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Zhang S, Tang Q, Zhang X, Chen X. Proximitomics by Reactive Species. ACS CENTRAL SCIENCE 2024; 10:1135-1147. [PMID: 38947200 PMCID: PMC11212136 DOI: 10.1021/acscentsci.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 07/02/2024]
Abstract
The proximitome is defined as the entire collection of biomolecules spatially in the proximity of a biomolecule of interest. More broadly, the concept of the proximitome can be extended to the totality of cells proximal to a specific cell type. Since the spatial organization of biomolecules and cells is essential for almost all biological processes, proximitomics has recently emerged as an active area of scientific research. One of the growing strategies for proximitomics leverages reactive species-which are generated in situ and spatially confined, to chemically tag and capture proximal biomolecules and cells for systematic analysis. In this Outlook, we summarize different types of reactive species that have been exploited for proximitomics and discuss their pros and cons for specific applications. In addition, we discuss the current challenges and future directions of this exciting field.
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Affiliation(s)
- Shaoran Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Qi Tang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
| | - Xu Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Xing Chen
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
- Synthetic
and Functional Biomolecules Center, Peking
University, Beijing 100871, People’s
Republic of China
- Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry
of Education, Peking University, Beijing 100871, People’s Republic of China
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2
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Nelson ZM, Kadiri O, Fehl C. GlycoID Proximity Labeling to Identify O-GlcNAcylated Protein Interactomes in Live Cells. Curr Protoc 2024; 4:e1052. [PMID: 38752278 PMCID: PMC11101149 DOI: 10.1002/cpz1.1052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
Cells continuously remodel their intracellular proteins with the monosaccharide O-linked N-acetylglucosamine (O-GlcNAc) to regulate metabolism, signaling, and stress. This protocol describes the use of GlycoID tools to capture O-GlcNAc dynamics in live cells. GlycoID constructs contain an O-GlcNAc binding domain linked to a proximity labeling domain and a subcellular localization sequence. When expressed in mammalian cells, GlycoID tracks changes in O-GlcNAc-modified proteins and their interactomes in response to chemical induction with biotin over time. Pairing the subcellular localization of GlycoID with the chemical induction of activity enables spatiotemporal studies of O-GlcNAc biology during cellular events such as insulin signaling. However, optimizing intracellular labeling experiments requires attention to several variables. Here, we describe two protocols to adapt GlycoID methods to a cell line and biological process of interest. Next, we describe how to conduct a semiquantitative proteomic analysis of O-GlcNAcylated proteins and their interactomes using insulin versus glucagon signaling as a sample application. This articles aims to establish baseline GlycoID protocols for new users and set the stage for widespread use over diverse cellular applications for the functional study of O-GlcNAc glycobiology. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Expression of targeted GlycoID constructs to verify subcellular location and labeling activity in mammalian cells Basic Protocol 2: GlycoID labeling in live HeLa cells for O-GlcNAc proteomic comparisons.
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Affiliation(s)
- Zachary M. Nelson
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, United States
| | - Oseni Kadiri
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, United States
| | - Charlie Fehl
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, United States
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3
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Stewart N, Daly J, Drummond-Guy O, Krishnamoorthy V, Stark JC, Riley NM, Williams KC, Bertozzi CR, Wisnovsky S. The glycoimmune checkpoint receptor Siglec-7 interacts with T-cell ligands and regulates T-cell activation. J Biol Chem 2024; 300:105579. [PMID: 38141764 PMCID: PMC10831161 DOI: 10.1016/j.jbc.2023.105579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/28/2023] [Indexed: 12/25/2023] Open
Abstract
Siglec-7 (sialic acid-binding immunoglobulin-like lectin 7) is a glycan-binding immune receptor that is emerging as a significant target of interest for cancer immunotherapy. The physiological ligands that bind Siglec-7, however, remain incompletely defined. In this study, we characterized the expression of Siglec-7 ligands on peripheral immune cell subsets and assessed whether Siglec-7 functionally regulates interactions between immune cells. We found that disialyl core 1 O-glycans are the major immune ligands for Siglec-7 and that these ligands are particularly highly expressed on naïve T-cells. Densely glycosylated sialomucins are the primary carriers of these glycans, in particular a glycoform of the cell-surface marker CD43. Biosynthesis of Siglec-7-binding glycans is dynamically controlled on different immune cell subsets through a genetic circuit involving the glycosyltransferase GCNT1. Siglec-7 blockade was found to increase activation of both primary T-cells and antigen-presenting dendritic cells in vitro, indicating that Siglec-7 binds T-cell glycans to regulate intraimmune signaling. Finally, we present evidence that Siglec-7 directly activates signaling pathways in T-cells, suggesting a new biological function for this receptor. These studies conclusively demonstrate the existence of a novel Siglec-7-mediated signaling axis that physiologically regulates T-cell activity. Going forward, our findings have significant implications for the design and implementation of therapies targeting immunoregulatory Siglec receptors.
