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Xie S, Leung AWS, Zheng Z, Zhang D, Xiao C, Luo R, Luo M, Zhang S. Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era. Innovation (N Y) 2021; 2:100153. [PMID: 34901902 PMCID: PMC8640597 DOI: 10.1016/j.xinn.2021.100153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
The Human Genome Project opened an era of (epi)genomic research, and also provided a platform for the development of new sequencing technologies. During and after the project, several sequencing technologies continue to dominate nucleic acid sequencing markets. Currently, Illumina (short-read), PacBio (long-read), and Oxford Nanopore (long-read) are the most popular sequencing technologies. Unlike PacBio or the popular short-read sequencers before it, which, as examples of the second or so-called Next-Generation Sequencing platforms, need to synthesize when sequencing, nanopore technology directly sequences native DNA and RNA molecules. Nanopore sequencing, therefore, avoids converting mRNA into cDNA molecules, which not only allows for the sequencing of extremely long native DNA and full-length RNA molecules but also document modifications that have been made to those native DNA or RNA bases. In this review on direct DNA sequencing and direct RNA sequencing using Oxford Nanopore technology, we focus on their development and application achievements, discussing their challenges and future perspective. We also address the problems researchers may encounter applying these approaches in their research topics, and how to resolve them.
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Affiliation(s)
- Shangqian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou 570228, China
| | - Amy Wing-Sze Leung
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Zhenxian Zheng
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Dake Zhang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangzhou 510060, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Ming Luo
- Agriculture and Biotechnology Research Center, Guangdong Provincial Key Laboratory of Applied Botany, Center of Economic Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shoudong Zhang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
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225
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Jung J, Enterina JR, Bui DT, Mozaneh F, Lin PH, Nitin, Kuo CW, Rodrigues E, Bhattacherjee A, Raeisimakiani P, Daskhan GC, St. Laurent CD, Khoo KH, Mahal LK, Zandberg WF, Huang X, Klassen JS, Macauley MS. Carbohydrate Sulfation As a Mechanism for Fine-Tuning Siglec Ligands. ACS Chem Biol 2021; 16:2673-2689. [PMID: 34661385 DOI: 10.1021/acschembio.1c00501] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The immunomodulatory family of Siglecs recognizes sialic acid-containing glycans as "self", which is exploited in cancer for immune evasion. The biochemical nature of Siglec ligands remains incompletely understood, with emerging evidence suggesting the importance of carbohydrate sulfation. Here, we investigate how specific sulfate modifications affect Siglec ligands by overexpressing eight carbohydrate sulfotransferases (CHSTs) in five cell lines. Overexpression of three CHSTs─CHST1, CHST2, or CHST4─significantly enhance the binding of numerous Siglecs. Unexpectedly, two other CHSTs (Gal3ST2 and Gal3ST3) diminish Siglec binding, suggesting a new mode to modulate Siglec ligands via sulfation. Results are cell type dependent, indicating that the context in which sulfated glycans are presented is important. Moreover, a pharmacological blockade of N- and O-glycan maturation reveals a cell-type-specific pattern of importance for either class of glycan. Production of a highly homogeneous Siglec-3 (CD33) fragment enabled a mass-spectrometry-based binding assay to determine ≥8-fold and ≥2-fold enhanced affinity for Neu5Acα2-3(6-O-sulfo)Galβ1-4GlcNAc and Neu5Acα2-3Galβ1-4(6-O-sulfo)GlcNAc, respectively, over Neu5Acα2-3Galβ1-4GlcNAc. CD33 shows significant additivity in affinity (≥28-fold) for the disulfated ligand, Neu5Acα2-3(6-O-sulfo)Galβ1-4(6-O-sulfo)GlcNAc. Moreover, joint overexpression of CHST1 with CHST2 in cells greatly enhanced the binding of CD33 and several other Siglecs. Finally, we reveal that CHST1 is upregulated in numerous cancers, correlating with poorer survival rates and sodium chlorate sensitivity for the binding of Siglecs to cancer cell lines. These results provide new insights into carbohydrate sulfation as a general mechanism for tuning Siglec ligands on cells, including in cancer.
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Affiliation(s)
- Jaesoo Jung
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | - Jhon R. Enterina
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, T6G 2J7, Canada
| | - Duong T. Bui
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | - Fahima Mozaneh
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | - Po-Han Lin
- Departments of Chemistry and Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Nitin
- Department of Chemistry, The University of British Columbia, Kelowna, V1V 1V7, Canada
| | - Chu-Wei Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Emily Rodrigues
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | | | | | - Gour C. Daskhan
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | | | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Lara K. Mahal
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | - Wesley F. Zandberg
- Department of Chemistry, The University of British Columbia, Kelowna, V1V 1V7, Canada
| | - Xuefei Huang
- Departments of Chemistry and Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - John S. Klassen
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | - Matthew S. Macauley
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, T6G 2J7, Canada
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226
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Bertok T, Pinkova Gajdosova V, Bertokova A, Svecova N, Kasak P, Tkac J. Breast cancer glycan biomarkers: their link to tumour cell metabolism and their perspectives in clinical practice. Expert Rev Proteomics 2021; 18:881-910. [PMID: 34711108 DOI: 10.1080/14789450.2021.1996231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Breast cancer (BCa) is the most common cancer type diagnosed in women and 5th most common cause of deaths among all cancer deaths despite the fact that screening program is at place. This is why novel diagnostics approaches are needed in order to decrease number of BCa cases and disease mortality. AREAS COVERED In this review paper, we aim to cover some basic aspects regarding cellular metabolism and signalling in BCa behind altered glycosylation. We also discuss novel exciting discoveries regarding glycan-based analysis, which can provide useful information for better understanding of the disease. The final part deals with clinical usefulness of glycan-based biomarkers and the clinical performance of such biomarkers is compared to already approved BCa biomarkers and diagnostic tools based on imaging. EXPERT OPINION Recent discoveries suggest that glycan-based biomarkers offer high accuracy for possible BCa diagnostics in blood, but also for better monitoring and management of BCa patients. The review article was written using Web of Science search engine to include articles published between 2019 and 2021.
