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Miao Y, Zhang C, Yang L, Zeng X, Hu Y, Xue X, Dai Y, Wei Z. The activation of PPARγ enhances Treg responses through up-regulating CD36/CPT1-mediated fatty acid oxidation and subsequent N-glycan branching of TβRII/IL-2Rα. Cell Commun Signal 2022; 20:48. [PMID: 35392915 PMCID: PMC8991706 DOI: 10.1186/s12964-022-00849-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/19/2022] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Peroxisome proliferator-activated receptor gamma (PPARγ) is an enhancer of Treg responses, but the mechanisms remain elusive. This study aimed to solve this problem in view of cellular metabolism. METHODS Three recognized PPARγ agonists (synthetic agonist: rosiglitazone; endogenous ligand: 15d-PGJ2; natural product: morin) were used as the tools to activate PPARγ. The fatty acid oxidation (FAO) was evaluated through the detection of fatty acid uptake, oxygen consumption rate, mitochondrial mass, mitochondrial membrane potential and acetyl-CoA level. The involvement of UDP-GlcNAc/N-linked glycosylation axis and the exact role of PPARγ in the action of PPARγ agonists were determined by flow cytometry, Q-PCR, western blotting, a commercial kit for enzyme activity and CRISPR/Cas9-mediated knockout. RESULTS Rosiglitazone, 15d-PGJ2 and morin all increased the frequency of CD4+Foxp3+ Treg cells generated from naïve CD4+ T cells, boosted the transcription of Foxp3, IL-10, CTLA4 and TIGIT, and facilitated the function of Treg cells. They significantly promoted FAO in differentiating Treg cells by up-regulating the levels of CD36 and CPT1 but not other enzymes involved in FAO such as ACADL, ACADM, HADHA or HADHB, and siCD36 or siCPT1 dampened PPARγ agonists-promoted Treg responses. Moreover, PPARγ agonists enhanced UDP-GlcNAc biosynthesis and subsequent N-linked glycosylation, but did not affect the expressions of N-glycan branching enzymes Mgat1, 2, 4 and 5. Notably, the enzyme activity of phosphofructokinase (PFK) was inhibited by PPARγ agonists and the effect was limited by siCD36 or siCPT1, implying PFK to be a link between PPARγ agonists-promoted FAO and UDP-GlcNAc biosynthesis aside from acetyl-CoA. Furthermore, PPARγ agonists facilitated the cell surface abundance of TβRII and IL-2Rα via N-linked glycosylation, thereby activating TGF-β/Smads and IL-2/STAT5 signaling, and the connection between N-linked glycosylation and Treg responses was revealed by tunicamycin. However, the increased surface abundance of CD36 was demonstrated to be mainly owing to PPARγ agonists-up-regulated overall expression. Finally, PPARγ antagonist GW9662 or CRISPR/Cas9-mediated knockout of PPARγ constrained the effects of rosiglitazone, 15d-PGJ2 and morin, confirming the exact role of PPARγ. CONCLUSIONS The activation of PPARγ enhances Treg responses through up-regulating CD36/CPT1-mediated fatty acid oxidation and subsequent N-glycan branching of TβRII/IL-2Rα, which is beneficial for inflammatory and autoimmune diseases. Video Abstract.
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Affiliation(s)
- Yumeng Miao
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China
| | - Changliu Zhang
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China
| | - Ling Yang
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China
| | - Xi Zeng
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China
| | - Yuxiao Hu
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China
| | - Xinru Xue
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China
| | - Yue Dai
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China.
| | - Zhifeng Wei
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China.
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2
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Mkhikian H, Hayama KL, Khachikyan K, Li C, Zhou RW, Pawling J, Klaus S, Tran PQN, Ly KM, Gong AD, Saryan H, Hai JL, Grigoryan D, Lee PL, Newton BL, Raffatellu M, Dennis JW, Demetriou M. Age-associated impairment of T cell immunity is linked to sex-dimorphic elevation of N-glycan branching. NATURE AGING 2022; 2:231-242. [PMID: 35528547 PMCID: PMC9075523 DOI: 10.1038/s43587-022-00187-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 02/02/2022] [Indexed: 11/08/2022]
Abstract
Impaired T cell immunity with aging increases mortality from infectious disease. The branching of Asparagine-linked glycans is a critical negative regulator of T cell immunity. Here we show that branching increases with age in females more than males, in naïve more than memory T cells, and in CD4+ more than CD8+ T cells. Female sex hormones and thymic output of naïve T cells (TN) decrease with age, however neither thymectomy nor ovariectomy altered branching. Interleukin-7 (IL-7) signaling was increased in old female more than male mouse TN cells, and triggered increased branching. N-acetylglucosamine, a rate-limiting metabolite for branching, increased with age in humans and synergized with IL-7 to raise branching. Reversing elevated branching rejuvenated T cell function and reduced severity of Salmonella infection in old female mice. These data suggest sex-dimorphic antagonistic pleiotropy, where IL-7 initially benefits immunity through TN maintenance but inhibits TN function by raising branching synergistically with age-dependent increases in N-acetylglucosamine.
