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Abraham BG, Haikarainen T, Vuorio J, Girych M, Virtanen AT, Kurttila A, Karathanasis C, Heilemann M, Sharma V, Vattulainen I, Silvennoinen O. Molecular basis of JAK2 activation in erythropoietin receptor and pathogenic JAK2 signaling. SCIENCE ADVANCES 2024; 10:eadl2097. [PMID: 38457493 PMCID: PMC10923518 DOI: 10.1126/sciadv.adl2097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
Abstract
Janus kinase 2 (JAK2) mediates type I/II cytokine receptor signaling, but JAK2 is also activated by somatic mutations that cause hematological malignancies by mechanisms that are still incompletely understood. Quantitative superresolution microscopy (qSMLM) showed that erythropoietin receptor (EpoR) exists as monomers and dimerizes upon Epo stimulation or through the predominant JAK2 pseudokinase domain mutations (V617F, K539L, and R683S). Crystallographic analysis complemented by kinase activity analysis and atomic-level simulations revealed distinct pseudokinase dimer interfaces and activation mechanisms for the mutants: JAK V617F activity is driven by dimerization, K539L involves both increased receptor dimerization and kinase activity, and R683S prevents autoinhibition and increases catalytic activity and drives JAK2 equilibrium toward activation state through a wild-type dimer interface. Artificial intelligence-guided modeling and simulations revealed that the pseudokinase mutations cause differences in the pathogenic full-length JAK2 dimers, particularly in the FERM-SH2 domains. A detailed molecular understanding of mutation-driven JAK2 hyperactivation may enable novel therapeutic approaches to selectively target pathogenic JAK2 signaling.
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Affiliation(s)
| | - Teemu Haikarainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
| | - Joni Vuorio
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Anniina T. Virtanen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Antti Kurttila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Christos Karathanasis
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Olli Silvennoinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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2
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Shamszadeh S, Shirvani A, Asgary S. The Role of Growth Factor Delivery Systems on Cellular Activities of Dental Stem Cells: A Systematic Review (Part II). Curr Stem Cell Res Ther 2024; 19:587-610. [PMID: 35692144 DOI: 10.2174/1574888x17666220609093939] [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: 03/01/2022] [Revised: 03/09/2022] [Accepted: 03/29/2022] [Indexed: 11/22/2022]
Abstract
OBJECTIVE The current systematic review aims to provide the available ex vivo evidence evaluating the biological interactions of dental stem cells (DSCs) and growth factor delivery systems. METHODS Following the Preferred Reporting Items for a Systematic Reviews and Meta-Analyses (PRISMA) guidelines, systematic search was conducted in the electronic databases (PubMed/Medline, Scopus, Web of Science, and Google Scholar) up to January 2022. Studies evaluating the biological interactions of DSCs and growth factor delivery systems were included. The outcome measures were cell cytocompatibility, mineralization, and differentiation. RESULTS Sixteen studies were selected for the qualitative synthesis. The following growth factor delivery systems exhibit adequate cytocompatibility, enhanced mineralization, and osteo/odontoblast differentiation potential of DSCs: 1) Fibroblast growth factor (FGF-2)-loaded-microsphere and silk fibroin, 2) Bone morphogenic protein-2 (BMP-2)-loaded-microsphere and mesoporous calcium silicate scaffold, 3) Transforming growth factor Beta 1 (TGF-ß1)-loaded-microsphere, glass ionomer cement (GIC), Bio-GIC and liposome, 4) TGF-ß1-loaded-nanoparticles/scaffold, 5) Vascular endothelial growth factor (VEGF)-loaded-fiber and hydrogel, 6) TGF-ß1/VEGF-loaded-nanocrystalline calcium sulfate/hydroxyapatite/calcium sulfate, 7) Epidermal growth factor-loaded- nanosphere, 8) Stem cell factor/DSCs-loaded-hydrogel and Silk fibroin, 9) VEGF/BMP-2/DSCs-loaded-Three-dimensional matrix, 10) VEGF/DSCs-loaded-microsphere/hydrogel, and 11) BMP-2/DSCs and VEGF/DSCs-loaded-Collagen matrices. The included delivery systems showed viability, except for Bio-GIC on day 3. The choice of specific growth factors and delivery systems (i.e., BMP-2-loaded-microsphere and VEGF-loaded-hydrogel) resulted in a greater gene expression. CONCLUSIONS This study, with low-level evidence obtained from ex vivo studies, suggests that growth factor delivery systems induce cell proliferation, mineralization, and differentiation toward a therapeutic potential in regenerative endodontics.
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Affiliation(s)
- Sayna Shamszadeh
- Iranian Center for Endodontic Research, Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Armin Shirvani
- Iranian Center for Endodontic Research, Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeed Asgary
- Iranian Center for Endodontic Research, Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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3
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Riege D, Herschel S, Fenkl T, Schade D. Small-Molecule Probes as Pharmacological Tools for the Bone Morphogenetic Protein Signaling Pathway. ACS Pharmacol Transl Sci 2023; 6:1574-1599. [PMID: 37974621 PMCID: PMC10644459 DOI: 10.1021/acsptsci.3c00170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 11/19/2023]
Abstract
The bone morphogenetic protein (BMP) pathway is highly conserved and plays central roles in health and disease. The quality and quantity of its signaling outputs are regulated at multiple levels, offering pharmacological options for targeted modulation. Both target-centric and phenotypic drug discovery (PDD) approaches were applied to identify small-molecule BMP inhibitors and stimulators. In this Review, we accumulated and systematically classified the different reported chemotypes based on their targets as well as modes-of-action, and herein we illustrate the discovery history of selected candidates. A comprehensive summary of available biochemical, cellular, and in vivo activities is provided for the most relevant BMP modulators, along with recommendations on their preferred use as chemical probes to study BMP-related (patho)physiological processes. There are a number of high-quality probes used as BMP inhibitors that potently and selectively interrogate the kinase activities of distinct type I (16 chemotypes available) and type II receptors (3 chemotypes available). In contrast, only a few high-quality BMP stimulator modalities have been introduced to the field due to a lack of profound target knowledge. FK506-derived macrolides such as calcineurin-sparing FKBP12 inhibitors currently represent the best-characterized chemical tools for direct activation of BMP-SMAD signaling at the receptor level. However, several PDD campaigns succeeded in expanding the druggable space of BMP stimulators. Albeit the majority of them do not entirely fulfill the strict chemical probe criteria, many chemotypes exhibit unique and unrecognized mechanisms as pathway potentiators or synergizers, serving as valuable pharmacological tools for BMP perturbation.
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Affiliation(s)
- Daniel Riege
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Sven Herschel
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Teresa Fenkl
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Dennis Schade
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
- Partner
Site Kiel, DZHK, German Center for Cardiovascular
Research, 24105 Kiel, Germany
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4
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Pogozheva ID, Cherepanov S, Park SJ, Raghavan M, Im W, Lomize AL. Structural Modeling of Cytokine-Receptor-JAK2 Signaling Complexes Using AlphaFold Multimer. J Chem Inf Model 2023; 63:5874-5895. [PMID: 37694948 DOI: 10.1021/acs.jcim.3c00926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Homodimeric class 1 cytokine receptors include the erythropoietin (EPOR), thrombopoietin (TPOR), granulocyte colony-stimulating factor 3 (CSF3R), growth hormone (GHR), and prolactin receptors (PRLR). These cell-surface single-pass transmembrane (TM) glycoproteins regulate cell growth, proliferation, and differentiation and induce oncogenesis. An active TM signaling complex consists of a receptor homodimer, one or two ligands bound to the receptor extracellular domains, and two molecules of Janus Kinase 2 (JAK2) constitutively associated with the receptor intracellular domains. Although crystal structures of soluble extracellular domains with ligands have been obtained for all of the receptors except TPOR, little is known about the structure and dynamics of the complete TM complexes that activate the downstream JAK-STAT signaling pathway. Three-dimensional models of five human receptor complexes with cytokines and JAK2 were generated here by using AlphaFold Multimer. Given the large size of the complexes (from 3220 to 4074 residues), the modeling required a stepwise assembly from smaller parts, with selection and validation of the models through comparisons with published experimental data. The modeling of active and inactive complexes supports a general activation mechanism that involves ligand binding to a monomeric receptor followed by receptor dimerization and rotational movement of the receptor TM α-helices, causing proximity, dimerization, and activation of associated JAK2 subunits. The binding mode of two eltrombopag molecules to the TM α-helices of the active TPOR dimer was proposed. The models also help elucidate the molecular basis of oncogenic mutations that may involve a noncanonical activation route. Models equilibrated in explicit lipids of the plasma membrane are publicly available.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stanislav Cherepanov
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sang-Jun Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Semper C, Savchenko A. Protein expression and purification of bioactive growth factors for use in cell culture and cellular agriculture. STAR Protoc 2023; 4:102351. [PMID: 37314918 PMCID: PMC10277608 DOI: 10.1016/j.xpro.2023.102351] [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: 12/21/2022] [Revised: 02/28/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Mitogenic growth factors are major cost drivers in serum-free media, contributing up to 95% of the total cost. Here, we present a streamlined workflow detailing cloning, expression testing, protein purification, and bioactivity screening that allows for low-cost production of bioactive growth factors including basic fibroblast growth factor and transforming growth factor β1. This generalized procedure can be used for multiple families of growth factors with minor modification, and the outputs are bioactive and suitable for cell culture applications. For complete details on the use and execution of this protocol, please refer to Venkatesan, et al.1.
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Affiliation(s)
- Cameron Semper
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada.