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Affiliation(s)
- Tomas Bertok
- Glycanostics Ltd., Bratislava, Slovak Republic.,Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Veronika Pinkova Gajdosova
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | | | - Natalia Svecova
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kasak
- Center for Advanced Materials, Qatar University, Doha, Qatar
| | - Jan Tkac
- Glycanostics Ltd., Bratislava, Slovak Republic.,Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
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227
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Wu J, Wu M, Zhang H, Zhan X, Wu N. An Oligomannuronic Acid-Sialic Acid Conjugate Capable of Inhibiting Aβ42 Aggregation and Alleviating the Inflammatory Response of BV-2 Microglia. Int J Mol Sci 2021; 22:ijms222212338. [PMID: 34830217 PMCID: PMC8621211 DOI: 10.3390/ijms222212338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
Oligomannuronic acid (MOS) from seaweed has antioxidant and anti-inflammatory activities. In this study, MOS was activated at the terminal to obtain three different graft complexes modified with sialic acid moiety (MOS-Sia). The results show that MOS-Sia addition can reduce the β-structure formation of Aβ42, and the binding effect of MOS-Sia3 is more obvious. MOS-Sia conjugates also have a better complexing effect with Ca2+ while reducing the formation of Aβ42 oligomers in solutions. MOS-Sia3 (25–50 μg/mL) can effectively inhibit the activation state of BV-2 cells stimulated by Aβ42, whereas a higher dose of MOS-Sia3 (>50 μg/mL) can inhibit the proliferation of BV-2 cells to a certain extent. A lower dose of MOS-Sia3 can also inhibit the expression of IL-1β, IL-6, TNF-α, and other proinflammatory factors in BV-2 cells induced by Aβ42 activation. In the future, the MOS-Sia3 conjugate can be used to treat Alzheimer’s disease.
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Affiliation(s)
- Jianrong Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (M.W.); (H.Z.); (X.Z.)
- Correspondence: ; Tel.: +86-510-85918299
| | - Miaosen Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (M.W.); (H.Z.); (X.Z.)
| | - Hongtao Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (M.W.); (H.Z.); (X.Z.)
| | - Xiaobei Zhan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (M.W.); (H.Z.); (X.Z.)
| | - Nian Wu
- Division of Histology and Embryology, International Joint Laboratory for Embryonic Development and Prenatal Medicine, Medical College, Jinan University, Guangzhou 510632, China;
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228
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TÜNCEL Ö, KARA M, YAYLAK B, ERDOĞAN İ, AKGÜL B. Noncoding RNAs in apoptosis: identification and function. Turk J Biol 2021; 46:1-40. [PMID: 37533667 PMCID: PMC10393110 DOI: 10.3906/biy-2109-35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/08/2022] [Accepted: 11/14/2021] [Indexed: 08/04/2023] Open
Abstract
Apoptosis is a vital cellular process that is critical for the maintenance of homeostasis in health and disease. The derailment of apoptotic mechanisms has severe consequences such as abnormal development, cancer, and neurodegenerative diseases. Thus, there exist complex regulatory mechanisms in eukaryotes to preserve the balance between cell growth and cell death. Initially, protein-coding genes were prioritized in the search for such regulatory macromolecules involved in the regulation of apoptosis. However, recent genome annotations and transcriptomics studies have uncovered a plethora of regulatory noncoding RNAs that have the ability to modulate not only apoptosis but also many other biochemical processes in eukaryotes. In this review article, we will cover a brief summary of apoptosis and detection methods followed by an extensive discussion on microRNAs, circular RNAs, and long noncoding RNAs in apoptosis.
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Affiliation(s)
- Özge TÜNCEL
- Non-coding RNA Laboratory, Department of Molecular Biology and Genetics, Faculty of Science, İzmir Institute of Technology, İzmir,
Turkey
| | - Merve KARA
- Non-coding RNA Laboratory, Department of Molecular Biology and Genetics, Faculty of Science, İzmir Institute of Technology, İzmir,
Turkey
| | - Bilge YAYLAK
- Non-coding RNA Laboratory, Department of Molecular Biology and Genetics, Faculty of Science, İzmir Institute of Technology, İzmir,
Turkey
| | - İpek ERDOĞAN
- Non-coding RNA Laboratory, Department of Molecular Biology and Genetics, Faculty of Science, İzmir Institute of Technology, İzmir,
Turkey
| | - Bünyamin AKGÜL
- Non-coding RNA Laboratory, Department of Molecular Biology and Genetics, Faculty of Science, İzmir Institute of Technology, İzmir,
Turkey
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229
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Cui C, Wu X, Zhou Y. GlyinsRNA: a webserver for predicting glycosylation sites on small RNAs. RNA Biol 2021; 18:600-603. [PMID: 34559595 DOI: 10.1080/15476286.2021.1982574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Versatile RNA modifications play important roles in post-transcriptional regulations of gene expression, among which glycosylation modifications on small RNAs emerge as a novel clade whose characteristics need further interrogations. Here, we demonstrated that the sequence pattern around RNA glycosylation sites was not random and could be exploited for glycosylation site prediction. A machine learning predictor, GlyinsRNA, which integrated multiple RNA sequence representation encodings, was established. GlyinsRNA achieved AUROC (area under the receiver operating characteristic curve) of 0.7933 and 0.7979 in five-fold cross-validation and independent tests, respectively. GlyinsRNA was implemented as an online webserver, where both the predicted glycosylation sites and the overrepresented RNA-binding protein (RBP)-related motifs were annotated to facilitate the users. GlyinsRNA webserver is freely available at http://www.rnanut.net/glyinsrna.