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Affiliation(s)
- Haik Mkhikian
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA
| | - Ken L Hayama
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, USA
| | - Khachik Khachikyan
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Carey Li
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Raymond W Zhou
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Judy Pawling
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Suzi Klaus
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, USA
| | - Phuong Q N Tran
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Kim M Ly
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Andrew D Gong
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Hayk Saryan
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Jasper L Hai
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - David Grigoryan
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Philip L Lee
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Barbara L Newton
- Department of Neurology, University of California, Irvine, Irvine, CA, USA
| | - Manuela Raffatellu
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, USA
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Mucosal Immunology, Allergy, and Vaccines, Chiba University-UC San Diego, La Jolla, CA, USA
| | - James W Dennis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Demetriou
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, USA.
- Department of Neurology, University of California, Irvine, Irvine, CA, USA.
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3
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Glycomic and Glycoproteomic Techniques in Neurodegenerative Disorders and Neurotrauma: Towards Personalized Markers. Cells 2022; 11:cells11030581. [PMID: 35159390 PMCID: PMC8834236 DOI: 10.3390/cells11030581] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022] Open
Abstract
The proteome represents all the proteins expressed by a genome, a cell, a tissue, or an organism at any given time under defined physiological or pathological circumstances. Proteomic analysis has provided unparalleled opportunities for the discovery of expression patterns of proteins in a biological system, yielding precise and inclusive data about the system. Advances in the proteomics field opened the door to wider knowledge of the mechanisms underlying various post-translational modifications (PTMs) of proteins, including glycosylation. As of yet, the role of most of these PTMs remains unidentified. In this state-of-the-art review, we present a synopsis of glycosylation processes and the pathophysiological conditions that might ensue secondary to glycosylation shortcomings. The dynamics of protein glycosylation, a crucial mechanism that allows gene and pathway regulation, is described. We also explain how-at a biomolecular level-mutations in glycosylation-related genes may lead to neuropsychiatric manifestations and neurodegenerative disorders. We then analyze the shortcomings of glycoproteomic studies, putting into perspective their downfalls and the different advanced enrichment techniques that emanated to overcome some of these challenges. Furthermore, we summarize studies tackling the association between glycosylation and neuropsychiatric disorders and explore glycoproteomic changes in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington disease, multiple sclerosis, and amyotrophic lateral sclerosis. We finally conclude with the role of glycomics in the area of traumatic brain injury (TBI) and provide perspectives on the clinical application of glycoproteomics as potential diagnostic tools and their application in personalized medicine.
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Galectins in Cancer and the Microenvironment: Functional Roles, Therapeutic Developments, and Perspectives. Biomedicines 2021; 9:biomedicines9091159. [PMID: 34572346 PMCID: PMC8465754 DOI: 10.3390/biomedicines9091159] [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: 07/30/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 12/15/2022] Open
Abstract
Changes in cell growth and metabolism are affected by the surrounding environmental factors to adapt to the cell’s most appropriate growth model. However, abnormal cell metabolism is correlated with the occurrence of many diseases and is accompanied by changes in galectin (Gal) performance. Gals were found to be some of the master regulators of cell–cell interactions that reconstruct the microenvironment, and disordered expression of Gals is associated with multiple human metabolic-related diseases including cancer development. Cancer cells can interact with surrounding cells through Gals to create more suitable conditions that promote cancer cell aggressiveness. In this review, we organize the current understanding of Gals in a systematic way to dissect Gals’ effect on human disease, including how Gals’ dysregulated expression affects the tumor microenvironment’s metabolism and elucidating the mechanisms involved in Gal-mediated diseases. This information may shed light on a more precise understanding of how Gals regulate cell biology and facilitate the development of more effective therapeutic strategies for cancer treatment by targeting the Gal family.
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Caldararu O, Ekberg V, Logan DT, Oksanen E, Ryde U. Exploring ligand dynamics in protein crystal structures with ensemble refinement. Acta Crystallogr D Struct Biol 2021; 77:1099-1115. [PMID: 34342282 PMCID: PMC8329865 DOI: 10.1107/s2059798321006513] [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: 03/17/2021] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein-ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein-ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and Rfree values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Vilhelm Ekberg
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Derek T. Logan
- Biochemistry and Structural Biology, Centre for Molecular Protein Science, Department of Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source Consortium ESS ERIC, PO Box 176, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
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6