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Affiliation(s)
- Natalie Stewart
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - John Daly
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Olivia Drummond-Guy
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vignesh Krishnamoorthy
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessica C Stark
- Department of Chemistry & Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Boston, Massachusetts, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Boston, Massachusetts, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Boston, Massachusetts, USA
| | - Nicholas M Riley
- Department of Chemistry & Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Karla C Williams
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carolyn R Bertozzi
- Department of Chemistry & Sarafan ChEM-H, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Simon Wisnovsky
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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4
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Takeuchi T, Oyama M, Tamura M, Arata Y, Hatanaka T. Reduced form of Galectin-1 Suppresses Osteoclastic Differentiation of Human Peripheral Blood Mononuclear Cells and Murine RAW264 Cells In Vitro. Biomolecules 2024; 14:121. [PMID: 38254721 PMCID: PMC10813495 DOI: 10.3390/biom14010121] [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: 11/28/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Galectin-1 (Gal-1) is an evolutionarily conserved sugar-binding protein found in intra- and extracellular spaces. Extracellularly, it binds to glycoconjugates with β-galactoside(s) and functions in various biological phenomena, including immunity, cancer, and differentiation. Under extracellular oxidative conditions, Gal-1 undergoes oxidative inactivation, losing its sugar-binding ability, although it exhibits sugar-independent functions. An age-related decrease in serum Gal-1 levels correlates with decreasing bone mass, and Gal-1 knockout promotes osteoclastic bone resorption and suppresses bone formation. However, the effect of extracellular Gal-1 on osteoclast differentiation remains unclear. Herein, we investigated the effects of extracellular Gal-1 on osteoclastogenesis in human peripheral blood mononuclear cells (PBMCs) and mouse macrophage RAW264 cells. Recombinant Gal-1 suppressed the macrophage colony-stimulating factor and receptor activator of nuclear factor-κB ligand-dependent osteoclast formation, actin ring formation, and bone-resorption activity of human PBMCs. Similar results were obtained for RAW264 cells. Gal-1 knockdown increased osteoclast-like cell formation, suggesting that it affected differentiation in an autocrine-like manner. Oxidized Gal-1 slightly affected differentiation, and in the presence of lactose, the differentiation inhibitory effect of galectin-1 was not observed. These findings suggest that extracellular Gal-1 inhibits osteoclast differentiation in a β-galactoside-dependent manner, and an age-related decrease in serum Gal-1 levels may contribute to reduced osteoclast activity and decreasing bone mass.
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Affiliation(s)
- Tomoharu Takeuchi
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado 350-0295, Saitama, Japan; (M.O.); (T.H.)
| | - Midori Oyama
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado 350-0295, Saitama, Japan; (M.O.); (T.H.)
| | - Mayumi Tamura
- Faculty of Pharma-Science, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; (M.T.); (Y.A.)
| | - Yoichiro Arata
- Faculty of Pharma-Science, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; (M.T.); (Y.A.)
| | - Tomomi Hatanaka
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado 350-0295, Saitama, Japan; (M.O.); (T.H.)