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6
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Rothschadl MJ, Sathyanesan M, Newton SS. Synergism of Carbamoylated Erythropoietin and Insulin-like Growth Factor-1 in Immediate Early Gene Expression. Life (Basel) 2023; 13:1826. [PMID: 37763230 PMCID: PMC10532867 DOI: 10.3390/life13091826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Trophic factors are secreted proteins that can modulate neuronal integrity, structure, and function. Previous preclinical studies have shown synergistic effects on decreasing apoptosis and improving behavioral performance after stroke when combining two such trophic factors, erythropoietin (EPO) and insulin-like growth factor-1 (IGF-1). However, EPO can elevate the hematocrit level, which can be life-threatening for non-anemic individuals. A chemically engineered derivative of EPO, carbamoylated EPO (CEPO), does not impact hematological parameters but retains neurotrophic effects similar to EPO. To obtain insight into CEPO and IGF-1 combination signaling, we examined immediate early gene (IEG) expression after treatment with CEPO, IGF-1, or CEPO + IGF-1 in rat pheochromocytoma (PC-12) cells and found that combining CEPO and IGF-1 produced a synergistic increase in IEG expression. An in vivo increase in the protein expression of Npas4 and Nptx2 was also observed in the rat hippocampus. We also examined which kinase signaling pathways might be mediating these effects and found that while AKT inhibition did not alter the pattern of IEG expression, both ERK and JAK2 inhibition significantly decreased IEG expression. These results begin to define the molecular effects of combining CEPO and IGF-1 and indicate the potential for these trophic factors to produce positive, synergistic effects.
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Affiliation(s)
| | | | - Samuel S. Newton
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069, USA; (M.J.R.); (M.S.)
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7
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Pogozheva ID, Cherepanov S, Park SJ, Raghavan M, Im W, Lomize AL. Structural modeling of cytokine-receptor-JAK2 signaling complexes using AlphaFold Multimer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544971. [PMID: 37398331 PMCID: PMC10312770 DOI: 10.1101/2023.06.14.544971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Homodimeric class 1 cytokine receptors include the erythropoietin (EPOR), thrombopoietin (TPOR), granulocyte colony-stimulating factor 3 (CSF3R), growth hormone (GHR), and prolactin receptors (PRLR). They are cell-surface single-pass transmembrane (TM) glycoproteins that regulate cell growth, proliferation, and differentiation and induce oncogenesis. An active TM signaling complex consists of a receptor homodimer, one or two ligands bound to the receptor extracellular domains and two molecules of Janus Kinase 2 (JAK2) constitutively associated with the receptor intracellular domains. Although crystal structures of soluble extracellular domains with ligands have been obtained for all the receptors except TPOR, little is known about the structure and dynamics of the complete TM complexes that activate the downstream JAK-STAT signaling pathway. Three-dimensional models of five human receptor complexes with cytokines and JAK2 were generated using AlphaFold Multimer. Given the large size of the complexes (from 3220 to 4074 residues), the modeling required a stepwise assembly from smaller parts with selection and validation of the models through comparisons with published experimental data. The modeling of active and inactive complexes supports a general activation mechanism that involves ligand binding to a monomeric receptor followed by receptor dimerization and rotational movement of the receptor TM α-helices causing proximity, dimerization, and activation of associated JAK2 subunits. The binding mode of two eltrombopag molecules to TM α-helices of the active TPOR dimer was proposed. The models also help elucidating the molecular basis of oncogenic mutations that may involve non-canonical activation route. Models equilibrated in explicit lipids of the plasma membrane are publicly available.
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Affiliation(s)
- Irina D. Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States
| | | | - Sang-Jun Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, PA 18015, United States
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, PA 18015, United States
| | - Andrei L. Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States
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8
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Wang Z, Xie S, Wu L, Chen F, Qiu L, Tan W. Aptamer-Functionalized Nanodevices for Dynamic Manipulation of Membrane Receptor Signaling in Living Cells. NANO LETTERS 2022; 22:7853-7859. [PMID: 36126113 DOI: 10.1021/acs.nanolett.2c02522] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The capacity to regulate the signaling amplitude of membrane receptors in a user-defined manner would open various opportunities for precise biological study and therapy. While partial agonists enabled downtuning of cellular responses, they required esoteric optimization of the ligand-receptor interface, limiting their practical applications. Herein, we developed an aptamer-functionalized, tweezer-like nanodevice to dynamically modulate the cellular behavior through control over the distance between receptors in the dimer with no need to involve complicated structural analysis. By combining a reversible conformation switch with aptamer-based molecular recognition, this nanodevice showed excellent performance on dynamic regulation of CD28 receptor-mediated T cell immunity. With the modular design, this nanodevice could be extended to dynamically modulate the activity of other membrane receptors (e.g., c-Met), expecting to offer a new paradigm for precise study and manipulation of specific molecular events in complex biological systems.
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Affiliation(s)
- Zhimin Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Sitao Xie
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Limei Wu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Fengming Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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9
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Wang G, Liu W, Wang C, Wang J, Liu H, Hao D, Zhang M. Molecular characterization and immunoregulatory analysis of suppressors of cytokine signaling 1 (SOCS1) in black rockfish, Sebastes schlegeli. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 130:104355. [PMID: 35077723 DOI: 10.1016/j.dci.2022.104355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/12/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
The suppressors of cytokine signaling (SOCS) family are important soluble mediators to inhibit signal transduction via the Janus kinase/signal transducer and activator of transcription (JAK-STAT) pathway in the innate and adaptive immune responses. SOCS1 is the primary regulator of a number of cytokines. In this study, two spliced transcripts of SOCS1 were identified and characterized from black rockfish (Sebastes schlegeli), named SsSOCS1a and SsSOCS1b. SsSOCS1a and SsSOCS1b contained conserved structural and functional domains including KIR region, ESS region, SH2 domain and SOCS box. SsSOCS1a and SsSOCS1b were distributed ubiquitously in all the detected tissues with the higher expression level in liver and spleen. After stimulation in vivo with Vibrio anguillarum and Edwardsiella tarda, the mRNA expression of SsSOCS1a and SsSOCS1b were induced in most of the immune-related tissues, including head kidney, spleen and liver. Meanwhile, poly I:C and IFNγ up-regulated the expression of SsSOCS1a and SsSOCS1b that reached the highest level at 24 h in macrophages in vitro. Luciferase assays in HEK293 cells showed SsSOCS1a and SsSOCS1b had the similar function in inhibiting ISRE activity after poly I:C and IFNγ treatment. Furthermore, KIR domain in black rockfish was determined to have a negative regulatory role in IFN signaling. SsSOCS1a and SsSOCS1b were found to interact strongly with each other by Co-immunoprecipitation analyses. These results indicated that the function of SOCS1 in the negative regulation of IFN signaling is conserved from teleost to mammals which will be helpful to further understanding of the biological functions of teleosts SOCS1 in innate immunity.
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Affiliation(s)
- Guanghua Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Wenqing Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Changbiao Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Jingjing Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Hongmei Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Dongfang Hao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Min Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266109, China.
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10
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Sotolongo Bellón J, Birkholz O, Richter CP, Eull F, Kenneweg H, Wilmes S, Rothbauer U, You C, Walter MR, Kurre R, Piehler J. Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane. CELL REPORTS METHODS 2022; 2:100165. [PMID: 35474965 PMCID: PMC9017138 DOI: 10.1016/j.crmeth.2022.100165] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/19/2021] [Accepted: 01/13/2022] [Indexed: 12/22/2022]
Abstract
Localization and tracking of individual receptors by single-molecule imaging opens unique possibilities to unravel the assembly and dynamics of signaling complexes in the plasma membrane. We present a comprehensive workflow for imaging and analyzing receptor diffusion and interaction in live cells at single molecule level with up to four colors. Two engineered, monomeric GFP variants, which are orthogonally recognized by anti-GFP nanobodies, are employed for efficient and selective labeling of target proteins in the plasma membrane with photostable fluorescence dyes. This labeling technique enables us to quantitatively resolve the stoichiometry and dynamics of the interferon-γ (IFNγ) receptor signaling complex in the plasma membrane of living cells by multicolor single-molecule imaging. Based on versatile spatial and spatiotemporal correlation analyses, we identify ligand-induced receptor homo- and heterodimerization. Multicolor single-molecule co-tracking and quantitative single-molecule Förster resonance energy transfer moreover reveals transient assembly of IFNγ receptor heterotetramers and confirms its structural architecture.
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Affiliation(s)
- Junel Sotolongo Bellón
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Oliver Birkholz
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Christian P. Richter
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Florian Eull
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Hella Kenneweg
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Stephan Wilmes
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
- Division of Cell Signalling and Immunology, University of Dundee, School of Life Sciences, Dundee, UK
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard-Karls-University, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Mark R. Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rainer Kurre
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
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11
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Li P, Li Q, Biswas N, Xin H, Diemer T, Liu L, Perez Gutierrez L, Paternostro G, Piermarocchi C, Domanskyi S, Wang RK, Ferrara N. LIF, a mitogen for choroidal endothelial cells, protects the choriocapillaris: implications for prevention of geographic atrophy. EMBO Mol Med 2022; 14:e14511. [PMID: 34779136 PMCID: PMC8749470 DOI: 10.15252/emmm.202114511] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/18/2022] Open
Abstract
In the course of our studies aiming to discover vascular bed-specific endothelial cell (EC) mitogens, we identified leukemia inhibitory factor (LIF) as a mitogen for bovine choroidal EC (BCE), although LIF has been mainly characterized as an EC growth inhibitor and an anti-angiogenic molecule. LIF stimulated growth of BCE while it inhibited, as previously reported, bovine aortic EC (BAE) growth. The JAK-STAT3 pathway mediated LIF actions in both BCE and BAE cells, but a caspase-independent proapoptotic signal mediated by cathepsins was triggered in BAE but not in BCE. LIF administration directly promoted activation of STAT3 and increased blood vessel density in mouse eyes. LIF also had protective effects on the choriocapillaris in a model of oxidative retinal injury. Analysis of available single-cell transcriptomic datasets shows strong expression of the specific LIF receptor in mouse and human choroidal EC. Our data suggest that LIF administration may be an innovative approach to prevent atrophy associated with AMD, through protection of the choriocapillaris.