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Brandt AU, Sy M, Bellmann-Strobl J, Newton BL, Pawling J, Zimmermann HG, Yu Z, Chien C, Dörr J, Wuerfel JT, Dennis JW, Paul F, Demetriou M. Association of a Marker of N-Acetylglucosamine With Progressive Multiple Sclerosis and Neurodegeneration. JAMA Neurol 2021; 78:842-852. [PMID: 33970182 PMCID: PMC8111565 DOI: 10.1001/jamaneurol.2021.1116] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Question Is the serum concentration of N-acetylglucosamine (GlcNAc) altered in patients with multiple sclerosis? Findings This cross-sectional study found that patients with a progressive multiple sclerosis subtype and more severe disease have reduced serum levels of a marker of GlcNAc. In addition, GlcNAc is a rate-limiting substrate for N-glycan branching, which has been shown to regulate immunoactivity and myelination. Meaning This study suggests that GlcNAc and N-glycan branching are associated with multiple sclerosis in general and progressive multiple sclerosis in particular. Importance N-glycan branching modulates cell surface receptor availability, and its deficiency in mice promotes inflammatory demyelination, reduced myelination, and neurodegeneration. N-acetylglucosamine (GlcNAc) is a rate-limiting substrate for N-glycan branching, but, to our knowledge, endogenous serum levels in patients with multiple sclerosis (MS) are unknown. Objective To investigate a marker of endogenous serum GlcNAc levels in patients with MS. Design, Setting, and Participants A cross-sectional discovery study and cross-sectional confirmatory study were conducted at 2 academic MS centers in the US and Germany. The discovery study recruited 54 patients with MS from an outpatient clinic as well as 66 healthy controls between April 20, 2010, and June 21, 2013. The confirmatory study recruited 180 patients with MS from screening visits at an academic MS study center between April 9, 2007, and February 29, 2016. Serum samples were analyzed from December 2, 2013, to March 2, 2015. Statistical analysis was performed from February 23, 2020, to March 18, 2021. Main Outcomes and Measures Serum levels of GlcNAc plus its stereoisomers, termed N-acetylhexosamine (HexNAc), were assessed using targeted tandem mass spectroscopy. Secondary outcomes (confirmatory study) comprised imaging and clinical disease markers. Results The discovery cohort included 66 healthy controls (38 women; mean [SD] age, 42 [20] years), 33 patients with relapsing-remitting MS (RRMS; 25 women; mean [SD] age, 50 [11] years), and 21 patients with progressive MS (PMS; 14 women; mean [SD] age, 55 [7] years). The confirmatory cohort included 125 patients with RRMS (83 women; mean [SD] age, 40 [9] years) and 55 patients with PMS (22 women; mean [SD] age, 49 [80] years). In the discovery cohort, the mean (SD) serum level of GlcNAc plus its stereoisomers (HexNAc) was 710 (174) nM in healthy controls and marginally reduced in patients with RRMS (mean [SD] level, 682 [173] nM; P = .04), whereas patients with PMS displayed markedly reduced levels compared with healthy controls (mean [SD] level, 548 [101] nM; P = 9.55 × 10−9) and patients with RRMS (P = 1.83 × 10−4). The difference between patients with RRMS (mean [SD] level, 709 [193] nM) and those with PMS (mean [SD] level, 405 [161] nM; P = 7.6 × 10−18) was confirmed in the independent confirmatory cohort. Lower HexNAc serum levels correlated with worse expanded disability status scale scores (ρ = –0.485; P = 4.73 × 10−12), lower thalamic volume (t = 1.7; P = .04), and thinner retinal nerve fiber layer (B = 0.012 [SE = 7.5 × 10−11]; P = .008). Low baseline serum HexNAc levels correlated with a greater percentage of brain volume loss at 18 months (t = 1.8; P = .04). Conclusions and Relevance This study suggests that deficiency of GlcNAc plus its stereoisomers (HexNAc) may be a biomarker for PMS. Previous preclinical, human genetic, and ex vivo human mechanistic studies revealed that N-glycan branching and/or GlcNAc may reduce proinflammatory responses, promote myelin repair, and decrease neurodegeneration. Combined, the data suggest that GlcNAc deficiency may be associated with progressive disease and neurodegeneration in patients with MS.
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Affiliation(s)
- Alexander U Brandt
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Neurology, University of California, Irvine, Irvine.,NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Sy
- Department of Neurology, University of California, Irvine, Irvine
| | - Judith Bellmann-Strobl
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Barbara L Newton
- Department of Neurology, University of California, Irvine, Irvine
| | - Judy Pawling
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Toronto, Ontario, Canada
| | - Hanna G Zimmermann
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Zhaoxia Yu
- Department of Statistics, University of California, Irvine, Irvine
| | - Claudia Chien
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jan Dörr
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jens Th Wuerfel
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Medical Image Analysis Center, Department of Biomedical Engineering, University Basel, Basel, Switzerland
| | - James W Dennis
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Friedemann Paul
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Demetriou
- Department of Neurology, University of California, Irvine, Irvine.,Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine
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Glimm T, Bhat R, Newman SA. Multiscale modeling of vertebrate limb development. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1485. [PMID: 32212250 DOI: 10.1002/wsbm.1485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 11/07/2022]
Abstract
We review the current state of mathematical modeling of cartilage pattern formation in vertebrate limbs. We place emphasis on several reaction-diffusion type models that have been proposed in the last few years. These models are grounded in more detailed knowledge of the relevant regulatory processes than previous ones but generally refer to different molecular aspects of these processes. Considering these models in light of comparative phylogenomics permits framing of hypotheses on the evolutionary order of appearance of the respective mechanisms and their roles in the fin-to-limb transition. This article is categorized under: Analytical and Computational Methods > Computational Methods Models of Systems Properties and Processes > Mechanistic Models Developmental Biology > Developmental Processes in Health and Disease Analytical and Computational Methods > Analytical Methods.