- School of Medicine, Tokai University, 143 Shimokasuya, Isehara 259-1193, Kanagawa, Japan
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5
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Troncoso MF, Elola MT, Blidner AG, Sarrias L, Espelt MV, Rabinovich GA. The universe of galectin-binding partners and their functions in health and disease. J Biol Chem 2023; 299:105400. [PMID: 37898403 PMCID: PMC10696404 DOI: 10.1016/j.jbc.2023.105400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/30/2023] Open
Abstract
Galectins, a family of evolutionarily conserved glycan-binding proteins, play key roles in diverse biological processes including tissue repair, adipogenesis, immune cell homeostasis, angiogenesis, and pathogen recognition. Dysregulation of galectins and their ligands has been observed in a wide range of pathologic conditions including cancer, autoimmune inflammation, infection, fibrosis, and metabolic disorders. Through protein-glycan or protein-protein interactions, these endogenous lectins can shape the initiation, perpetuation, and resolution of these processes, suggesting their potential roles in disease monitoring and treatment. However, despite considerable progress, a full understanding of the biology and therapeutic potential of galectins has not been reached due to their diversity, multiplicity of cell targets, and receptor promiscuity. In this article, we discuss the multiple galectin-binding partners present in different cell types, focusing on their contributions to selected physiologic and pathologic settings. Understanding the molecular bases of galectin-ligand interactions, particularly their glycan-dependency, the biochemical nature of selected receptors, and underlying signaling events, might contribute to designing rational therapeutic strategies to control a broad range of pathologic conditions.
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Affiliation(s)
- María F Troncoso
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química y Fisicoquímica Biológicas (IQUIFIB) Prof Alejandro C. Paladini, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María T Elola
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química y Fisicoquímica Biológicas (IQUIFIB) Prof Alejandro C. Paladini, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ada G Blidner
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina
| | - Luciana Sarrias
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química y Fisicoquímica Biológicas (IQUIFIB) Prof Alejandro C. Paladini, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María V Espelt
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química y Fisicoquímica Biológicas (IQUIFIB) Prof Alejandro C. Paladini, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gabriel A Rabinovich
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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6
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Nguyễn KB, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. Cell Chem Biol 2023; 30:811-827.e7. [PMID: 37419112 PMCID: PMC10510412 DOI: 10.1016/j.chembiol.2023.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/01/2023] [Accepted: 06/07/2023] [Indexed: 07/09/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxICAT, Biotin Switch, and SP3-Rox, these methods typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. Here we establish the local cysteine capture (Cys-LoC) and local cysteine oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole-cell proteomic analysis. Application of the Cys-LOx method to LPS-stimulated immortalized murine bone marrow-derived macrophages (iBMDM), revealed previously unidentified, mitochondrially localized cysteine oxidative modifications upon pro-inflammatory activation, including those associated with oxidative mitochondrial metabolism.
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Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Ashley R Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Andréa B Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Lisa M Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Alexandra C Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Kaitlyn B Nguyễn
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Stephanie L Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Heta S Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
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7
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Reeves AE, Huang ML. Proximity labeling technologies to illuminate glycan-protein interactions. Curr Opin Chem Biol 2023; 72:102233. [PMID: 36493526 PMCID: PMC9870929 DOI: 10.1016/j.cbpa.2022.102233] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
Glycosylation is a ubiquitous post-translational modification read by glycan-binding proteins (GBP) to encode important functions, but a robust understanding of these interactions and their consequences can be challenging to uncover. Glycan-GBP interactions are transient and weak, making them difficult to capture, and glycosylation is dynamic and heterogenous, necessitating study in native cellular environments to identify endogenous ligands. Proximity labeling, an experimental innovation that labels biomolecules close to a protein of interest, has recently emerged as a powerful strategy to overcome these limitations, allowing interactors to be tagged in cells for subsequent enrichment and identification by mass spectrometry-based proteomics. We will describe this nascent technique and discuss its applications in the last five years with different GBP classes, including Siglecs, galectins, and non-human lectins.