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Affiliation(s)
- Chunmei Cui
- Department of Biomedical Informatics, Moe Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Xiaobin Wu
- Department of Biomedical Informatics, Moe Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yuan Zhou
- Department of Biomedical Informatics, Moe Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China
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230
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Tomé-Carneiro J, de Las Hazas MCL, Boughanem H, Böttcher Y, Cayir A, Macias González M, Dávalos A. Up-to-date on the evidence linking miRNA-related epitranscriptomic modifications and disease settings. Can these modifications affect cross-kingdom regulation? RNA Biol 2021; 18:586-599. [PMID: 34843412 DOI: 10.1080/15476286.2021.2002003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The field of epitranscriptomics is rapidly developing. Several modifications (e.g. methylations) have been identified for different RNA types. Current evidence shows that chemical RNA modifications can influence the whole molecule's secondary structure, translatability, functionality, stability, and degradation, and some are dynamically and reversibly modulated. miRNAs, in particular, are not only post-transcriptional modulators of gene expression but are themselves submitted to regulatory mechanisms. Understanding how these modifications are regulated and the resulting pathological consequences when dysregulation occurs is essential for the development of new therapeutic targets. In humans and other mammals, dietary components have been shown to affect miRNA expression and may also induce chemical modifications in miRNAs. The identification of chemical modifications in miRNAs (endogenous and exogenous) that can impact host gene expression opens up an alternative way to select new specific therapeutic targets.Hence, the aim of this review is to briefly address how RNA epitranscriptomic modifications can affect miRNA biogenesis and to summarize the existing evidence showing the connection between the (de)regulation of these processes and disease settings. In addition, we hypothesize on the potential effect certain chemical modifications could have on the potential cross-kingdom journey of dietary plant miRNAs.
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Affiliation(s)
- João Tomé-Carneiro
- Laboratory of Functional Foods, Madrid Institute for Advanced Studies (IMDEA)-food, CEI UAM + CSIM, Spain
| | | | - Hatim Boughanem
- Instituto de Investigación Biomédica de Málaga (Ibima), Unidad de Gestión Clínica de Endocrinología Y Nutrición Del Hospital Virgen de La Victoria, Málaga, Spain.,Instituto de Salud Carlos Iii (Isciii), Consorcio Ciber, M.p. Fisiopatología de La Obesidad Y Nutrición (Ciberobn), Madrid, Spain.,Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Yvonne Böttcher
- Institute of Clinical Medicine, Department of Clinical Molecular Biology (EpiGen), University of Oslo, Oslo, Norway.,Department of Medical Services and Techniques (EpiGen), Akershus Universitetssykehus, Lørenskog, Norway
| | - Akin Cayir
- Institute of Clinical Medicine, Department of Clinical Molecular Biology (EpiGen), University of Oslo, Oslo, Norway.,Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Manuel Macias González
- Instituto de Investigación Biomédica de Málaga (Ibima), Unidad de Gestión Clínica de Endocrinología Y Nutrición Del Hospital Virgen de La Victoria, Málaga, Spain.,Instituto de Salud Carlos Iii (Isciii), Consorcio Ciber, M.p. Fisiopatología de La Obesidad Y Nutrición (Ciberobn), Madrid, Spain
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-food, CEI UAM + CSIC, Spain
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231
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De Bisschop G, Allouche D, Frezza E, Masquida B, Ponty Y, Will S, Sargueil B. Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure. Noncoding RNA 2021; 7:71. [PMID: 34842779 PMCID: PMC8628965 DOI: 10.3390/ncrna7040071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 01/04/2023] Open
Abstract
As more sequencing data accumulate and novel puzzling genetic regulations are discovered, the need for accurate automated modeling of RNA structure increases. RNA structure modeling from chemical probing experiments has made tremendous progress, however accurately predicting large RNA structures is still challenging for several reasons: RNA are inherently flexible and often adopt many energetically similar structures, which are not reliably distinguished by the available, incomplete thermodynamic model. Moreover, computationally, the problem is aggravated by the relevance of pseudoknots and non-canonical base pairs, which are hardly predicted efficiently. To identify nucleotides involved in pseudoknots and non-canonical interactions, we scrutinized the SHAPE reactivity of each nucleotide of the 188 nt long lariat-capping ribozyme under multiple conditions. Reactivities analyzed in the light of the X-ray structure were shown to report accurately the nucleotide status. Those that seemed paradoxical were rationalized by the nucleotide behavior along molecular dynamic simulations. We show that valuable information on intricate interactions can be deduced from probing with different reagents, and in the presence or absence of Mg2+. Furthermore, probing at increasing temperature was remarkably efficient at pointing to non-canonical interactions and pseudoknot pairings. The possibilities of following such strategies to inform structure modeling software are discussed.