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Affiliation(s)
- Tilmann Glimm
- Department of Mathematics, Western Washington University, Bellingham, Washington
| | - Ramray Bhat
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, New York
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8
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Caldararu O, Misini Ignjatović M, Oksanen E, Ryde U. Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures. RSC Adv 2020; 10:8435-8443. [PMID: 35497843 PMCID: PMC9049968 DOI: 10.1039/c9ra09601a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/18/2020] [Indexed: 01/13/2023] Open
Abstract
The function of proteins is influenced not only by the atomic structure but also by the detailed structure of the solvent surrounding it. Computational studies of protein structure also critically depend on the water structure around the protein. Herein we compare the water structure obtained from molecular dynamics (MD) simulations of galectin-3 in complex with two ligands to crystallographic water molecules observed in the corresponding crystal structures. We computed MD trajectories both in a water box, which mimics a protein in solution, and in a crystallographic unit cell, which mimics a protein in a crystal. The calculations were compared to crystal structures obtained at both cryogenic and room temperature. Two types of analyses of the MD simulations were performed. First, the positions of the crystallographic water molecules were compared to peaks in the MD density after alignment of the protein in each snapshot. The results of this analysis indicate that all simulations reproduce the crystallographic water structure rather poorly. However, if we define the crystallographic water sites based on their distances to nearby protein atoms and follow these sites throughout the simulations, the MD simulations reproduce the crystallographic water sites much better. This shows that the failure of MD simulations to reproduce the water structure around proteins in crystal structures observed both in this and previous studies is caused by the problem of identifying water sites for a flexible and dynamic protein (traditionally done by overlaying the structures). Our local clustering approach solves the problem and shows that the MD simulations reasonably reproduce the water structure observed in crystals. Furthermore, analysis of the crystal MD simulations indicates a few water molecules that are close to unmodeled electron density peaks in the crystal structures, suggesting that crystal MD could be used as a complementary tool for identifying and modelling water in protein crystallography.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre P. O. Box 124 SE-221 00 Lund Sweden +46-46-2228648 +46-46-2224502
| | - Majda Misini Ignjatović
- Department of Theoretical Chemistry, Lund University, Chemical Centre P. O. Box 124 SE-221 00 Lund Sweden +46-46-2228648 +46-46-2224502
| | - Esko Oksanen
- Instruments Division, European Spallation Source Consortium ESS ERIC P. O. Box 176 SE-221 00 Lund Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre P. O. Box 124 SE-221 00 Lund Sweden +46-46-2228648 +46-46-2224502
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9
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Caldararu O, Manzoni F, Oksanen E, Logan DT, Ryde U. Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Acta Crystallogr D Struct Biol 2019; 75:368-380. [PMID: 30988254 PMCID: PMC6465982 DOI: 10.1107/s205979831900175x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/30/2019] [Indexed: 11/20/2022] Open
Abstract
Neutron crystallography is a powerful method to determine the positions of H atoms in macromolecular structures. However, it is sometimes hard to judge what would constitute a chemically reasonable model, and the geometry of H atoms depends more on the surroundings (for example the formation of hydrogen bonds) than heavy atoms, so that the empirical geometry information for the H atoms used to supplement the experimental data is often less accurate. These problems may be reduced by using quantum-mechanical calculations. A method has therefore been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. A first validation of this method is provided by re-refining the structure of the galectin-3 carbohydrate-recognition domain in complex with lactose. The geometry is improved, in particular for water molecules, for which the method leads to better-resolved hydrogen-bonding interactions. The method has also been applied to the active copper site of lytic polysaccharide monooxygenase and shows that the protonation state of the amino-terminal histidine residue can be determined.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Francesco Manzoni
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
- Instruments Division, European Spallation Source ESS ERIC, PO Box 176, SE-221 00 Lund, Sweden
| | - Derek T. Logan
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
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10
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Wang Y, Park H, Lin H, Kitova EN, Klassen JS. Multipronged ESI–MS Approach for Studying Glycan-Binding Protein Interactions with Glycoproteins. Anal Chem 2019; 91:2140-2147. [DOI: 10.1021/acs.analchem.8b04673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yilin Wang
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Heajin Park
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Hong Lin
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N. Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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11
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Demetriou M, Nabi IR, Dennis JW. Galectins as Adaptors: Linking Glycosylation and Metabolism with Extracellular Cues. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1732.1se] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Ivan R. Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia
| | - James W. Dennis
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital
- Department of Molecular Genetics, & Department of Laboratory Medicine and Pathology, Department of Medicine, University of Toronto
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12
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Manzoni F, Ryde U. Assessing the stability of free-energy perturbation calculations by performing variations in the method. J Comput Aided Mol Des 2018. [PMID: 29536221 PMCID: PMC5889414 DOI: 10.1007/s10822-018-0110-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We have calculated relative binding affinities for eight tetrafluorophenyl-triazole-thiogalactoside inhibitors of galectin-3 with the alchemical free-energy perturbation approach. We obtain a mean absolute deviation from experimental estimates of only 2-3 kJ/mol and a correlation coefficient (R2) of 0.5-0.8 for seven relative affinities spanning a range of up to 11 kJ/mol. We also studied the effect of using different methods to calculate the charges of the inhibitor and different sizes of the perturbed group (the atoms that are described by soft-core potentials and are allowed to have differing coordinates). However, the various approaches gave rather similar results and it is not possible to point out one approach as consistently and significantly better than the others. Instead, we suggest that such small and reasonable variations in the computational method can be used to check how stable the calculated results are and to obtain a more accurate estimate of the uncertainty than if performing only one calculation with a single computational setup.