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Affiliation(s)
- Abigail E Reeves
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Mia L Huang
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
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8
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525042. [PMID: 36711448 PMCID: PMC9882296 DOI: 10.1101/2023.01.22.525042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxiCat, Biotin Switch, and SP3-Rox, they typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. To obviate requirements for laborious biochemical fractionation, here, we develop and apply an unprecedented two step cysteine capture method to establish the Local Cysteine Capture (Cys-LoC), and Local Cysteine Oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole cell proteomic analysis. Application of the Cys-LOx method to LPS stimulated murine immortalized bone marrow-derived macrophages (iBMDM), revealed previously unidentified mitochondria-specific inflammation-induced cysteine oxidative modifications including those associated with oxidative phosphorylation. These findings shed light on post-translational mechanisms regulating mitochondrial function during the cellular innate immune response.
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Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Ashley R. Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Anthony E. Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Andréa B. Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Lisa M. Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Alexandra C. Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Stephanie L. Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Heta S. Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Ajit S. Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M. Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA.,DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA.,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
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9
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Laderach DJ, Compagno D. Inhibition of galectins in cancer: Biological challenges for their clinical application. Front Immunol 2023; 13:1104625. [PMID: 36703969 PMCID: PMC9872792 DOI: 10.3389/fimmu.2022.1104625] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Galectins play relevant roles in tumor development, progression and metastasis. Accordingly, galectins are certainly enticing targets for medical intervention in cancer. To date, however, clinical trials based on galectin inhibitors reported inconclusive results. This review summarizes the galectin inhibitors currently being evaluated and discusses some of the biological challenges that need to be addressed to improve these strategies for the benefit of cancer patients.
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Affiliation(s)
- Diego José Laderach
- Molecular and Functional Glyco-Oncology Laboratory, Instituto de Química Biológica de la Facutad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET), Buenos Aires, Argentina,Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina,Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina,*Correspondence: Diego José Laderach,
| | - Daniel Compagno
- Molecular and Functional Glyco-Oncology Laboratory, Instituto de Química Biológica de la Facutad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET), Buenos Aires, Argentina,Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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10
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Wisnovsky S, Bertozzi CR. Reading the glyco-code: New approaches to studying protein-carbohydrate interactions. Curr Opin Struct Biol 2022; 75:102395. [PMID: 35653954 PMCID: PMC9811956 DOI: 10.1016/j.sbi.2022.102395] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/06/2022] [Accepted: 04/16/2022] [Indexed: 01/07/2023]
Abstract
The surface of all living cells is decorated with carbohydrate molecules. Hundreds of functional proteins bind to these glycosylated ligands; such binding events subsequently modulate many aspects of protein and cell function. Identifying ligands for glycan-binding proteins (GBPs) is a defining challenge of glycoscience research. Here, we review recent advances that are allowing protein-carbohydrate interactions to be dissected with an unprecedented level of precision. We specifically highlight how cell-based glycan arrays and glyco-genomic profiling are being used to define the structural determinants of glycan-protein interactions in living cells. Going forward, these methods create exciting new opportunities for the study of glycans in physiology and disease.
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Affiliation(s)
- Simon Wisnovsky
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA,Howard Hughes Medical Institute, Stanford, CA, 94305, USA
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11
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Griffin ME, Hsieh-Wilson LC. Tools for mammalian glycoscience research. Cell 2022; 185:2657-2677. [PMID: 35809571 PMCID: PMC9339253 DOI: 10.1016/j.cell.2022.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Cellular carbohydrates or glycans are critical mediators of biological function. Their remarkably diverse structures and varied activities present exciting opportunities for understanding many areas of biology. In this primer, we discuss key methods and recent breakthrough technologies for identifying, monitoring, and manipulating glycans in mammalian systems.
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Affiliation(s)
- Matthew E. Griffin
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Linda C. Hsieh-Wilson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 92115, USA,Correspondence: (L.C.H.W.)
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12
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Critcher M, Huang ML. Excavating proteoglycan structure-function relationships: Modern approaches to capture the interactions of ancient biomolecules. Am J Physiol Cell Physiol 2022; 323:C415-C422. [PMID: 35759439 PMCID: PMC9359657 DOI: 10.1152/ajpcell.00222.2022] [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: 11/22/2022]
Abstract
Proteoglycans are now well regarded as key facilitators of cell biology. While a majority of their interactions and functions are attributed to the decorating glycosaminoglycan chains, there is a growing appreciation for the roles of the proteoglycan core protein and for considering proteoglycans as replete protein-glycan conjugates. This appreciation, seeded by early work in proteoglycan biology, is now being advanced and exalted by modern approaches in chemical glycobiology. In this review, we discuss up-and-coming methods to unearth the fine-scale architecture of proteoglycans that modulate their functions and interactions. Crucial to these efforts is the production of chemically defined materials, including semi-synthetic proteoglycans and the in situ capture of interacting proteins. Together, the integration of chemical biology approaches promises to expedite the dissection of the structural heterogeneity of proteoglycans and deliver refined insight into their functions.
