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Lv Y, Qi J, Babon JJ, Cao L, Fan G, Lang J, Zhang J, Mi P, Kobe B, Wang F. The JAK-STAT pathway: from structural biology to cytokine engineering. Signal Transduct Target Ther 2024; 9:221. [PMID: 39169031 PMCID: PMC11339341 DOI: 10.1038/s41392-024-01934-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/12/2024] [Accepted: 07/16/2024] [Indexed: 08/23/2024] Open
Abstract
The Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway serves as a paradigm for signal transduction from the extracellular environment to the nucleus. It plays a pivotal role in physiological functions, such as hematopoiesis, immune balance, tissue homeostasis, and surveillance against tumors. Dysregulation of this pathway may lead to various disease conditions such as immune deficiencies, autoimmune diseases, hematologic disorders, and cancer. Due to its critical role in maintaining human health and involvement in disease, extensive studies have been conducted on this pathway, ranging from basic research to medical applications. Advances in the structural biology of this pathway have enabled us to gain insights into how the signaling cascade operates at the molecular level, laying the groundwork for therapeutic development targeting this pathway. Various strategies have been developed to restore its normal function, with promising therapeutic potential. Enhanced comprehension of these molecular mechanisms, combined with advances in protein engineering methodologies, has allowed us to engineer cytokines with tailored properties for targeted therapeutic applications, thereby enhancing their efficiency and safety. In this review, we outline the structural basis that governs key nodes in this pathway, offering a comprehensive overview of the signal transduction process. Furthermore, we explore recent advances in cytokine engineering for therapeutic development in this pathway.
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Affiliation(s)
- You Lv
- Center for Molecular Biosciences and Non-communicable Diseases Research, Xi'an University of Science and Technology, Xi'an, Shaanxi, 710054, China
- Xi'an Amazinggene Co., Ltd, Xi'an, Shaanxi, 710026, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100080, China
| | - Jeffrey J Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Longxing Cao
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
| | - Guohuang Fan
- Immunophage Biotech Co., Ltd, No. 10 Lv Zhou Huan Road, Shanghai, 201112, China
| | - Jiajia Lang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Jin Zhang
- Xi'an Amazinggene Co., Ltd, Xi'an, Shaanxi, 710026, China
| | - Pengbing Mi
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - Faming Wang
- Center for Molecular Biosciences and Non-communicable Diseases Research, Xi'an University of Science and Technology, Xi'an, Shaanxi, 710054, China.
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2
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Mravic M, He L, Kratochvil HT, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. De novo-designed transmembrane proteins bind and regulate a cytokine receptor. Nat Chem Biol 2024; 20:751-760. [PMID: 38480980 PMCID: PMC11142920 DOI: 10.1038/s41589-024-01562-z] [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] [Received: 02/14/2023] [Accepted: 01/25/2024] [Indexed: 05/30/2024]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has the potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking the binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom-designed topologies.
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Affiliation(s)
- Marco Mravic
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Li He
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Huong T Kratochvil
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Hailin Hu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Sarah E Nick
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Weiya Bai
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Anne Edwards
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.
- Yale Cancer Center, New Haven, CT, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
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3
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Metallinou C, Staneloudi C, Nikolettos K, Asimakopoulos B. NGF, EPO, and IGF-1 in the Male Reproductive System. J Clin Med 2024; 13:2918. [PMID: 38792459 PMCID: PMC11122040 DOI: 10.3390/jcm13102918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/09/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Several studies have demonstrated interesting results considering the implication of three growth factors (GFs), namely nerve growth factor (NGF), erythropoietin (EPO), and the insulin-like growth factor-I (IGF-1) in the physiology of male reproductive functions. This review provides insights into the effects of NGF, EPO, and IGF-1 on the male reproductive system, emphasizing mainly their effects on sperm motility and vitality. In the male reproductive system, the expression pattern of the NGF system varies according to the species and testicular development, playing a crucial role in morphogenesis and spermatogenesis. In humans, it seems that NGF positively affects sperm motility parameters and NGF supplementation in cryopreservation media improves post-thaw sperm motility. In animals, EPO is found in various male reproductive tissues, and in humans, the protein is present in seminal plasma and testicular germ cells. EPO receptors have been discovered in the plasma membrane of human spermatozoa, suggesting potential roles in sperm motility and vitality. In humans, IGF-1 is expressed mainly in Sertoli cells and is present in seminal plasma, contributing to cell development and the maturation of spermatozoa. IGF-1 seems to modulate sperm motility, and treatment with IGF-1 has a positive effect on sperm motility and vitality. Furthermore, lower levels of NGF or IGF-1 in seminal plasma are associated with infertility. Understanding the mechanisms of actions of these GFs in the male reproductive system may improve the outcome of sperm processing techniques.