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Affiliation(s)
- Francesco Manzoni
- Theoretical Chemistry, Department of Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden
| | - Ulf Ryde
- Theoretical Chemistry, Department of Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden.
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13
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Farhad M, Rolig AS, Redmond WL. The role of Galectin-3 in modulating tumor growth and immunosuppression within the tumor microenvironment. Oncoimmunology 2018; 7:e1434467. [PMID: 29872573 PMCID: PMC5980349 DOI: 10.1080/2162402x.2018.1434467] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/25/2018] [Accepted: 01/25/2018] [Indexed: 01/11/2023] Open
Abstract
The efficacy of cancer immunotherapy is limited, in part, by the multitude of immunosuppressive mechanisms present within the tumor microenvironment (TME). Galectin-3 (Gal-3) is a lectin that contributes to TME immunosuppression and regulates diverse functions including cellular homeostasis and cancer biology. Increased Gal-3 expression during cancer progression augments tumor growth, invasiveness, metastatic potential, and immune suppression, which highlights the potential use of Gal-3 as a therapeutic target capable of modulating anti-tumor immunity. Here, we discuss the mechanisms by which Gal-3 regulates lymphocytes, the role of Gal-3 in lung and prostate tumors, and the contribution of Gal-3 to TME immunosuppression.
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Affiliation(s)
- Mohammad Farhad
- Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, OR.,Cell, Developmental, and Cancer Biology Department, Oregon Health and Science University, Portland, OR
| | - Annah S Rolig
- Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, OR
| | - William L Redmond
- Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, OR
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14
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Steelman AJ, Li J. Astrocyte galectin-9 potentiates microglial TNF secretion. J Neuroinflammation 2014; 11:144. [PMID: 25158758 PMCID: PMC4158089 DOI: 10.1186/s12974-014-0144-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 07/31/2014] [Indexed: 12/31/2022] Open
Abstract
Background Aberrant neuroinflammation is suspected to contribute to the pathogenesis of myriad neurological diseases. As such, determining the pathways that promote or inhibit glial activation is of interest. Activation of the surface glycoprotein T-cell immunoglobulin and mucin-domain containing protein 3 (Tim-3) by the lectin galectin-9 has been implicated in promoting innate immune cell activation by potentiating or synergizing toll-like receptor (TLR) signaling. In the present study we examined the role of the Tim-3/galectin-9 pathway in glial activation in vitro. Method Primary monocultures of microglia or astrocytes, co-cultures containing microglia and astrocytes, and mixed glial cultures consisting of microglia, astrocytes and oligodendrocytes were stimulated with poly(I:C) or LPS, and galectin-9 up-regulation was determined. The effect of endogenous galectin-9 production on microglial activation was examined using cultures from wild-type and Lgals9 null mice. The ability for recombinant galectin-9 to promote microglia activation was also assessed. Tim-3 expression on microglia and BV2 cells was examined by qPCR and flow cytometry and its necessity in transducing the galectin-9 signal was determined using a Tim-3 specific neutralizing antibody or recombinant soluble Tim-3. Result Astrocytes potentiated TNF production from microglia following TLR stimulation. Poly(I:C) stimulation increased galectin-9 expression in microglia and microglial-derived factors promoted galectin-9 up-regulation in astrocytes. Astrocyte-derived galectin-9 in turn enhanced microglial TNF production. Similarly, recombinant galectin-9 enhanced poly(I:C)-induced microglial TNF and IL-6 production. Inhibition of Tim-3 did not alter TNF production in mixed glial cultures stimulated with poly(I:C). Conclusion Galectin-9 functions as an astrocyte-microglia communication signal and promotes cytokine production from microglia in a Tim-3 independent manner. Activation of CNS galectin-9 likely modulates neuroinflammatory processes in which TNF and IL-6 contribute to either pathology or reparation. Electronic supplementary material The online version of this article (doi:10.1186/s12974-014-0144-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jianrong Li
- Department of Veterinary Integrative Biosciences and Institute for Neuroscience, Texas A&M University, Mail Stop 4458, College Station 77843, TX, USA.
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15
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Copits BA, Vernon CG, Sakai R, Swanson GT. Modulation of ionotropic glutamate receptor function by vertebrate galectins. J Physiol 2014; 592:2079-96. [PMID: 24614744 DOI: 10.1113/jphysiol.2013.269597] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
AMPA and kainate receptors are glutamate-gated ion channels whose function is known to be altered by a variety of plant oligosaccharide-binding proteins, or lectins, but the physiological relevance of this activity has been uncertain because no lectins with analogous allosteric modulatory effects have been identified in animals. We report here that members of the prototype galectin family, which are β-galactoside-binding lectins, exhibit subunit-specific allosteric modulation of desensitization of recombinant homomeric and heteromeric AMPA and kainate receptors. Galectin modulation of GluK2 kainate receptors was dependent upon complex oligosaccharide processing of N-glycosylation sites in the amino-terminal domain and downstream linker region. The sensitivity of GluA4 AMPA receptors to human galectin-1 could be enhanced by supplementation of culture media with uridine and N-acetylglucosamine (GlcNAc), precursors for the hexosamine pathway that supplies UDP-GlcNAc for synthesis of complex oligosaccharides. Neuronal kainate receptors in dorsal root ganglia were sensitive to galectin modulation, whereas AMPA receptors in cultured hippocampal neurons were insensitive, which could be a reflection of differential N-glycan processing or receptor subunit selectivity. Because glycan content of integral proteins can be modified dynamically, we postulate that physiological or pathological conditions in the CNS could arise in which galectins alter excitatory neurotransmission or neuronal excitability through their actions on AMPA or kainate receptors.