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Affiliation(s)
- Grégoire De Bisschop
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Delphine Allouche
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
- Institut Necker-Enfants Malades (INEM), Inserm U1151, 156 rue de Vaugirard, CEDEX 15, 75015 Paris, France
| | - Elisa Frezza
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
| | - Benoît Masquida
- Université de Strasbourg, CNRS UMR7156 GMGM, 67084 Strasbourg, France;
| | - Yann Ponty
- Ecole Polytechnique, CNRS UMR 7161, LIX, 91120 Palaiseau, France; (Y.P.); (S.W.)
| | - Sebastian Will
- Ecole Polytechnique, CNRS UMR 7161, LIX, 91120 Palaiseau, France; (Y.P.); (S.W.)
| | - Bruno Sargueil
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
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232
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233
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Clark KD, Rubakhin SS, Sweedler JV. Single-Neuron RNA Modification Analysis by Mass Spectrometry: Characterizing RNA Modification Patterns and Dynamics with Single-Cell Resolution. Anal Chem 2021; 93:14537-14544. [PMID: 34672536 PMCID: PMC8608286 DOI: 10.1021/acs.analchem.1c03507] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The entire collection of post-transcriptional modifications to RNA, known as the epitranscriptome, has been increasingly recognized as a critical regulatory layer in the cellular translation machinery. However, contemporary methods for the analysis of RNA modifications are limited to the detection of highly abundant modifications in bulk tissue samples, potentially obscuring unique epitranscriptomes of individual cells with population averages. We developed an approach, single-neuron RNA modification analysis by mass spectrometry (SNRMA-MS), that enables the detection and quantification of numerous post-transcriptionally modified nucleosides in single cells. When compared to a conventional RNA extraction approach that does not allow detection of RNA modifications in single cells, SNRMA-MS leverages an optimized sample preparation approach to detect up to 16 RNA modifications in individual neurons from the central nervous system of Aplysia californica. SNRMA-MS revealed that the RNA modification profiles of identified A. californica neurons with different physiological functions were mostly cell specific. However, functionally homologous neurons tended to demonstrate similar modification patterns. Stable isotope labeling with CD3-Met showed significant differences in RNA methylation rates that were dependent on the identity of the modification and the cell, with metacerebral cells (MCCs) displaying the fastest incorporation of CD3 groups into endogenous RNAs. Quantitative SNRMA-MS showed higher intracellular concentrations for 2'-O-methyladenosine and 2'-O-methylcytidine in homologous R2/LPl1 cell pairs than in MCCs. Overall, SNRMA-MS is the first analytical approach capable of simultaneously quantifying numerous RNA modifications in single neurons and revealing cell-specific modification profiles.
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Affiliation(s)
- Kevin D. Clark
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stanislav S. Rubakhin
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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234
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Chiu KY, Wang Q, Gunawardena HP, Held M, Faik A, Chen H. Desalting Paper Spay Mass Spectrometry (DPS-MS) for Rapid Detection of Glycans and Glycoconjugates. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 469:116688. [PMID: 35386843 PMCID: PMC8981528 DOI: 10.1016/j.ijms.2021.116688] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The detection of glycans and glycoconjugates has gained increasing attention in biological fields. Traditional mass spectrometry (MS)-based methods for glycoconjugate analysis are challenged with poor intensity when dealing with complex biological samples. We developed a desalting paper spray mass spectrometry (DPS-MS) strategy to overcome the issue of signal suppression of carbohydrates in salted buffer. Glycans and glycoconjugates (i.e., glycopeptides, nucleotide sugars, etc.) in non-volatile buffer (e.g., Tris buffer) can be loaded on the paper substrate from which buffers can be removed by washing with ACN/H2O (90/10 v/v) solution. Glycans or glycoconjugates can then be eluted and spray ionized by adding ACN/H2O/formic acid (FA) (10/90/1 v/v/v) solvent and applying a high voltage (HV) to the paper substrate. This work also showed that DPS-MS is applicable for direct detection of intact glycopeptides and nucleotide sugars as well as determination of glycosylation profiling of antibody, such as NIST monoclonal antibody IgG (NISTmAb). NISTmAb was deglycosylated with PNGase F to release N-linked oligosaccharides. Twenty-six N-linked oligosaccharides were detected by DPS-MS within a 5-minute timeframe without the need for further enrichment or derivatization. This work demonstrates that DPS-MS allows fast and sensitive detection of glycans/oligosaccharides and glycosylated species in complex matrices and has great potential in bioanalysis.