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Affiliation(s)
- Pin Li
- Department of PathologyUniversity of California San DiegoLa JollaCAUSA
| | - Qin Li
- Department of OphthalmologyUniversity of California San DiegoLa JollaCAUSA
| | - Nilima Biswas
- Department of PathologyUniversity of California San DiegoLa JollaCAUSA
| | - Hong Xin
- Department of PathologyUniversity of California San DiegoLa JollaCAUSA
| | - Tanja Diemer
- Department of PathologyUniversity of California San DiegoLa JollaCAUSA
| | - Lixian Liu
- Department of PathologyUniversity of California San DiegoLa JollaCAUSA
| | | | | | - Carlo Piermarocchi
- Department of Physics and AstronomyMichigan State UniversityEast LansingMIUSA
| | - Sergii Domanskyi
- Department of Physics and AstronomyMichigan State UniversityEast LansingMIUSA
| | - Ruikang K Wang
- Department of BioengineeringUniversity of WashingtonSeattleWAUSA
| | - Napoleone Ferrara
- Department of PathologyUniversity of California San DiegoLa JollaCAUSA
- Department of OphthalmologyUniversity of California San DiegoLa JollaCAUSA
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12
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Identification and localization of growth factor genes in the sea cucumber , Holothuria scabra. Heliyon 2021; 7:e08370. [PMID: 34825084 PMCID: PMC8605306 DOI: 10.1016/j.heliyon.2021.e08370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 11/23/2022] Open
Abstract
The sea cucumber Holothuria scabra is both an economically important species in Asian countries and an emerging experimental model for research studies in regeneration and medicinal bioactives. Growth factors and their receptors are known to be key components that guide tissue repair and renewal, yet validation of their presence in H. scabra has not been established. We performed a targeted in silico search of H. scabra transcriptome data to elucidate conserved growth factor family and receptor genes. In total, 42 transcripts were identified, of which 9 were validated by gene cloning and sequencing. The H. scabra growth factor genes, such as bone morphogenetic protein 2A (BMP 2A), bone morphogenetic protein 5-like (BMP5-like), neurotrophin (NT) and fibroblast growth factor 18 (FGF18), were selected for further analyses, including phylogenetic comparison and spatial gene expression using RT-PCR and in situ hybridization. Expression of all genes investigated were widespread in multiple tissues. However, BMP 2A, BMP5-like and NT were found extensively in the radial nerve cord cells, while FGF18 was highly expressed in connective tissue layer of the body wall. Our identification and expression analysis of the H. scabra growth factor genes provided the molecular information of growth factors in this species which may ultimately complement the research in regenerative medicine.
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13
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Drees C, Rühl P, Czerny J, Chandra G, Bajorath J, Haase M, Heinemann SH, Piehler J. Diffraction-Unlimited Photomanipulation at the Plasma Membrane via Specifically Targeted Upconversion Nanoparticles. NANO LETTERS 2021; 21:8025-8034. [PMID: 34519216 DOI: 10.1021/acs.nanolett.1c02267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Engineered UCNP are used to trigger rapid photoconversion of the fluorescent protein Dendra2 with nanoscopic precision and over longer distances in mammalian cells. By exploiting the synergy of high-level thulium doping with core-shell design and elevated excitation intensities, intense UCNP emission is achieved, allowing fast photoconversion of Dendra2 with <10 nm resolution. A tailored biocompatible surface coating and functionalization with a derivate of green fluorescent protein (GFP) for recognition of antiGFP nanobodies are developed. Highly specific targeting of UCNP to fusion proteins of antiGFP on the surface of mammalian cells is demonstrated. UCNP bound to extracellular Dendra2 enable rapid photoconversion selectively in molecular proximity and thus unambiguous detection of cytokine receptor dimerization in the plasma membrane and in endosomes. Remarkably, UCNPs are also suited for manipulating intracellular Dendra2 across the plasma membrane. This study thus establishes UCNP-controlled photomanipulation with nanoscale precision, opening exciting opportunities for bioanalytical applications in cell biology.
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Affiliation(s)
- Christoph Drees
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Philipp Rühl
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, 07745 Jena, Germany
| | - Jacqueline Czerny
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Gemini Chandra
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, 07745 Jena, Germany
| | - Janosch Bajorath
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Markus Haase
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Stefan H Heinemann
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, 07745 Jena, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
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14
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Akiyama M, Ueki R, Yanagawa M, Abe M, Hiroshima M, Sako Y, Sando S. DNA‐Based Synthetic Growth Factor Surrogates with Fine‐Tuned Agonism**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Momoko Akiyama
- Department of Chemistry and Biotechnology The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Masataka Yanagawa
- Cellular Informatics Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Mitsuhiro Abe
- Cellular Informatics Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Michio Hiroshima
- Cellular Informatics Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Laboratory for Cell Signaling Dynamics RIKEN Center for, Biosystems Dynamics Research 6-2-3, Furuedai, Suita Osaka 565-0874 Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Department of Bioengineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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15
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Optimal ligand discrimination by asymmetric dimerization and turnover of interferon receptors. Proc Natl Acad Sci U S A 2021; 118:2103939118. [PMID: 34507994 DOI: 10.1073/pnas.2103939118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
In multicellular organisms, antiviral defense mechanisms evoke a reliable collective immune response despite the noisy nature of biochemical communication between tissue cells. A molecular hub of this response, the interferon I receptor (IFNAR), discriminates between ligand types by their affinity regardless of concentration. To understand how ligand type can be decoded robustly by a single receptor, we frame ligand discrimination as an information-theoretic problem and systematically compare the major classes of receptor architectures: allosteric, homodimerizing, and heterodimerizing. We demonstrate that asymmetric heterodimers achieve the best discrimination power over the entire physiological range of local ligand concentrations. This design enables sensing of ligand presence and type, and it buffers against moderate concentration fluctuations. In addition, receptor turnover, which drives the receptor system out of thermodynamic equilibrium, allows alignment of activation points for ligands of different affinities and thereby makes ligand discrimination practically independent of concentration. IFNAR exhibits this optimal architecture, and our findings thus suggest that this specialized receptor can robustly decode digital messages carried by its different ligands.
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16
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Akiyama M, Ueki R, Yanagawa M, Abe M, Hiroshima M, Sako Y, Sando S. DNA-Based Synthetic Growth Factor Surrogates with Fine-Tuned Agonism*. Angew Chem Int Ed Engl 2021; 60:22745-22752. [PMID: 34142433 DOI: 10.1002/anie.202105314] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/16/2021] [Indexed: 11/06/2022]
Abstract
Designing synthetic surrogates of functional proteins is an important, albeit challenging, task in the field of chemistry. A strategy toward the design of synthetic agonists for growth factor or cytokine receptors that elicit a desired signal activity has been in high demand, as such ligands hold great promise as safer and more effective therapeutics. In the present study, we used a DNA aptamer as a building block and described the strategy-guided design of a synthetic receptor agonist with fine-tuned agonism. The developed synthetic partial agonist can regulate therapeutically relevant cellular activities by eliciting fine-tuned receptor signaling.
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Affiliation(s)
- Momoko Akiyama
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masataka Yanagawa
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mitsuhiro Abe
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Michio Hiroshima
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Laboratory for Cell Signaling Dynamics, RIKEN Center for, Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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17
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Distaffen HE, Jones CW, Abraham BL, Nilsson BL. Multivalent display of chemical signals on
self‐assembled
peptide scaffolds. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Lee J, Vernet A, Gruber NG, Kready KM, Burrill DR, Way JC, Silver PA. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Eng Des Sel 2021; 34:6414420. [PMID: 34725710 DOI: 10.1093/protein/gzab025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/04/2021] [Accepted: 09/01/2021] [Indexed: 12/16/2022] Open
Abstract
Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10-14 M, allowing an estimate of the number of receptor-ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia.
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Affiliation(s)
- Jungmin Lee
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Andyna Vernet
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Nathalie G Gruber
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.,Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Kasia M Kready
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Devin R Burrill
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Jeffrey C Way
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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19
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Modulation of Human Mesenchymal Stem Cells by Electrical Stimulation Using an Enzymatic Biofuel Cell. Catalysts 2021. [DOI: 10.3390/catal11010062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Enzymatic biofuel cells (EBFCs) have excellent potential as components in bioelectronic devices, especially as active biointerfaces to regulate stem cell behavior for regenerative medicine applications. However, it remains unclear to what extent EBFC-generated electrical stimulation can regulate the functional behavior of human adipose-derived mesenchymal stem cells (hAD-MSCs) at the morphological and gene expression levels. Herein, we investigated the effect of EBFC-generated electrical stimulation on hAD-MSC cell morphology and gene expression using next-generation RNA sequencing. We tested three different electrical currents, 127 ± 9, 248 ± 15, and 598 ± 75 nA/cm2, in mesenchymal stem cells. We performed transcriptome profiling to analyze the impact of EBFC-derived electrical current on gene expression using next generation sequencing (NGS). We also observed changes in cytoskeleton arrangement and analyzed gene expression that depends on the electrical stimulation. The electrical stimulation of EBFC changes cell morphology through cytoskeleton re-arrangement. In particular, the results of whole transcriptome NGS showed that specific gene clusters were up- or down-regulated depending on the magnitude of applied electrical current of EBFC. In conclusion, this study demonstrates that EBFC-generated electrical stimulation can influence the morphological and gene expression properties of stem cells; such capabilities can be useful for regenerative medicine applications such as bioelectronic devices.