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Affiliation(s)
- Bryan A Copits
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Claire G Vernon
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Ryuichi Sakai
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611, Japan
| | - Geoffrey T Swanson
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
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16
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Bucior I, Abbott J, Song Y, Matthay MA, Engel JN. Sugar administration is an effective adjunctive therapy in the treatment of Pseudomonas aeruginosa pneumonia. Am J Physiol Lung Cell Mol Physiol 2013; 305:L352-63. [PMID: 23792737 DOI: 10.1152/ajplung.00387.2012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Treatment of acute and chronic pulmonary infections caused by opportunistic pathogen Pseudomonas aeruginosa is limited by the increasing frequency of multidrug bacterial resistance. Here, we describe a novel adjunctive therapy in which administration of a mix of simple sugars-mannose, fucose, and galactose-inhibits bacterial attachment, limits lung damage, and potentiates conventional antibiotic therapy. The sugar mixture inhibits adhesion of nonmucoid and mucoid P. aeruginosa strains to bronchial epithelial cells in vitro. In a murine model of acute pneumonia, treatment with the sugar mixture alone diminishes lung damage, bacterial dissemination to the subpleural alveoli, and neutrophil- and IL-8-driven inflammatory responses. Remarkably, the sugars act synergistically with anti-Pseudomonas antibiotics, including β-lactams and quinolones, to further reduce bacterial lung colonization and damage. To probe the mechanism, we examined the effects of sugars in the presence or absence of antibiotics during growth in liquid culture and in an ex vivo infection model utilizing freshly dissected mouse tracheas and lungs. We demonstrate that the sugar mixture induces rapid but reversible formation of bacterial clusters that exhibited enhanced susceptibility to antibiotics compared with individual bacteria. Our findings reveal that sugar inhalation, an inexpensive and safe therapeutic, could be used in combination with conventional antibiotic therapy to more effectively treat P. aeruginosa lung infections.
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Affiliation(s)
- Iwona Bucior
- Department of Medicine, University of California, San Francisco, CA, USA
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17
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Abstract
The recognition of peptide/MHC antigens by T-cells has continued to challenge the imagination of immunologists, biochemists, and cell biologists alike. This is at least in part because T-cell recognition connects a diversity of issues and transcends many scientific disciplines. A fundamental unsolved issue is how T-cells manage to detect even a single molecule of an agonist pMHC complex, which is vastly outnumbered by endogenous pMHCs, many of which involve the same MHC molecule. They do so although TCRs are cross-reactive and typically low in affinity when measured in isolation. Importantly, T-cell antigen recognition takes place within the contact zone between a T-cell and the antigen-presenting cell, termed the immunological synapse. This bimembrane structure sets the stage for the antigen-binding events and all subsequent molecular recognition events. There is increasing evidence that the molecular dynamics of receptor-ligand interactions are not only dependent on the intrinsic properties of the binding partners but also become transformed by cell biological parameters such as the geometrical constraints within the immune synapse, mechanical forces, and local molecular crowding. To appreciate the complete picture, we think a multidisciplinary approach is imperative, which includes genetics, biochemistry, and structure determination and also biophysical analyses and the latest molecular imaging techniques. Here, we review earlier pioneering work and also recent developments in the fascinating and interdisciplinary science of T-cell antigen recognition. In many ways, this work may present a useful "roadmap" for work in other systems of cell-cell recognition, which underlie many fundamental biological phenomenons of interest.
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18
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Belardi B, O'Donoghue GP, Smith AW, Groves JT, Bertozzi CR. Investigating cell surface galectin-mediated cross-linking on glycoengineered cells. J Am Chem Soc 2012; 134:9549-52. [PMID: 22540968 PMCID: PMC3374418 DOI: 10.1021/ja301694s] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
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The galectin family of glycan-binding proteins is thought
to mediate
many cellular processes by oligomerizing cell surface glycoproteins
and glycolipids into higher-order aggregates. This hypothesis reflects
the known oligomeric states of the galectins themselves and their
binding properties with multivalent ligands in vitro, but direct evidence of their ability to cross-link ligands on a
cell surface is lacking. A major challenge in fundamental studies
of galectin–ligand interactions is that their natural ligands
comprise a heterogeneous collection of glycoconjugates that share
related glycan structures but disparate underlying scaffolds. Consequently,
there is no obvious means to selectively monitor the behaviors of
natural galectin ligands on live cell surfaces. Here we describe an
approach for probing the galectin-induced multimerization of glycoconjugates
on cultured cells. Using RAFT polymerization, we synthesized well-defined
glycopolymers (GPs) functionalized with galectin-binding glycans along
the backbone, a lipid group on one end and a fluorophore on the other.