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Affiliation(s)
- Kai-Yuan Chiu
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA, 07102
| | - Qi Wang
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA, 07102
| | - Harsha P Gunawardena
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania, USA, 19477
| | - Michael Held
- Deparment of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, Ohio USA, 45701
| | - Ahmed Faik
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, Ohio USA, 45701
- Department of Environmental and Plant Biology, Ohio University, Athens Ohio, USA, 45701
| | - Hao Chen
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA, 07102
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235
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Georgeson J, Schwartz S. The ribosome epitranscriptome: inert-or a platform for functional plasticity? RNA (NEW YORK, N.Y.) 2021; 27:1293-1301. [PMID: 34312287 PMCID: PMC8522695 DOI: 10.1261/rna.078859.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A universal property of all rRNAs explored to date is the prevalence of post-transcriptional ("epitranscriptional") modifications, which expand the chemical and topological properties of the four standard nucleosides. Are these modifications an inert, constitutive part of the ribosome? Or could they, in part, also regulate the structure or function of the ribosome? In this review, we summarize emerging evidence that rRNA modifications are more heterogeneous than previously thought, and that they can also vary from one condition to another, such as in the context of a cellular response or a developmental trajectory. We discuss the implications of these results and key open questions on the path toward connecting such heterogeneity with function.
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Affiliation(s)
- Joseph Georgeson
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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236
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Thompson MG, Sacco MT, Horner SM. How RNA modifications regulate the antiviral response. Immunol Rev 2021; 304:169-180. [PMID: 34405413 PMCID: PMC8616813 DOI: 10.1111/imr.13020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 12/25/2022]
Abstract
Induction of the antiviral innate immune response is highly regulated at the RNA level, particularly by RNA modifications. Recent discoveries have revealed how RNA modifications play key roles in cellular surveillance of nucleic acids and in controlling gene expression in response to viral infection. These modifications have emerged as being essential for a functional antiviral response and maintaining cellular homeostasis. In this review, we will highlight these and other discoveries that describe how the antiviral response is controlled by modifications to both viral and cellular RNA, focusing on how mRNA cap modifications, N6-methyladenosine, and RNA editing all contribute to coordinating an efficient response that properly controls viral infection.
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Affiliation(s)
- Matthew G Thompson
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Matthew T Sacco
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Stacy M Horner
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
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237
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Dragomir MP, Knutsen E, Calin GA. Classical and noncanonical functions of miRNAs in cancers. Trends Genet 2021; 38:379-394. [PMID: 34728089 DOI: 10.1016/j.tig.2021.10.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022]
Abstract
Alterations in microRNAs (miRNAs) expression are causative in the initiation and progression of human cancers. The molecular events responsible for the widespread differential expression of miRNAs in malignancy are exemplified by their location in cancer-associated genomic regions, epigenetic mechanisms, transcriptional dysregulation, chemical modifications and editing, and alterations in miRNA biogenesis proteins. The classical miRNA function is synonymous with post-transcriptional repression of target protein genes. However, several studies have reported miRNAs functioning outside this paradigm and some of these novel modes of regulation of gene expression have been implicated in cancers. Here, we summarize key aspects of miRNA involvement in cancer, with a special focus on these lesser-studied mechanisms of action.
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Affiliation(s)
- Mihnea P Dragomir
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway.
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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238
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Li Z, Zhang J, Ai HW. Genetically Encoded Green Fluorescent Biosensors for Monitoring UDP-GlcNAc in Live Cells. ACS CENTRAL SCIENCE 2021; 7:1763-1770. [PMID: 34729420 PMCID: PMC8554846 DOI: 10.1021/acscentsci.1c00745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) is a nucleotide sugar used by glycosyltransferases to synthesize glycoproteins, glycosaminoglycans, glycolipids, and glycoRNA. UDP-GlcNAc also serves as the donor substrate for forming O-GlcNAc, a dynamic intracellular protein modification involved in diverse signaling and disease processes. UDP-GlcNAc is thus a central metabolite connecting nutrition, metabolism, signaling, and disease. There is a great interest in monitoring UDP-GlcNAc in biological systems. Here, we present the first genetically encoded, green fluorescent UDP-GlcNAc sensor (UGAcS), an optimized insertion of a circularly permuted green fluorescent protein (cpGFP) into an inactive mutant of an Escherichia coli UDP-GlcNAc transferase, for ratiometric monitoring of UDP-GlcNAc dynamics in live mammalian cells. Although UGAcS responds to UDP-GlcNAc quite selectively among various nucleotide sugars, UDP and uridine triphosphate (UTP) interfere with the response. We thus developed another biosensor named UXPS, which is responsive to UDP and UTP but not UDP-GlcNAc. We demonstrated the use of the biosensors to follow UDP-GlcNAc levels in cultured mammalian cells perturbed with nutritional changes, pharmacological inhibition, and knockdown or overexpression of key enzymes in the UDP-GlcNAc synthesis pathway. We further utilized the biosensors to monitor UDP-GlcNAc concentrations in pancreatic MIN6 β-cells under various culture conditions.
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239
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Thomès L, Bojar D. The Role of Fucose-Containing Glycan Motifs Across Taxonomic Kingdoms. Front Mol Biosci 2021; 8:755577. [PMID: 34631801 PMCID: PMC8492980 DOI: 10.3389/fmolb.2021.755577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
The extraordinary diversity of glycans leads to large differences in the glycomes of different kingdoms of life. Yet, while most monosaccharides are solely found in certain taxonomic groups, there is a small set of monosaccharides with widespread distribution across nearly all domains of life. These general monosaccharides are particularly relevant for glycan motifs, as they can readily be used by commensals and pathogens to mimic host glycans or hijack existing glycan recognition systems. Among these, the monosaccharide fucose is especially interesting, as it frequently presents itself as a terminal monosaccharide, primed for interaction with proteins. Here, we analyze fucose-containing glycan motifs across all taxonomic kingdoms. Using a hereby presented large species-specific glycan dataset and a plethora of methods for glycan-focused bioinformatics and machine learning, we identify characteristic as well as shared fucose-containing glycan motifs for various taxonomic groups, demonstrating clear differences in fucose usage. Even within domains, fucose is used differentially based on an organism’s physiology and habitat. We particularly highlight differences in fucose-containing motifs between vertebrates and invertebrates. With the example of pathogenic and non-pathogenic Escherichia coli strains, we also demonstrate the importance of fucose-containing motifs in molecular mimicry and thereby pathogenic potential. We envision that this study will shed light on an important class of glycan motifs, with potential new insights into the role of fucosylated glycans in symbiosis, pathogenicity, and immunity.