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20
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Yuan J, Zhao R, Xu J, Cheng M, Qin Z, Kou X, Fang X. Analyzing protein dynamics from fluorescence intensity traces using unsupervised deep learning network. Commun Biol 2020; 3:669. [PMID: 33184459 PMCID: PMC7665068 DOI: 10.1038/s42003-020-01389-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 10/13/2020] [Indexed: 11/09/2022] Open
Abstract
We propose an unsupervised deep learning network to analyze the dynamics of membrane proteins from the fluorescence intensity traces. This system was trained in an unsupervised manner with the raw experimental time traces and synthesized ones, so neither predefined state number nor pre-labelling were required. With the bidirectional Long Short-Term Memory (biLSTM) networks as the hidden layers, both the past and future context can be used fully to improve the prediction results and can even extract information from the noise distribution. The method was validated with the synthetic dataset and the experimental dataset of monomeric fluorophore Cy5, and then applied to extract the membrane protein interaction dynamics from experimental data successfully.
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Affiliation(s)
- Jinghe Yuan
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.
| | - Rong Zhao
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, 100029, Beijing, China
| | - Jiachao Xu
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
| | - Ming Cheng
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
| | - Zidi Qin
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaolong Kou
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
| | - Xiaohong Fang
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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21
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Schreiber G. The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19. Front Immunol 2020; 11:595739. [PMID: 33117408 PMCID: PMC7561359 DOI: 10.3389/fimmu.2020.595739] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022] Open
Abstract
Type I interferons (IFN-I) were first discovered over 60 years ago in a classical experiment by Isaacs and Lindenman, who showed that IFN-Is possess antiviral activity. Later, it became one of the first approved protein drugs using heterologous protein expression systems, which allowed its large-scale production. It has been approved, and widely used in a pleiotropy of diseases, including multiple-sclerosis, hepatitis B and C, and some forms of cancer. Preliminary clinical data has supported its effectiveness against potential pandemic pathogens such as Ebola and SARS. Still, more efficient and specific drugs have taken its place in treating such diseases. The COVID-19 global pandemic has again lifted the status of IFN-Is to become one of the more promising drug candidates, with initial clinical trials showing promising results in reducing the severity and duration of the disease. Although SARS-CoV-2 inhibits the production of IFNβ and thus obstructs the innate immune response to this virus, it is sensitive to the antiviral activity of externally administrated IFN-Is. In this review I discuss the diverse modes of biological actions of IFN-Is and how these are related to biophysical parameters of IFN-I-receptor interaction and cell-type specificity in light of the large variety of binding affinities of the different IFN-I subtypes towards the common interferon receptor. Furthermore, I discuss how these may guide the optimized use IFN-Is in combatting COVID-19.
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Affiliation(s)
- Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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22
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Chataigner LMP, Leloup N, Janssen BJC. Structural Perspectives on Extracellular Recognition and Conformational Changes of Several Type-I Transmembrane Receptors. Front Mol Biosci 2020; 7:129. [PMID: 32850948 PMCID: PMC7427315 DOI: 10.3389/fmolb.2020.00129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Type-I transmembrane proteins represent a large group of 1,412 proteins in humans with a multitude of functions in cells and tissues. They are characterized by an extracellular, or luminal, N-terminus followed by a single transmembrane helix and a cytosolic C-terminus. The domain composition and structures of the extracellular and intercellular segments differ substantially amongst its members. Most of the type-I transmembrane proteins have roles in cell signaling processes, as ligands or receptors, and in cellular adhesion. The extracellular segment often determines specificity and can control signaling and adhesion. Here we focus on recent structural understanding on how the extracellular segments of several diverse type-I transmembrane proteins engage in interactions and can undergo conformational changes for their function. Interactions at the extracellular side by proteins on the same cell or between cells are enhanced by the transmembrane setting. Extracellular conformational domain rearrangement and structural changes within domains alter the properties of the proteins and are used to regulate signaling events. The combination of structural properties and interactions can support the formation of larger-order assemblies on the membrane surface that are important for cellular adhesion and intercellular signaling.
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Affiliation(s)
- Lucas M P Chataigner
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nadia Leloup
- Structural Biology and Protein Biochemistry, Morphic Therapeutic, Waltham, MA, United States
| | - Bert J C Janssen
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
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23
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Ding M, Tegel H, Sivertsson Å, Hober S, Snijder A, Ormö M, Strömstedt PE, Davies R, Holmberg Schiavone L. Secretome-Based Screening in Target Discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:535-551. [PMID: 32425085 PMCID: PMC7309359 DOI: 10.1177/2472555220917113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
Abstract
Secreted proteins and their cognate plasma membrane receptors regulate human physiology by transducing signals from the extracellular environment into cells resulting in different cellular phenotypes. Systematic use of secretome proteins in assays enables discovery of novel biology and signaling pathways. Several secretome-based phenotypic screening platforms have been described in the literature and shown to facilitate target identification in drug discovery. In this review, we summarize the current status of secretome-based screening. This includes annotation, production, quality control, and sample management of secretome libraries, as well as how secretome libraries have been applied to discover novel target biology using different disease-relevant cell-based assays. A workflow for secretome-based screening is shared based on the AstraZeneca experience. The secretome library offers several advantages compared with other libraries used for target discovery: (1) screening using a secretome library directly identifies the active protein and, in many cases, its cognate receptor, enabling a rapid understanding of the disease pathway and subsequent formation of target hypotheses for drug discovery; (2) the secretome library covers significant areas of biological signaling space, although the size of this library is small; (3) secretome proteins can be added directly to cells without additional manipulation. These factors make the secretome library ideal for testing in physiologically relevant cell types, and therefore it represents an attractive approach to phenotypic target discovery.
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Affiliation(s)
- Mei Ding
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Hanna Tegel
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Arjan Snijder
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Mats Ormö
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Erik Strömstedt
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Rick Davies
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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24
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Khan M, Maryam A, Saleem MZ, Shakir HA, Qazi JI, Li Y, Ma T. Brevilin A induces ROS-dependent apoptosis and suppresses STAT3 activation by direct binding in human lung cancer cells. J Cancer 2020; 11:3725-3735. [PMID: 32328177 PMCID: PMC7171504 DOI: 10.7150/jca.40983] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/06/2020] [Indexed: 12/30/2022] Open
Abstract
Sesquiterpene lactones have been shown to be promising leads for anticancer drug development. Brevilin A (BLN-A), a sesquiterpene lactone compound of Centipeda minima has been shown to exhibit anticancer effects against various cancer cells. However, the anticancer mechanism and cellular targets of BLN-A remain elusive. Here in this study, BLN-A inhibits proliferation and induces cell morphological changes in A549 and NCI-H1650 non-small cell lung cancer cells in a dose-dependent manner. Moreover, BLN-A increased ROS generation and bax/bcl-2 ratio while decreased intracellular glutathione (GSH), and mitochondrial membrane potential which resulted in induction of apoptosis as evident by annexin-V/FITC staining, caspase-3 activation and PARP cleavage. Supplementation of cells with NAC (ROS Scavenger) effectively protected the cells from BLN-A-induced apoptosis. Finally, BLN-A inhibited constitutive as well as IL-6- and EGF-induced STAT3 activation at Tyr705. Using molecular docking and SPR analyses, we found that BLN-A directly binds with STAT3 and thereby inhibits its activation. Knocking down of STAT3 by stable transfection with shRNA suppressed growth and augmented cytotoxicity of BLN-A, indicating the key role of STAT3 in BLN-A-mediated apoptosis. Cumulative findings suggest that BLN-A is a promising lead structure for developing it into a potent STAT3 inhibitor and therapeutic agent against NSCLC as well.