After insertion into live cell membranes, the GPs’ fluorescence
lifetime and diffusion time were measured in the presence and absence
of galectin-1. We observed direct evidence for galectin-1-mediated
extended cross-linking on the engineered cells, a phenomenon that
was dependent on glycan structure. This platform offers a new approach
to exploring the “galectin lattice” hypothesis and to
defining galectin ligand specificity in a physiologically relevant
context.
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Affiliation(s)
- Brian Belardi
- Department of Chemistry, and Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California 94720, USA
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19
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Sano M, Korekane H, Ohtsubo K, Yamaguchi Y, Kato M, Shibukawa Y, Tajiri M, Adachi H, Wada Y, Asahi M, Taniguchi N. N-glycans of SREC-I (scavenger receptor expressed by endothelial cells): essential role for ligand binding, trafficking and stability. Glycobiology 2012; 22:714-24. [PMID: 22279061 DOI: 10.1093/glycob/cws010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Scavenger receptor expressed by endothelial cells (SREC-I) mediates the endocytosis of chemically modified lipoproteins such as acetylated low-density lipoprotein (Ac-LDL) and oxidized LDL and is implicated in atherogenesis. We produced recombinant SREC-I in Chinese hamster ovary-K1 cells and identified three potential glycosylation sites, Asn(289), Asn(382) and Asn(393), which were all glycosylated. To determine the function of N-glycans in SREC-I, we characterized SREC-I mutant proteins by intracellular distribution and the cellular incorporation rate of Ac-LDL. N382Q/N393Q and N289Q/N382Q/N393Q were sequestered in the endoplasmic reticulum, resulting in a severe reduction in the cellular incorporation of Ac-LDL. N382Q showed a normal cell surface residency and an enhanced affinity for Ac-LDL, resulting in an elevated Ac-LDL cellular incorporation. These results indicate that the N-glycan of Asn(393) regulates the intracellular sorting of SREC-I and that the N-glycan of Asn(382) controls ligand-binding affinity. Furthermore, we detected an enhanced trypsin sensitivity of the N289Q. Glycan structure analyses revealed that the core-fucosylated bi-antennary is the common major structure at all glycosylation sites. In addition, tri- and tetra-antennary were detected as minor constituents at Asn(289). A bisecting GlcNAc was also detected at Asn(382) and Asn(393). Structural analyses and homology modeling of SREC-I suggest that the N-glycan bearing a β1-6GlcNAc branch at Asn(289) protects from proteinase attack and thus confers a higher stability on SREC-I. These data indicate that Asn(289)-, Asn(382)- and Asn(393)-linked N-glycans of SREC-I have distinct functions in regulating proteolytic resistance, ligand-binding affinity and subcellular localization, all of which might be involved in the development of atherogenesis.
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Affiliation(s)
- Masahiro Sano
- Department of Disease Glycomics, Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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20
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The CD3-zeta chimeric antigen receptor overcomes TCR Hypo-responsiveness of human terminal late-stage T cells. PLoS One 2012; 7:e30713. [PMID: 22292024 PMCID: PMC3264628 DOI: 10.1371/journal.pone.0030713] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 12/20/2011] [Indexed: 12/17/2022] Open
Abstract
Adoptive therapy of malignant diseases with tumor-specific cytotoxic T cells showed remarkable efficacy in recent trials. Repetitive T cell receptor (TCR) engagement of target antigen, however, inevitably ends up in hypo-responsive cells with terminally differentiated KLRG-1+ CD57+ CD7− phenotype limiting their therapeutic efficacy. We here revealed that hypo-responsiveness of CMV-specific late-stage CD8+ T cells is due to reduced TCR synapse formation compared to younger cells. Membrane anchoring of TCR components contributes to T cell hypo-responsiveness since dislocation of galectin-3 from the synapse by swainsonine restored both TCR synapse formation and T cell response. Transgenic expression of a CD3-zeta signaling chimeric antigen receptor (CAR) recovered hypo-responsive T cells to full effector functions indicating that the defect is restricted to TCR membrane components while synapse formation of the transgenic CAR was not blocked. CAR engineered late-stage T cells released cytokines and mediated redirected cytotoxicity as efficiently as younger effector T cells. Our data provide a rationale for TCR independent, CAR mediated activation in the adoptive cell therapy to avoid hypo-responsiveness of late-stage T cells upon repetitive antigen encounter.