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Affiliation(s)
- Luc Thomès
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Bojar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
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240
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Mesnage R, Mahmud N, Mein CA, Antoniou MN. Alterations in small RNA profiles in liver following a subchronic exposure to a low-dose pesticide mixture in Sprague-Dawley rats. Toxicol Lett 2021; 353:20-26. [PMID: 34626815 DOI: 10.1016/j.toxlet.2021.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/17/2021] [Accepted: 10/04/2021] [Indexed: 02/07/2023]
Abstract
Small RNAs have emerged as a promising new type of biomarker to monitor health status and track the development of diseases. Here we report changes in the levels of small RNAs in the liver of rats exposed to a mixture of six pesticides frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole). Multivariate analysis with OPLS-DA methods showed that small RNA profiles can discriminate samples from pesticide treated rats from their concurrent controls. A total of 9 miRNAs were found to have their levels altered in the liver of the pesticide-treated rats in comparison to the controls, which included 7 that were downregulated (miR-22-5p, miR-193a-3p, miR-32-5p, miR-33-5p, miR-122-5p, miR-22-3p, miR-130a-3p) and 2 that were upregulated (miR-486-5p, miR-146a-5p). These miRNAs were predicted to regulate genes, which were found to have their expression altered by the pesticide mixture and have known health implications in the regulation of hepatic metabolism. This supports and extends our recent conclusions that high- throughput 'omics' analyses can reveal molecular perturbations, which can potentially act as sensitive and accurate markers of health risks arising from exposure to environmental pollutants such as pesticides.
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Affiliation(s)
- Robin Mesnage
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, Guy's Hospital, London, SE1 9RT, United Kingdom
| | - Nadiya Mahmud
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London, E1 2AT, United Kingdom
| | - Charles A Mein
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London, E1 2AT, United Kingdom
| | - Michael N Antoniou
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, Guy's Hospital, London, SE1 9RT, United Kingdom.
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241
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Welch LG, Peak-Chew SY, Begum F, Stevens TJ, Munro S. GOLPH3 and GOLPH3L are broad-spectrum COPI adaptors for sorting into intra-Golgi transport vesicles. J Cell Biol 2021; 220:e202106115. [PMID: 34473204 PMCID: PMC8421267 DOI: 10.1083/jcb.202106115] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
The fidelity of Golgi glycosylation is, in part, ensured by compartmentalization of enzymes within the stack. The COPI adaptor GOLPH3 has been shown to interact with the cytoplasmic tails of a subset of Golgi enzymes and direct their retention. However, other mechanisms of retention, and other roles for GOLPH3, have been proposed, and a comprehensive characterization of the clientele of GOLPH3 and its paralogue GOLPH3L is lacking. GOLPH3's role is of particular interest as it is frequently amplified in several solid tumor types. Here, we apply two orthogonal proteomic methods to identify GOLPH3+3L clients and find that they act in diverse glycosylation pathways or have other roles in the Golgi. Binding studies, bioinformatics, and a Golgi retention assay show that GOLPH3+3L bind the cytoplasmic tails of their clients through membrane-proximal positively charged residues. Furthermore, deletion of GOLPH3+3L causes multiple defects in glycosylation. Thus, GOLPH3+3L are major COPI adaptors that impinge on most, if not all, of the glycosylation pathways of the Golgi.
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Affiliation(s)
| | | | | | | | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK
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242
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Guzman NA, Guzman DE. Immunoaffinity Capillary Electrophoresis in the Era of Proteoforms, Liquid Biopsy and Preventive Medicine: A Potential Impact in the Diagnosis and Monitoring of Disease Progression. Biomolecules 2021; 11:1443. [PMID: 34680076 PMCID: PMC8533156 DOI: 10.3390/biom11101443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/08/2023] Open
Abstract
Over the years, multiple biomarkers have been used to aid in disease screening, diagnosis, prognosis, and response to therapy. As of late, protein biomarkers are gaining strength in their role for early disease diagnosis and prognosis in part due to the advancements in identification and characterization of a distinct functional pool of proteins known as proteoforms. Proteoforms are defined as all of the different molecular forms of a protein derived from a single gene caused by genetic variations, alternative spliced RNA transcripts and post-translational modifications. Monitoring the structural changes of each proteoform of a particular protein is essential to elucidate the complex molecular mechanisms that guide the course of disease. Clinical proteomics therefore holds the potential to offer further insight into disease pathology, progression, and prevention. Nevertheless, more technologically advanced diagnostic methods are needed to improve the reliability and clinical applicability of proteomics in preventive medicine. In this manuscript, we review the use of immunoaffinity capillary electrophoresis (IACE) as an emerging powerful diagnostic tool to isolate, separate, detect and characterize proteoform biomarkers obtained from liquid biopsy. IACE is an affinity capture-separation technology capable of isolating, concentrating and analyzing a wide range of biomarkers present in biological fluids. Isolation and concentration of target analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. IACE has the potential to generate rapid results with significant accuracy, leading to reliability and reproducibility in diagnosing and monitoring disease. Additionally, IACE has the capability of monitoring the efficacy of therapeutic agents by quantifying companion and complementary protein biomarkers. With advancements in telemedicine and artificial intelligence, the implementation of proteoform biomarker detection and analysis may significantly improve our capacity to identify medical conditions early and intervene in ways that improve health outcomes for individuals and populations.