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Affiliation(s)
- Muhammad Khan
- Department of Zoology, University of the Punjab, Quaid-e-Azam Campus, Lahore-54590, Pakistan
| | - Amara Maryam
- Department of Zoology, University of the Punjab, Quaid-e-Azam Campus, Lahore-54590, Pakistan
| | | | - Hafiz Abdullah Shakir
- Department of Zoology, University of the Punjab, Quaid-e-Azam Campus, Lahore-54590, Pakistan
| | - Javed Iqbal Qazi
- Department of Zoology, University of the Punjab, Quaid-e-Azam Campus, Lahore-54590, Pakistan
| | - Yongming Li
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, P.R. China
| | - Tonghui Ma
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, P.R. China
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25
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Mossner S, Phan HT, Triller S, Moll JM, Conrad U, Scheller J. Multimerization strategies for efficient production and purification of highly active synthetic cytokine receptor ligands. PLoS One 2020; 15:e0230804. [PMID: 32236103 PMCID: PMC7112226 DOI: 10.1371/journal.pone.0230804] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/09/2020] [Indexed: 01/28/2023] Open
Abstract
Cytokine signaling is transmitted by cell surface receptors which act as natural biological switches to control cellular functions such as immune reactions. Recently, we have designed synthetic cytokine receptors (SyCyRs) consisting of green fluorescent protein (GFP)- and mCherry-nanobodies fused to the transmembrane and intracellular domains of cytokine receptors. Following stimulation with homo- and heterodimeric GFP-mCherry fusion proteins, the resulting receptors phenocopied signaling induced by physiologically occurring cytokines. GFP and mCherry fusion proteins were produced in E. coli or CHO-K1 cells, but the overall yield and stability was low. Therefore, we applied two alternative multimerization strategies and achieved immunoglobulin Fc-mediated dimeric and coiled-coil GCN4pII-mediated trimeric assemblies. GFP- and/or mCherry-Fc homodimers activated synthetic gp130 cytokine receptors, which naturally respond to Interleukin 6 family cytokines. Activation of these synthetic gp130 receptors resulted in STAT3 and ERK phosphorylation and subsequent proliferation of Ba/F3-gp130 cells. Half-maximal effective concentrations (EC50) of 8.1 ng/ml and 0.64 ng/ml were determined for dimeric GFP-Fc and mCherry-Fc, respectively. This is well within the expected EC50 range of the native cytokines. Moreover, we generated tetrameric and hexameric GFP-mCherry-Fc fusion proteins, which were also biologically active. This highlighted the importance of close juxtaposition of two cytokine receptors for efficient receptor activation. Finally, we used a trimeric GCN4pII motif to generate homo-trimeric GFP and mCherry complexes. These synthetic cytokines showed improved EC50 values (GFP3: 0.58 ng/ml; mCherrry3: 0.37 ng/ml), over dimeric Fc fused variants. In conclusion, we successfully generated highly effective and stable multimeric synthetic cytokine receptor ligands for activation of synthetic cytokine receptors.
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Affiliation(s)
- Sofie Mossner
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Hoang T. Phan
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Gatersleben, Germany
| | - Saskia Triller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Gatersleben, Germany
| | - Jens M. Moll
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Udo Conrad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Gatersleben, Germany
| | - Jürgen Scheller
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail:
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26
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Tissue Engineering Approaches for Enamel, Dentin, and Pulp Regeneration: An Update. Stem Cells Int 2020; 2020:5734539. [PMID: 32184832 PMCID: PMC7060883 DOI: 10.1155/2020/5734539] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
Stem/progenitor cells are undifferentiated cells characterized by their exclusive ability for self-renewal and multilineage differentiation potential. In recent years, researchers and investigations explored the prospect of employing stem/progenitor cell therapy in regenerative medicine, especially stem/progenitor cells originating from the oral tissues. In this context, the regeneration of the lost dental tissues including enamel, dentin, and the dental pulp are pivotal targets for stem/progenitor cell therapy. The present review elaborates on the different sources of stem/progenitor cells and their potential clinical applications to regenerate enamel, dentin, and the dental pulpal tissues.
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27
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Wilmes S, Hafer M, Vuorio J, Tucker JA, Winkelmann H, Löchte S, Stanly TA, Pulgar Prieto KD, Poojari C, Sharma V, Richter CP, Kurre R, Hubbard SR, Garcia KC, Moraga I, Vattulainen I, Hitchcock IS, Piehler J. Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations. Science 2020; 367:643-652. [PMID: 32029621 PMCID: PMC8117407 DOI: 10.1126/science.aaw3242] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022]
Abstract
Homodimeric class I cytokine receptors are assumed to exist as preformed dimers that are activated by ligand-induced conformational changes. We quantified the dimerization of three prototypic class I cytokine receptors in the plasma membrane of living cells by single-molecule fluorescence microscopy. Spatial and spatiotemporal correlation of individual receptor subunits showed ligand-induced dimerization and revealed that the associated Janus kinase 2 (JAK2) dimerizes through its pseudokinase domain. Oncogenic receptor and hyperactive JAK2 mutants promoted ligand-independent dimerization, highlighting the formation of receptor dimers as the switch responsible for signal activation. Atomistic modeling and molecular dynamics simulations based on a detailed energetic analysis of the interactions involved in dimerization yielded a mechanistic blueprint for homodimeric class I cytokine receptor activation and its dysregulation by individual mutations.
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Affiliation(s)
- Stephan Wilmes
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Maximillian Hafer
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Joni Vuorio
- Department of Physics, University of Helsinki, Helsinki, Finland
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Julie A Tucker
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hauke Winkelmann
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Tess A Stanly
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Katiuska D Pulgar Prieto
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Chetan Poojari
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Christian P Richter
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Stevan R Hubbard
- Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ignacio Moraga
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland.
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Ian S Hitchcock
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - Jacob Piehler
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany.
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28
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Neutrophil extracellular trap-associated RNA and LL37 enable self-amplifying inflammation in psoriasis. Nat Commun 2020; 11:105. [PMID: 31913271 PMCID: PMC6949246 DOI: 10.1038/s41467-019-13756-4] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/13/2019] [Indexed: 12/21/2022] Open
Abstract
Psoriasis is an inflammatory skin disease with strong neutrophil (PMN) infiltration and high levels of the antimicrobial peptide, LL37. LL37 in complex with DNA and RNA is thought to initiate disease exacerbation via plasmacytoid dendritic cells. However, the source of nucleic acids supposed to start this initial inflammatory event remains unknown. We show here that primary murine and human PMNs mount a fulminant and self-propagating neutrophil extracellular trap (NET) and cytokine response, but independently of the canonical NET component, DNA. Unexpectedly, RNA, which is abundant in NETs and psoriatic but not healthy skin, in complex with LL37 triggered TLR8/TLR13-mediated cytokine and NET release by PMNs in vitro and in vivo. Transfer of NETs to naive human PMNs prompts additional NET release, promoting further inflammation. Our study thus uncovers a self-propagating vicious cycle contributing to chronic inflammation in psoriasis, and NET-associated RNA (naRNA) as a physiologically relevant NET component.
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29
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Belle NM, Ji Y, Herbine K, Wei Y, Park J, Zullo K, Hung LY, Srivatsa S, Young T, Oniskey T, Pastore C, Nieves W, Somsouk M, Herbert DR. TFF3 interacts with LINGO2 to regulate EGFR activation for protection against colitis and gastrointestinal helminths. Nat Commun 2019; 10:4408. [PMID: 31562318 PMCID: PMC6764942 DOI: 10.1038/s41467-019-12315-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 08/26/2019] [Indexed: 12/14/2022] Open
Abstract
Intestinal epithelial cells (IEC) have important functions in nutrient absorption, barrier integrity, regeneration, pathogen-sensing, and mucus secretion. Goblet cells are a specialized cell type of IEC that secrete Trefoil factor 3 (TFF3) to regulate mucus viscosity and wound healing, but whether TFF3-responsiveness requires a receptor is unclear. Here, we show that leucine rich repeat receptor and nogo-interacting protein 2 (LINGO2) is essential for TFF3-mediated functions. LINGO2 immunoprecipitates with TFF3, co-localizes with TFF3 on the cell membrane of IEC, and allows TFF3 to block apoptosis. We further show that TFF3-LINGO2 interactions disrupt EGFR-LINGO2 complexes resulting in enhanced EGFR signaling. Excessive basal EGFR activation in Lingo2 deficient mice increases disease severity during colitis and augments immunity against helminth infection. Conversely, TFF3 deficiency reduces helminth immunity. Thus, TFF3-LINGO2 interactions de-repress inhibitory LINGO2-EGFR complexes, allowing TFF3 to drive wound healing and immunity.
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Affiliation(s)
- Nicole Maloney Belle
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19140, USA
| | - Yingbiao Ji
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19140, USA
| | - Karl Herbine
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19140, USA
| | - Yun Wei
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, 94110, USA.,Department of Inflammation and Oncology, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA, 94080, USA
| | - JoonHyung Park
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19140, USA
| | - Kelly Zullo
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19140, USA
| | - Li-Yin Hung
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19140, USA.,Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, 94110, USA
| | - Sriram Srivatsa
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19140, USA
| | - Tanner Young
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19140, USA
| | - Taylor Oniskey
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, 94110, USA
| | - Christopher Pastore
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19140, USA
| | - Wildaliz Nieves
- Division of Gastroenterology at ZSFG, University of California, San Francisco, San Francisco, CA, 94110, USA
| | - Ma Somsouk
- Division of Gastroenterology at ZSFG, University of California, San Francisco, San Francisco, CA, 94110, USA
| | - De'Broski R Herbert
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19140, USA. .,Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, 94110, USA.
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30
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Human adipose liquid extract induces angiogenesis and adipogenesis: a novel cell-free therapeutic agent. Stem Cell Res Ther 2019; 10:252. [PMID: 31412933 DOI: 10.1186/s13287-019-1356-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Taking advantage of cellular paracrine mechanisms, the secretome of adipose-derived stem cells (ADSCs) and adipose tissue has been demonstrated to induce tissue repair and regeneration in various ischemic and impaired conditions. However, these cell-based therapies have been hindered by issues, such as inherent safety and cost-efficiency for clinical applications. In this study, we prepared a liquid cell-free extract from human adipose tissue [adipose liquid extract (ALE)] and evaluated its potential therapeutic efficacy. METHODS ALE was prepared from human subcutaneous adipose tissue using a rapid and physical approach, and the protein components in ALE were identified using mass spectrometry analysis. In vivo, the therapeutic effect of this agent was investigated on wound healing in C57BL/6 mice, and wound healing rate, vessel density, and neo-adipocyte formation in wounded skins were measured at days 3, 7, 11, and 14. In vitro, the effect of ALE on the viability of human ADSCs, tube formation of human umbilical vein endothelial cells (HUVECs), and adipogenic differentiation of ADSCs were tested. RESULTS The results demonstrated that ALE contained a variety of growth factors and did not affect cell viability. ALE-treated wounds exhibited accelerated wound healing with increased vessel density and formation of neo-adipocytes compared to that of control wounds. Moreover, when added as a cell culture supplement, ALE effectively induced tube formation of HUVECs and lipid accumulation in ADSCs. ALE-treated ADSCs also exhibited elevated levels of adipogenic gene expression. CONCLUSIONS ALE is a novel growth-rich therapeutic agent that is cell-free and easy to produce. Besides, it is also able to induce angiogenesis and adipogenesis both in vitro and in vivo, thus indicating that it could be used for wound repair and soft tissue regeneration.