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21
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Saraboji K, Håkansson M, Genheden S, Diehl C, Qvist J, Weininger U, Nilsson UJ, Leffler H, Ryde U, Akke M, Logan DT. The carbohydrate-binding site in galectin-3 is preorganized to recognize a sugarlike framework of oxygens: ultra-high-resolution structures and water dynamics. Biochemistry 2011; 51:296-306. [PMID: 22111949 PMCID: PMC3255464 DOI: 10.1021/bi201459p] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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The recognition of carbohydrates by proteins is a fundamental aspect of communication within and between living cells. Understanding the molecular basis of carbohydrate–protein interactions is a prerequisite for the rational design of synthetic ligands. Here we report the high- to ultra-high-resolution crystal structures of the carbohydrate recognition domain of galectin-3 (Gal3C) in the ligand-free state (1.08 Å at 100 K, 1.25 Å at 298 K) and in complex with lactose (0.86 Å) or glycerol (0.9 Å). These structures reveal striking similarities in the positions of water and carbohydrate oxygen atoms in all three states, indicating that the binding site of Gal3C is preorganized to coordinate oxygen atoms in an arrangement that is nearly optimal for the recognition of β-galactosides. Deuterium nuclear magnetic resonance (NMR) relaxation dispersion experiments and molecular dynamics simulations demonstrate that all water molecules in the lactose-binding site exchange with bulk water on a time scale of nanoseconds or shorter. Nevertheless, molecular dynamics simulations identify transient water binding at sites that agree well with those observed by crystallography, indicating that the energy landscape of the binding site is maintained in solution. All heavy atoms of glycerol are positioned like the corresponding atoms of lactose in the Gal3C complexes. However, binding of glycerol to Gal3C is insignificant in solution at room temperature, as monitored by NMR spectroscopy or isothermal titration calorimetry under conditions where lactose binding is readily detected. These observations make a case for protein cryo-crystallography as a valuable screening method in fragment-based drug discovery and further suggest that identification of water sites might inform inhibitor design.
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Affiliation(s)
- Kadhirvel Saraboji
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Box 124, Lund University, SE-221 00 Lund, Sweden
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22
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Grigorian A, Araujo L, Naidu NN, Place DJ, Choudhury B, Demetriou M. N-acetylglucosamine inhibits T-helper 1 (Th1)/T-helper 17 (Th17) cell responses and treats experimental autoimmune encephalomyelitis. J Biol Chem 2011; 286:40133-41. [PMID: 21965673 PMCID: PMC3220534 DOI: 10.1074/jbc.m111.277814] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/26/2011] [Indexed: 01/25/2023] Open
Abstract
Current treatments and emerging oral therapies for multiple sclerosis (MS) are limited by effectiveness, cost, and/or toxicity. Genetic and environmental factors that alter the branching of Asn (N)-linked glycans result in T cell hyperactivity, promote spontaneous inflammatory demyelination and neurodegeneration in mice, and converge to regulate the risk of MS. The sugar N-acetylglucosamine (GlcNAc) enhances N-glycan branching and inhibits T cell activity and adoptive transfer experimental autoimmune encephalomyelitis (EAE). Here, we report that oral GlcNAc inhibits T-helper 1 (Th1) and T-helper 17 (Th17) responses and attenuates the clinical severity of myelin oligodendrocyte glycoprotein (MOG)-induced EAE when administered after disease onset. Oral GlcNAc increased expression of branched N-glycans in T cells in vivo as shown by high pH anion exchange chromatography, MALDI-TOF mass spectroscopy and FACS analysis with the plant lectin l-phytohemagglutinin. Initiating oral GlcNAc treatment on the second day of clinical disease inhibited MOG-induced EAE as well as secretion of interferon-γ, tumor necrosis factor-α, interleukin-17, and interleukin-22. In the more severe 2D2 T cell receptor transgenic EAE model, oral GlcNAc initiated after disease onset also inhibits clinical disease, except for those with rapid lethal progression. These data suggest that oral GlcNAc may provide an inexpensive and nontoxic oral therapeutic agent for MS that directly targets an underlying molecular mechanism causal of disease.
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Affiliation(s)
- Ani Grigorian
- From the Departments of Neurology and
- Institute for Immunology, University of California, Irvine, California 92697 and
| | | | - Nandita N. Naidu
- Glycotechnology Core Resource, University of California at San Diego, La Jolla, California 92093
| | | | - Biswa Choudhury
- Glycotechnology Core Resource, University of California at San Diego, La Jolla, California 92093
| | - Michael Demetriou
- From the Departments of Neurology and
- Microbiology and Molecular Genetics
- Institute for Immunology, University of California, Irvine, California 92697 and
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23
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Shibui A, Doi J, Tolba MEM, Shiraishi C, Sato Y, Ishikawa S, Watanabe J, Nogami S, Nakae S, Sugano S, Hozumi N. N-acetylglucosaminyltransferase V-deficiency increases susceptibility to murine malaria. Exp Parasitol 2011; 129:318-21. [PMID: 21767537 DOI: 10.1016/j.exppara.2011.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 06/23/2011] [Accepted: 07/01/2011] [Indexed: 11/30/2022]
Abstract
It is considered that several glycoproteins on erythrocytes in mammalian species are involved in malaria parasite infection. To elucidate the role of N-glycans on malaria parasite infection, we induced experimental murine malaria infection (using Plasmodium berghei ANKA) in mice deficient in N-acetylglucosaminyltransferase V (Mgat5), which is one of the enzymes involved in β1,6-GlcNAc N-glycan biosynthesis. After infection, Mgat5(-/-) mice showed severe body weight loss and parasitemia compared with wild-type mice. The Mgat5(-/-) mice, but not wild-type mice, also showed severe pathology accompanied by marked infiltration of plasma cells into the lungs and liver. These results suggest that β1,6-GlcNAc N-glycans on/in host erythrocytes may interfere with invasion of the parasites and progression to severe malaria.
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Affiliation(s)
- Akiko Shibui
- Department of Medical Genomics, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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