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Affiliation(s)
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08543, USA;
- Division of Hospital Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
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243
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Ren J, Sherry AD. 31 P-MRS of healthy human brain: Measurement of guanosine diphosphate mannose at 7 T. NMR IN BIOMEDICINE 2021; 34:e4576. [PMID: 34155714 DOI: 10.1002/nbm.4576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/01/2021] [Accepted: 06/05/2021] [Indexed: 06/13/2023]
Abstract
Guanosine diphosphate mannose (GDP-Man) is the donor substrate required for mannosylation in the synthesis of glycoproteins, glycolipids and the newly discovered glycoRNA. Normal GDP-Man biosynthesis plays a crucial role in support of a variety of cellular functions, including cell recognition, cell communication and immune responses against viruses. Here, we report the detection of GDP-Man in human brain for the first time, using 31 P MRS at 7 T. The presence of GDP-Man is evidenced by the detection of a weak 31 P doublet at -10.7 ppm that can be assigned to the phosphomannosyl group (Pβ) of the GDP-Man molecule. This weak but well-resolved signal lies 0.9 ppm upfield of UDP(G) Pβ-multiplet from a mixture of UDP-Glc, UDP-Gal, UDP-GlcNAc and UDP-GalNAc. In reference to ATP (2.8 mM), the concentration of GDP-Man in human brain was estimated to be 0.02 ± 0.01 mM, about 15-fold lower than the total concentration of UDP(G) (0.30 ± 0.04, N = 17) and consistent with previous reports of UDP-Man in cells and brain tissue extracts measured by high-performance liquid chromatography. The reproducibility of the measured GDP-Man between test and 2-week retest was 21% ± 15% compared with 5% ± 4% for UDP(G) (N = 7). The measured concentrations of GDP-Man and UDP(G) are linearly correlated ([UDP(G)] = 4.3 [GDP-Man] + 0.02, with R = 0.66 and p = 0.0043), likely reflecting the effect of shared sugar precursors, which may vary among individuals in response to variation in nutritional intake and consumption. Given that GDP-Man has another set of doublet (Pα) at -8.3 ppm that overlaps with NAD(H) and UDP(G)-Pα signals, the amount of GDP-Man could potentially interfere with the deconvolution of these mixed signals in composition analysis. Importantly, this new finding may be useful in advancing our understanding of glycosylation and its role in the development of cancer, as well as infectious and neurodegenerative diseases.
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Affiliation(s)
- Jimin Ren
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - A Dean Sherry
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Chemistry, University of Texas at Dallas, Richardson, Texas, USA
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244
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García-García A, Hicks T, El Qaidi S, Zhu C, Hardwidge PR, Angulo J, Hurtado-Guerrero R. NleB/SseK-catalyzed arginine-glycosylation and enteropathogen virulence are finely tuned by a single variable position contiguous to the catalytic machinery. Chem Sci 2021; 12:12181-12191. [PMID: 34667584 PMCID: PMC8457375 DOI: 10.1039/d1sc04065k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/12/2021] [Indexed: 01/18/2023] Open
Abstract
NleB/SseK effectors are arginine-GlcNAc-transferases expressed by enteric bacterial pathogens that modify host cell proteins to disrupt signaling pathways. While the conserved Citrobacter rodentium NleB and E. coli NleB1 proteins display a broad selectivity towards host proteins, Salmonella enterica SseK1, SseK2, and SseK3 have a narrowed protein substrate selectivity. Here, by combining computational and biophysical experiments, we demonstrate that the broad protein substrate selectivity of NleB relies on Tyr284NleB/NleB1, a second-shell residue contiguous to the catalytic machinery. Tyr284NleB/NleB1 is important in coupling protein substrate binding to catalysis. This is exemplified by S286YSseK1 and N302YSseK2 mutants, which become active towards FADD and DR3 death domains, respectively, and whose kinetic properties match those of enterohemorrhagic E. coli NleB1. The integration of these mutants into S. enterica increases S. enterica survival in macrophages, suggesting that better enzymatic kinetic parameters lead to enhanced virulence. Our findings provide insights into how these enzymes finely tune arginine-glycosylation and, in turn, bacterial virulence. In addition, our data show how promiscuous glycosyltransferases preferentially glycosylate specific protein substrates. The NleB and SseK glycosyltransferases glycosylate arginine residues of mammalian proteins with different substrate specificities. We uncover that these differences rely on a particular second-shell residue contiguous to the catalytic machinery.![]()
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Affiliation(s)
- Ana García-García
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D Zaragoza Spain
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University Manhattan KS 66506 USA
| | - Congrui Zhu
- College of Veterinary Medicine, Kansas State University Manhattan KS 66506 USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University Manhattan KS 66506 USA
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia Norwich Research Park Norwich NR4 7TJ UK.,Departamento de Química Orgánica, Universidad de Sevilla Sevilla 41012 Spain .,Instituto de Investigaciones Químicas (CSIC-US) Sevilla 41092 Spain
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D Zaragoza Spain .,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen Copenhagen Denmark.,Fundación ARAID Zaragoza Spain
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245
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The Non-Coding RNA Journal Club: Highlights on Recent Papers-9. Noncoding RNA 2021; 7:ncrna7030058. [PMID: 34564320 PMCID: PMC8482151 DOI: 10.3390/ncrna7030058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022] Open
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246
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Donohoo KB, Wang J, Goli M, Yu A, Peng W, Hakim MA, Mechref Y. Advances in mass spectrometry-based glycomics-An update covering the period 2017-2021. Electrophoresis 2021; 43:119-142. [PMID: 34505713 DOI: 10.1002/elps.202100199] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022]
Abstract
The wide variety of chemical properties and biological functions found in proteins is attained via post-translational modifications like glycosylation. Covalently bonded to proteins, glycans play a critical role in cell activity. Complex structures with microheterogeneity, the glycan structures that are associated with proteins are difficult to analyze comprehensively. Recent advances in sample preparation methods, separation techniques, and MS have facilitated the quantitation and structural elucidation of glycans. This review focuses on highlighting advances in MS-based techniques for glycomic analysis that occurred over the last 5 years (2017-2021) as an update to the previous review on the subject. The topics of discussion will include progress in glycomic workflow such as glycan release, purification, derivatization, and separation as well as the topics of ionization, tandem MS, and separation techniques that can be coupled with MS. Additionally, bioinformatics tools used for the analysis of glycans will be described.