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31
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Wang B, Wangkahart E, Secombes CJ, Wang T. Insights into the Evolution of the Suppressors of Cytokine Signaling (SOCS) Gene Family in Vertebrates. Mol Biol Evol 2019; 36:393-411. [PMID: 30521052 PMCID: PMC6368001 DOI: 10.1093/molbev/msy230] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The SOCS family are key negative regulators of cytokine and growth factor signaling. Typically, 8-17 SOCS genes are present in vertebrate species with eight known in mammals, classified as type I (SOCS4-7) and type II (CISH and SOCS1-3) SOCS. It was believed that the type II SOCS were expanded through the two rounds of whole genome duplication (1R and 2R WGDs) from a single CISH/SOCS1-3 precursor. Previously, 12 genes were identified in rainbow trout but here we report 15 additional loci are present, and confirm 26 of the genes are expressed, giving rainbow trout the largest SOCS gene repertoire identified to date. The discovery of the additional SOCS genes in trout has led to a novel model of SOCS family evolution, whereby the vertebrate SOCS gene family was derived from CISH/SOCS2, SOCS1/SOCS3, SOCS4/5, SOCS6, and SOCS7 ancestors likely present before the two WGD events. It is also apparent that teleost SOCS2b, SOCS4, and SOCS5b molecules are not true orthologues of mammalian SOCS2, SOCS4, and SOCS5, respectively. The rate of SOCS gene structural changes increased from 2R vertebrates, to 4R rainbow trout, and the genes with structural changes show large differences and low correlation coefficient of expression levels relative to their paralogues, suggesting a role of structural changes in expression and functional diversification. This study has important impacts in the functional prediction and understanding of the SOCS gene family in different vertebrates, and provides a framework for determining how many SOCS genes could be expected in a particular vertebrate species/lineage.
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Affiliation(s)
- Bei Wang
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, P.R. China.,Scottish Fish Immunology Research Centre, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Eakapol Wangkahart
- Scottish Fish Immunology Research Centre, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.,Research Unit of Excellence for Tropical Fisheries and Technology, Division of Fisheries, Department of Agricultural Technology, Faculty of Technology, Mahasarakham University, Khamriang Sub-District, Kantarawichai, Mahasarakham, Thailand
| | - Christopher J Secombes
- Scottish Fish Immunology Research Centre, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Tiehui Wang
- Scottish Fish Immunology Research Centre, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
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32
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Eswaramoorthy SD, Ramakrishna S, Rath SN. Recent advances in three-dimensional bioprinting of stem cells. J Tissue Eng Regen Med 2019; 13:908-924. [PMID: 30866145 DOI: 10.1002/term.2839] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 02/01/2019] [Accepted: 02/21/2019] [Indexed: 12/29/2022]
Abstract
In spite of being a new field, three-dimensional (3D) bioprinting has undergone rapid growth in the recent years. Bioprinting methods offer a unique opportunity for stem cell distribution, positioning, and differentiation at the microscale to make the differentiated architecture of any tissue while maintaining precision and control over the cellular microenvironment. Bioprinting introduces a wide array of approaches to modify stem cell fate. This review discusses these methodologies of 3D bioprinting stem cells. Fabricating a fully operational tissue or organ construct with a long life will be the most significant challenge of 3D bioprinting. Once this is achieved, a whole human organ can be fabricated for the defect place at the site of surgery.
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Affiliation(s)
- Sindhuja D Eswaramoorthy
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad (IITH), Sangareddy, Telangana, India
| | - Seeram Ramakrishna
- Centre for Nanofibers & Nanotechnology, NUS Nanoscience & Nanotechnology Initiative, Singapore
| | - Subha N Rath
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad (IITH), Sangareddy, Telangana, India
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33
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Xu J, Qin G, Luo F, Wang L, Zhao R, Li N, Yuan J, Fang X. Automated Stoichiometry Analysis of Single-Molecule Fluorescence Imaging Traces via Deep Learning. J Am Chem Soc 2019; 141:6976-6985. [DOI: 10.1021/jacs.9b00688] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jiachao Xu
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gege Qin
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Luo
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Wang
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Zhao
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Li
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghe Yuan
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohong Fang
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Abstract
Cell surface transmembrane receptors often form nanometer- to micrometer-scale clusters to initiate signal transduction in response to environmental cues. Extracellular ligand oligomerization, domain-domain interactions, and binding to multivalent proteins all contribute to cluster formation. Here we review the current understanding of mechanisms driving cluster formation in a series of representative receptor systems: glycosylated receptors, immune receptors, cell adhesion receptors, Wnt receptors, and receptor tyrosine kinases. We suggest that these clusters share properties of systems that undergo liquid-liquid phase separation and could be investigated in this light.
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Affiliation(s)
- Lindsay B Case
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , ,
| | - Jonathon A Ditlev
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , ,
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , ,
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35
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Barak R, Yom-Tov G, Guez-Haddad J, Gasri-Plotnitsky L, Maimon R, Cohen-Berkman M, McCarthy AA, Perlson E, Henis-Korenblit S, Isupov MN, Opatowsky Y. Structural Principles in Robo Activation and Auto-inhibition. Cell 2019; 177:272-285.e16. [PMID: 30853216 DOI: 10.1016/j.cell.2019.02.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/06/2018] [Accepted: 02/06/2019] [Indexed: 01/28/2023]
Abstract
Proper brain function requires high-precision neuronal expansion and wiring, processes controlled by the transmembrane Roundabout (Robo) receptor family and their Slit ligands. Despite their great importance, the molecular mechanism by which Robos' switch from "off" to "on" states remains unclear. Here, we report a 3.6 Å crystal structure of the intact human Robo2 ectodomain (domains D1-8). We demonstrate that Robo cis dimerization via D4 is conserved through hRobo1, 2, and 3 and the C. elegans homolog SAX-3 and is essential for SAX-3 function in vivo. The structure reveals two levels of auto-inhibition that prevent premature activation: (1) cis blocking of the D4 dimerization interface and (2) trans interactions between opposing Robo receptors that fasten the D4-blocked conformation. Complementary experiments in mouse primary neurons and C. elegans support the auto-inhibition model. These results suggest that Slit stimulation primarily drives the release of Robo auto-inhibition required for dimerization and activation.
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Affiliation(s)
- Reut Barak
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Galit Yom-Tov
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | | | - Roy Maimon
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Moran Cohen-Berkman
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | | | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | | | | | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel.
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36
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Li LJ, Ma J, Li SB, Chen X, Zhang J. Vascular endothelial growth factor B inhibits lipid accumulation in C2C12 myotubes incubated with fatty acids. Growth Factors 2019; 37:76-84. [PMID: 31215273 DOI: 10.1080/08977194.2019.1626851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To investigate (1) the effect of vascular endothelial growth factor B (VEGFB) on lipid accumulation and the alteration of fatty acids and fatty acid-related enzymes in C2C12 myotubes incubated with fatty acids and (2) the regulatory effect of VEGFB on skeletal muscle lipid metabolism. Mouse C2C12 myotubes were incubated with oleic acid (OA) and palmitic acid (PA), and differentiated mature C2C12 myotubes were treated with VEGFB. Oil-red O staining, BODIPY staining and cell triglycerides (TG) content were examined. Total RNA was isolated, and real-time PCR analysis was performed. Treatment with 100 μM OA and 50 μM PA induced lipid droplet accumulation and increased TG content (p < .01), and 100 ng/mL VEGFB reduced lipid droplet accumulation and decreased TG content (p < .01). Treatment with 100 ng/mL VEGFB significantly induced the mRNA expression of fatty acid transport protein 1 (FATP1) (p < .01) and FATP4 (p < .01). Treatment with 100 ng/mL VEGFB significantly induced the mRNA expression of adipose TG lipase and hormone-sensitive lipase (p < .01) as well as carnitine palmitoyltransferase I (p < .01), peroxisome proliferator-activated receptor-γ coactivator-1α (p < .01), acyl-coa dehydrogenase very long chain (p < .05), acyl-coa synthetase long-chain family member 1 (p < .01), peroxisomal acyl-coenzyme A oxidase 1 (p < .05), and mitochondrial uncoupling protein 3 (p < .01). VEGFB enhanced FATP1and FATP4 expression, promoted C2C12 myotube fatty acid oxidation and TG decomposition, and inhibited C2C12 myotube fatty acid re-esterification, thus inhibiting lipid accumulation in C2C12 myotubes incubated with fatty acids.