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Affiliation(s)
- Meg Critcher
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, CA.,Department of Molecular Medicine, Scripps Research, La Jolla, CA
| | - Mia L Huang
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, CA.,Department of Molecular Medicine, Scripps Research, La Jolla, CA.,Department of Chemistry, Scripps Research, La Jolla, CA
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O'Leary TR, Critcher M, Stephenson TN, Yang X, Hassan AA, Bartfield NM, Hawkins R, Huang ML. Chemical editing of proteoglycan architecture. Nat Chem Biol 2022; 18:634-642. [PMID: 35551261 PMCID: PMC9205196 DOI: 10.1038/s41589-022-01023-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 03/29/2022] [Indexed: 12/21/2022]
Abstract
Proteoglycans are heterogeneous macromolecular glycoconjugates that orchestrate many important cellular processes. While much attention has focused on the poly-sulfated glycosaminoglycan chains that decorate proteoglycans, other important elements of their architecture, such as core proteins and membrane localization, have garnered less emphasis. Hence, comprehensive structure-function relationships that consider the replete proteoglycan architecture as glycoconjugates are limited. Here we present an extensive approach to study proteoglycan structure and biology by fabricating defined semisynthetic modular proteoglycans that can be tailored for cell surface display. The expression of proteoglycan core proteins with unnatural amino acids permits bioorthogonal click chemistry with functionalized glycosaminoglycans for methodical dissection of the parameters required for optimal binding and function of various proteoglycan-binding proteins. We demonstrate that these sophisticated materials can recapitulate the functions of native proteoglycan ectodomains in mouse embryonic stem cell differentiation and cancer cell spreading while permitting the analysis of the contributing architectural elements toward function.
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Affiliation(s)
- Timothy R O'Leary
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - Meg Critcher
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, CA, USA
| | | | - Xueyi Yang
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, CA, USA
| | - Abdullah A Hassan
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - Noah M Bartfield
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - Richard Hawkins
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - Mia L Huang
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA.
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, CA, USA.
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
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Critcher M, Hassan AA, Huang ML. Seeing the forest through the trees: characterizing the glycoproteome. Trends Biochem Sci 2022; 47:492-505. [DOI: 10.1016/j.tibs.2022.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 12/14/2022]
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Jiang HS, Zhuang SC, Lam CH, Chang LY, Angata T. Recent Progress in the Methodologies to Identify Physiological Ligands of Siglecs. Front Immunol 2021; 12:813082. [PMID: 34956244 PMCID: PMC8702521 DOI: 10.3389/fimmu.2021.813082] [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: 11/11/2021] [Accepted: 11/23/2021] [Indexed: 11/28/2022] Open
Abstract
Siglecs, a family of receptor-like lectins, recognize glycoproteins and/or glycolipids containing sialic acid in the extracellular space and transduce intracellular signaling. Recently, researchers uncovered significant contributions of Siglecs in cancer immunity, renewing interest in this family of proteins. Previous extensive studies have defined how Siglecs recognize glycan epitopes (glycotopes). Nevertheless, the biological role of these glycotopes has not been fully evaluated. Recent studies using live cells have begun unraveling the constituents of Siglec ligands. These studies demonstrated that glycoprotein scaffolds (counter-receptors) displaying glycotopes are sometimes just as important as the glycotope itself. These new insights may guide future efforts to develop therapeutic agents to target the Siglec – ligand axis.
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Affiliation(s)
- Huei-Syuan Jiang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Shao-Chien Zhuang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chak Hin Lam
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Lan-Yi Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Takashi Angata
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
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