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Affiliation(s)
- Kaitlyn B Donohoo
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Md Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
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247
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Cortés-Hernández LE, Eslami-S Z, Costa-Silva B, Alix-Panabières C. Current Applications and Discoveries Related to the Membrane Components of Circulating Tumor Cells and Extracellular Vesicles. Cells 2021; 10:2221. [PMID: 34571870 PMCID: PMC8465935 DOI: 10.3390/cells10092221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
In cancer, many analytes can be investigated through liquid biopsy. They play fundamental roles in the biological mechanisms underpinning the metastatic cascade and provide clinical information that can be monitored in real time during the natural course of cancer. Some of these analytes (circulating tumor cells and extracellular vesicles) share a key feature: the presence of a phospholipid membrane that includes proteins, lipids and possibly nucleic acids. Most cell-to-cell and cell-to-matrix interactions are modulated by the cell membrane composition. To understand cancer progression, it is essential to describe how proteins, lipids and nucleic acids in the membrane influence these interactions in cancer cells. Therefore, assessing such interactions and the phospholipid membrane composition in different liquid biopsy analytes might be important for future diagnostic and therapeutic strategies. In this review, we briefly describe some of the most important surface components of circulating tumor cells and extracellular vesicles as well as their interactions, putting an emphasis on how they are involved in the different steps of the metastatic cascade and how they can be exploited by the different liquid biopsy technologies.
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Affiliation(s)
- Luis Enrique Cortés-Hernández
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, CEDEX 5, 34295 Montpellier, France; (L.E.C.-H.); (Z.E.-S.)
- CREEC/CANECEV, MIVEGEC (CREES), Université de Montpellier, CNRS, IRD, 34000 Montpellier, France
| | - Zahra Eslami-S
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, CEDEX 5, 34295 Montpellier, France; (L.E.C.-H.); (Z.E.-S.)
- CREEC/CANECEV, MIVEGEC (CREES), Université de Montpellier, CNRS, IRD, 34000 Montpellier, France
| | - Bruno Costa-Silva
- Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal;
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, CEDEX 5, 34295 Montpellier, France; (L.E.C.-H.); (Z.E.-S.)
- CREEC/CANECEV, MIVEGEC (CREES), Université de Montpellier, CNRS, IRD, 34000 Montpellier, France
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248
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Affiliation(s)
- Sigrid Nachtergaele
- From the Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT (S.N.); and the Department of Chemistry and the Grossman Institute of Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago (Y.K.)
| | - Yamuna Krishnan
- From the Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT (S.N.); and the Department of Chemistry and the Grossman Institute of Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago (Y.K.)
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249
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Russo L. Glycans and diagnostics in nanomedicine. Nanomedicine (Lond) 2021; 16:1839-1842. [PMID: 34348476 DOI: 10.2217/nnm-2021-0173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Laura Russo
- Department of Biotechnology & Biosciences, University of Milano-Bicocca, 20126, Milan, Italy.,BioNanoMedicine Center, University of Milano-Bicocca, Via Follereau 3, 20854, Vedano al Lambro (MB), Italy.,CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, H91 W2TY, Galway, Ireland
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250
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Chevet E, De Matteis MA, Eskelinen EL, Farhan H. RNA, a new member in the glycan-club that gets exposed at the cell surface. Traffic 2021; 22:362-363. [PMID: 34338403 DOI: 10.1111/tra.12810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/27/2022]
Abstract
In this article we discuss implications of the recent discovery of glycoRNAs found to be present at the cell surface of mammalian cells which was reported by Flynn et al. Cell 2021.
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Affiliation(s)
- Eric Chevet
- INSERM U1242, University of Rennes 1, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II-Medical School, Naples, Italy
| | | | - Hesso Farhan
- Institute of Pathophysiology, Medical University of Innsbruck, Innsbruck, Austria
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