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Affiliation(s)
- Ling-Jie Li
- a College of P.E. and Sports, Beijing Normal University , Beijing , China
| | - Jin Ma
- a College of P.E. and Sports, Beijing Normal University , Beijing , China
| | - Song-Bo Li
- b China Academy of Sport and Health Science, Beijing Sport University , Beijing , China
| | - Xuefei Chen
- a College of P.E. and Sports, Beijing Normal University , Beijing , China
| | - Jing Zhang
- a College of P.E. and Sports, Beijing Normal University , Beijing , China
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37
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Approaching the Roundabout: cis and trans Robo1 Contacts Revealed. Structure 2019; 26:183-184. [PMID: 29413320 DOI: 10.1016/j.str.2018.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this issue of Structure,Aleksandrova et al. (2018) present low- and high-resolution structures of Robo1, a key player in axonal guidance. The structures shed light on the arrangement of Robo1 at the plasma membrane and provide evidence for back-to-back trans Robo1 contacts.
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Scheide-Noeth JP, Rosen M, Baumstark D, Dietz H, Mueller TD. Structural Basis of Interleukin-5 Inhibition by the Small Cyclic Peptide AF17121. J Mol Biol 2018; 431:714-731. [PMID: 30529748 DOI: 10.1016/j.jmb.2018.11.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
Interleukin-5 (IL-5) is a T-helper cell of subtype 2 cytokine involved in many aspects of eosinophil life. Eosinophilic granulocytes play a pathogenic role in the progression of atopic diseases, such as allergy, asthma and atopic dermatitis and hypereosinophilic syndromes. Here, eosinophils upon activation degranulate leading to the release of proinflammatory proteins and mediators stored in intracellular vesicles termed granula thereby causing local inflammation, which when persisting leads to tissue damage and organ failure. As a key regulator of eosinophil function, IL-5 therefore presents a major pharmaceutical target and approaches to interfere with IL-5 receptor activation are of great interest. Here we present the structure of the IL-5 inhibiting peptide AF17121 bound to the extracellular domain of the IL-5 receptor IL-5Rα. The small 18mer cyclic peptide snugly fits into the wrench-like cleft of the IL-5 receptor, thereby blocking access of key residues for IL-5 binding. While AF17121 and IL-5 seemingly bind to a similar epitope at IL-5Rα, functional studies show that recognition and binding of both ligands differ. Using the structure data, peptide variants with improved IL-5 inhibition have been generated, which might present valuable starting points for superior peptide-based IL-5 antagonists.
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Affiliation(s)
- Jan-Philipp Scheide-Noeth
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute of the University Wuerzburg, Julius-von-Sachs-Platz 2, D-97082, Wuerzburg, Germany
| | - Maximilian Rosen
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute of the University Wuerzburg, Julius-von-Sachs-Platz 2, D-97082, Wuerzburg, Germany
| | - David Baumstark
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute of the University Wuerzburg, Julius-von-Sachs-Platz 2, D-97082, Wuerzburg, Germany
| | - Harald Dietz
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute of the University Wuerzburg, Julius-von-Sachs-Platz 2, D-97082, Wuerzburg, Germany
| | - Thomas D Mueller
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute of the University Wuerzburg, Julius-von-Sachs-Platz 2, D-97082, Wuerzburg, Germany.
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Engineered systems to study the synergistic signaling between integrin-mediated mechanotransduction and growth factors (Review). Biointerphases 2018; 13:06D302. [DOI: 10.1116/1.5045231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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40
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MacDonald RJ, Yen A. CXCR5 overexpression in HL-60 cells enhances chemotaxis toward CXCL13 without anticipated interaction partners or enhanced MAPK signaling. In Vitro Cell Dev Biol Anim 2018; 54:725-735. [PMID: 30276608 DOI: 10.1007/s11626-018-0293-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 09/06/2018] [Indexed: 01/09/2023]
Abstract
CXCR5 is a serpentine receptor implicated in cell migration in lymphocytes and differentiation in leukocytes. It causes MAPK pathway activation and has known membrane partners for signaling. CXCR5 mRNA is reportedly expressed in neutrophils following isolation, but its role in this cellular context is unknown. CXCR5 is also expressed in HL-60 cells, a human acute myeloid leukemia line, following treatment with all-trans retinoic acid, which induces differentiation toward a neutrophil-like state. CXCR5 is necessary for this process; differentiation was crippled in CXCR5 knockout cells and enhanced in cells ectopically expressing it. Since CXCR5 has various membrane protein partners, we investigated whether CXCR5-driven all-trans retinoic acid-induced differentiation depends on its association with such partners. Pursuing this, we generated HL-60 cells overexpressing the protein. We found that CXCR5 drove migration toward its ligand, CXCL13, and probed for interactions with several candidates using flow cytometry-based Förster resonance energy transfer. Surprisingly, we did not detect interactions with any candidates, including three reported in other cellular contexts. Additionally, we observed no significant changes in all-trans retinoic acid-induced differentiation; this may be due to the stoichiometry of CXCR5 and partner receptors or CXCL13. The anticipated membrane partnerings were surprisingly apparently unnecessary for downstream CXCR5 signaling and all-trans retinoic acid-induced differentiation.
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Affiliation(s)
- Robert J MacDonald
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Veterinary Research Tower T4008A, Box 11, Ithaca, NY, 14853, USA
| | - Andrew Yen
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Veterinary Research Tower T4008A, Box 11, Ithaca, NY, 14853, USA.
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Gorby C, Martinez-Fabregas J, Wilmes S, Moraga I. Mapping Determinants of Cytokine Signaling via Protein Engineering. Front Immunol 2018; 9:2143. [PMID: 30319612 PMCID: PMC6170656 DOI: 10.3389/fimmu.2018.02143] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/30/2018] [Indexed: 12/21/2022] Open
Abstract
Cytokines comprise a large family of secreted ligands that are critical for the regulation of immune homeostasis. Cytokines initiate signaling via dimerization or oligomerization of the cognate receptor subunits, triggering the activation of the Janus Kinases (JAKs)/ signal transducer and activator of transcription (STATs) pathway and the induction of specific gene expression programs and bioactivities. Deregulation of cytokines or their downstream signaling pathways are at the root of many human disorders including autoimmunity and cancer. Identifying and understanding the mechanistic principles that govern cytokine signaling will, therefore, be highly important in order to harness the therapeutic potential of cytokines. In this review, we will analyze how biophysical (ligand-receptor binding geometry and affinity) and cellular (receptor trafficking and intracellular abundance of signaling molecules) parameters shape the cytokine signalosome and cytokine functional pleiotropy; from the initial cytokine binding to its receptor to the degradation of the cytokine receptor complex in the proteasome and/or lysosome. We will also discuss how combining advanced protein engineering with detailed signaling and functional studies has opened promising avenues to tackle complex questions in the cytokine signaling field.
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Affiliation(s)
- Claire Gorby
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jonathan Martinez-Fabregas
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Stephan Wilmes
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ignacio Moraga
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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42
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Kumar S, Jain S. Immune signalling by supramolecular assemblies. Immunology 2018; 155:435-445. [PMID: 30144032 DOI: 10.1111/imm.12995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
Formation of supramolecular assemblies appears to be a general mechanism in immune signalling pathways. These supramolecular assemblies appear to form through a nucleated polymerization mechanism. This review examines selected immune signalling pathways that involve supramolecular assemblies, describes the concepts of protein polymerization, and discusses how those concepts of protein polymerization implicate new elegant ways for signal amplification, setting threshold and noise reduction in these pathways.
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Affiliation(s)
- Santosh Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Shweta Jain
- Department of Neurology and Graduate Programs in Neuroscience and Biomedical Sciences, University of California at San Francisco, San Francisco, CA, USA
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43
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Structural insights into SorCS2-Nerve Growth Factor complex formation. Nat Commun 2018; 9:2979. [PMID: 30061605 PMCID: PMC6065357 DOI: 10.1038/s41467-018-05405-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 07/04/2018] [Indexed: 01/09/2023] Open
Abstract
Signaling of SorCS receptors by proneurotrophin ligands regulates neuronal plasticity, induces apoptosis and is associated with mental disorders. The detailed structure of SorCS2 and its extracellular specificity are unresolved. Here we report crystal structures of the SorCS2–NGF complex and unliganded SorCS2 ectodomain, revealing cross-braced SorCS2 homodimers with two NGF dimers bound in a 2:4 stoichiometry. Five out of six SorCS2 domains directly contribute to dimer formation and a C-terminal membrane proximal unreported domain, with an RNA recognition motif fold, locks the dimer in an intermolecular head-to-tail interaction. The complex structure shows an altered SorCS2 conformation indicating substantial structural plasticity. Both NGF dimer chains interact exclusively with the top face of a SorCS2 β-propeller. Biophysical experiments reveal that NGF, proNGF, and proBDNF bind at this site on SorCS2. Taken together, our data reveal a structurally flexible SorCS2 receptor that employs the large β-propeller as a ligand binding platform. The Sortilin-related CNS-expressed receptor 2 (SorCS2)–proneurotrophin signaling system regulates neuronal plasticity and its dysfunction is linked to schizophrenia. Here the authors present the structures of the SorCS2 ectodomain alone and in complex with Nerve Growth Factor, which provides insights into SorCS2 ligand binding and signaling.
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Gungor-Ozkerim PS, Inci I, Zhang YS, Khademhosseini A, Dokmeci MR. Bioinks for 3D bioprinting: an overview. Biomater Sci 2018; 6:915-946. [PMID: 29492503 PMCID: PMC6439477 DOI: 10.1039/c7bm00765e] [Citation(s) in RCA: 585] [Impact Index Per Article: 97.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioprinting is an emerging technology with various applications in making functional tissue constructs to replace injured or diseased tissues. It is a relatively new approach that provides high reproducibility and precise control over the fabricated constructs in an automated manner, potentially enabling high-throughput production. During the bioprinting process, a solution of a biomaterial or a mixture of several biomaterials in the hydrogel form, usually encapsulating the desired cell types, termed the bioink, is used for creating tissue constructs. This bioink can be cross-linked or stabilized during or immediately after bioprinting to generate the final shape, structure, and architecture of the designed construct. Bioinks may be made from natural or synthetic biomaterials alone, or a combination of the two as hybrid materials. In certain cases, cell aggregates without any additional biomaterials can also be adopted for use as a bioink for bioprinting processes. An ideal bioink should possess proper mechanical, rheological, and biological properties of the target tissues, which are essential to ensure correct functionality of the bioprinted tissues and organs. In this review, we provide an in-depth discussion of the different bioinks currently employed for bioprinting, and outline some future perspectives in their further development.
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Affiliation(s)
- P Selcan Gungor-Ozkerim
- Biomaterials Innovation Research Center, Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA
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45
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Krüger CL, Zeuner MT, Cottrell GS, Widera D, Heilemann M. Quantitative single-molecule imaging of TLR4 reveals ligand-specific receptor dimerization. Sci Signal 2017; 10:10/503/eaan1308. [DOI: 10.1126/scisignal.aan1308] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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46
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Ligand-induced type II interleukin-4 receptor dimers are sustained by rapid re-association within plasma membrane microcompartments. Nat Commun 2017; 8:15976. [PMID: 28706306 PMCID: PMC5519985 DOI: 10.1038/ncomms15976] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 05/16/2017] [Indexed: 12/14/2022] Open
Abstract
The spatiotemporal organization of cytokine receptors in the plasma membrane is still debated with models ranging from ligand-independent receptor pre-dimerization to ligand-induced receptor dimerization occurring only after receptor uptake into endosomes. Here, we explore the molecular and cellular determinants governing the assembly of the type II interleukin-4 receptor, taking advantage of various agonists binding the receptor subunits with different affinities and rate constants. Quantitative kinetic studies using artificial membranes confirm that receptor dimerization is governed by the two-dimensional ligand–receptor interactions and identify a critical role of the transmembrane domain in receptor dimerization. Single molecule localization microscopy at physiological cell surface expression levels, however, reveals efficient ligand-induced receptor dimerization by all ligands, largely independent of receptor binding affinities, in line with the similar STAT6 activation potencies observed for all IL-4 variants. Detailed spatiotemporal analyses suggest that kinetic trapping of receptor dimers in actin-dependent microcompartments sustains robust receptor dimerization and signalling. The contribution of ligands for cytokine receptor dimerization is still not fully understood. Here, the authors show the efficient ligand-induced dimerization of type II interleukin-4 receptor at the plasma membrane and the kinetic trapping of signalling complexes by actin-dependent membrane microdomains.
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47
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Feng QY, Hu ZX, Song XL, Pan HW. Aberrant expression of genes and proteins in pterygium and their implications in the pathogenesis. Int J Ophthalmol 2017; 10:973-981. [PMID: 28730091 DOI: 10.18240/ijo.2017.06.22] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/11/2017] [Indexed: 12/29/2022] Open
Abstract
Pterygium is a common ocular surface disease induced by a variety of factors. The exact pathogenesis of pterygium remains unclear. Numbers of genes and proteins are discovered in pterygium and they function differently in the occurrence and development of this disease. We searched the Web of Science and PubMed throughout history for literatures about the subject. The keywords we used contain pterygium, gene, protein, angiogenesis, fibrosis, proliferation, inflammation, pathogenesis and therapy. In this review, we summarize the aberrant expression of a range of genes and proteins in pterygium compared with normal conjunctiva or cornea, including growth factors, matrix metalloproteinases and tissue inhibitors of metalloproteinases, interleukins, tumor suppressor genes, proliferation related proteins, apoptosis related proteins, cell adhesion molecules, extracellular matrix proteins, heat shock proteins and tight junction proteins. We illustrate their possible mechanisms in the pathogenesis of pterygium as well as the related intervention based on them for pterygium therapy.
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Affiliation(s)
- Qing-Yang Feng
- Department of Ophthalmology, the First Affiliated Hospital of Jinan University, Guangzhou 510630, Guangdong Province, China
| | - Zi-Xuan Hu
- Department of Public Health and Preventive Medicine, Jinan University, Guangzhou 510632, Guangdong Province, China
| | - Xi-Ling Song
- Department of Public Health and Preventive Medicine, Jinan University, Guangzhou 510632, Guangdong Province, China
| | - Hong-Wei Pan
- Department of Ophthalmology, the First Affiliated Hospital of Jinan University, Guangzhou 510630, Guangdong Province, China.,Department of Public Health and Preventive Medicine, Jinan University, Guangzhou 510632, Guangdong Province, China.,Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou 510632, Guangdong Province, China
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48
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Ho CCM, Chhabra A, Starkl P, Schnorr PJ, Wilmes S, Moraga I, Kwon HS, Gaudenzio N, Sibilano R, Wehrman TS, Gakovic M, Sockolosky JT, Tiffany MR, Ring AM, Piehler J, Weissman IL, Galli SJ, Shizuru JA, Garcia KC. Decoupling the Functional Pleiotropy of Stem Cell Factor by Tuning c-Kit Signaling. Cell 2017; 168:1041-1052.e18. [PMID: 28283060 DOI: 10.1016/j.cell.2017.02.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/20/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022]
Abstract
Most secreted growth factors and cytokines are functionally pleiotropic because their receptors are expressed on diverse cell types. While important for normal mammalian physiology, pleiotropy limits the efficacy of cytokines and growth factors as therapeutics. Stem cell factor (SCF) is a growth factor that acts through the c-Kit receptor tyrosine kinase to elicit hematopoietic progenitor expansion but can be toxic when administered in vivo because it concurrently activates mast cells. We engineered a mechanism-based SCF partial agonist that impaired c-Kit dimerization, truncating downstream signaling amplitude. This SCF variant elicited biased activation of hematopoietic progenitors over mast cells in vitro and in vivo. Mouse models of SCF-mediated anaphylaxis, radioprotection, and hematopoietic expansion revealed that this SCF partial agonist retained therapeutic efficacy while exhibiting virtually no anaphylactic off-target effects. The approach of biasing cell activation by tuning signaling thresholds and outputs has applications to many dimeric receptor-ligand systems.
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Affiliation(s)
- Chia Chi M Ho
- Department of Bioengineering, Stanford University School of Engineering, 443 Via Ortega, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Akanksha Chhabra
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Philipp Starkl
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine I, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Peter-John Schnorr
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Stephan Wilmes
- Department of Biology, University of Osnabruck, Barbarastr. 11, 49076 Osnabruck, Germany
| | - Ignacio Moraga
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Hye-Sook Kwon
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Nicolas Gaudenzio
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Riccardo Sibilano
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Tom S Wehrman
- Primity Bio, 48383 Fremont Blvd, Suite 118, Fremont, CA 94538, USA
| | - Milica Gakovic
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Jonathan T Sockolosky
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Matthew R Tiffany
- Department of Pediatrics and Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Aaron M Ring
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
| | - Jacob Piehler
- Department of Biology, University of Osnabruck, Barbarastr. 11, 49076 Osnabruck, Germany
| | - Irving L Weissman
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Stephen J Galli
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
| | - Judith A Shizuru
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA.
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49
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Chuartzman SG, Nevo R, Waichman S, Shental D, Piehler J, Levy Y, Reich Z, Kapon R. Binding of interferon reduces the force of unfolding for interferon receptor 1. PLoS One 2017; 12:e0175413. [PMID: 28403186 PMCID: PMC5389645 DOI: 10.1371/journal.pone.0175413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/24/2017] [Indexed: 11/19/2022] Open
Abstract
Differential signaling of the type I interferon receptor (IFNAR) has been correlated with the ability of its subunit, IFNAR1, to differentially recognize a large spectrum of different ligands, which involves intricate conformational re-arrangements of multiple interacting domains. To shed light onto the structural determinants governing ligand recognition, we compared the force-induced unfolding of the IFNAR1 ectodomain when bound to interferon and when free, using the atomic force microscope and steered molecular dynamics simulations. Unexpectedly, we find that IFNAR1 is easier to mechanically unfold when bound to interferon than when free. Analysis of the structures indicated that the origin of the reduction in unfolding forces is a conformational change in IFNAR1 induced by ligand binding.
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Affiliation(s)
- Silvia G. Chuartzman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Reinat Nevo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon Waichman
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Dalit Shental
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Reich
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (RK); (ZR)
| | - Ruti Kapon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (RK); (ZR)
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50
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Corbett MSP, Poger D, Mark AE. Revisiting the scissor-like mechanism of activation for the erythropoietin receptor. FEBS Lett 2016; 590:3083-8. [PMID: 27490140 DOI: 10.1002/1873-3468.12340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 01/28/2023]
Abstract
An interpretation of alternative crystal structures of the erythropoietin receptor, with and without ligand, led to the proposal of a scissor-like mechanism of activation. This model has been propagated in the literature and is still being used to interpret crystal structures of related type-I cytokine receptors. Here, we assess whether the model remains compatible with current knowledge on the family of type-I cytokine receptors, and consider whether the model, as initially presented, is truly supported by the crystal structures on which it was originally based.
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Affiliation(s)
- Michael S P Corbett
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
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