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Affiliation(s)
- Chryssa Metallinou
- Laboratory of Physiology, Faculty of Medicine, School of Health Sciences, Democritus University of Thrace, 69100 Alexandroupolis, Greece; (C.M.); (K.N.)
| | - Chrysovalanto Staneloudi
- Laboratory of Exercise Physiology and Biochemistry, Department of Physical Education and Sport Science at Serres, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Konstantinos Nikolettos
- Laboratory of Physiology, Faculty of Medicine, School of Health Sciences, Democritus University of Thrace, 69100 Alexandroupolis, Greece; (C.M.); (K.N.)
| | - Byron Asimakopoulos
- Laboratory of Physiology, Faculty of Medicine, School of Health Sciences, Democritus University of Thrace, 69100 Alexandroupolis, Greece; (C.M.); (K.N.)
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4
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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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5
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Sarson-Lawrence KTG, Hardy JM, Iaria J, Stockwell D, Behrens K, Saiyed T, Tan C, Jebeli L, Scott NE, Dite TA, Nicola NA, Leis AP, Babon JJ, Kershaw NJ. Cryo-EM structure of the extracellular domain of murine Thrombopoietin Receptor in complex with Thrombopoietin. Nat Commun 2024; 15:1135. [PMID: 38326297 PMCID: PMC10850085 DOI: 10.1038/s41467-024-45356-2] [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: 09/01/2023] [Accepted: 01/19/2024] [Indexed: 02/09/2024] Open
Abstract
Thrombopoietin (Tpo) is the primary regulator of megakaryocyte and platelet numbers and is required for haematopoetic stem cell maintenance. Tpo functions by binding its receptor (TpoR, a homodimeric Class I cytokine receptor) and initiating cell proliferation or differentiation. Here we characterise the murine Tpo:TpoR signalling complex biochemically and structurally, using cryo-electron microscopy. Tpo uses opposing surfaces to recruit two copies of receptor, forming a 1:2 complex. Although it binds to the same, membrane-distal site on both receptor chains, it does so with significantly different affinities and its highly glycosylated C-terminal domain is not required. In one receptor chain, a large insertion, unique to TpoR, forms a partially structured loop that contacts cytokine. Tpo binding induces the juxtaposition of the two receptor chains adjacent to the cell membrane. The therapeutic agent romiplostim also targets the cytokine-binding site and the characterisation presented here supports the future development of improved TpoR agonists.
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Affiliation(s)
- Kaiseal T G Sarson-Lawrence
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Joshua M Hardy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
| | - Josephine Iaria
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Dina Stockwell
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Kira Behrens
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Tamanna Saiyed
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Cyrus Tan
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Victoria, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Victoria, Australia
| | - Toby A Dite
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Nicos A Nicola
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Andrew P Leis
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
| | - Jeffrey J Babon
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia.
| | - Nadia J Kershaw
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia.
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6
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Pardridge WM. Treatment of Parkinson's disease with biologics that penetrate the blood-brain barrier via receptor-mediated transport. Front Aging Neurosci 2023; 15:1276376. [PMID: 38035276 PMCID: PMC10682952 DOI: 10.3389/fnagi.2023.1276376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Parkinson's disease (PD) is characterized by neurodegeneration of nigral-striatal neurons in parallel with the formation of intra-neuronal α-synuclein aggregates, and these processes are exacerbated by neuro-inflammation. All 3 components of PD pathology are potentially treatable with biologics. Neurotrophins, such as glial derived neurotrophic factor or erythropoietin, can promote neural repair. Therapeutic antibodies can lead to disaggregation of α-synuclein neuronal inclusions. Decoy receptors can block the activity of pro-inflammatory cytokines in brain. However, these biologic drugs do not cross the blood-brain barrier (BBB). Biologics can be made transportable through the BBB following the re-engineering of the biologic as an IgG fusion protein, where the IgG domain targets an endogenous receptor-mediated transcytosis (RMT) system within the BBB, such as the insulin receptor or transferrin receptor. The receptor-specific antibody domain of the fusion protein acts as a molecular Trojan horse to ferry the biologic into brain via the BBB RMT pathway. This review describes the re-engineering of all 3 classes of biologics (neurotrophins, decoy receptor, therapeutic antibodies) for BBB delivery and treatment of PD. Targeting the RMT pathway at the BBB also enables non-viral gene therapy of PD using lipid nanoparticles (LNP) encapsulated with plasmid DNA encoding therapeutic genes. The surface of the lipid nanoparticle is conjugated with a receptor-specific IgG that triggers RMT of the LNP across the BBB in vivo.
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7
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Mesev EV, Lin AE, Guare EG, Heller BL, Douam F, Adamson B, Toettcher JE, Ploss A. Membrane-proximal motifs encode differences in signaling strength between type I and III interferon receptors. Sci Signal 2023; 16:eadf5494. [PMID: 37816090 PMCID: PMC10939449 DOI: 10.1126/scisignal.adf5494] [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] [Received: 11/16/2022] [Accepted: 09/09/2023] [Indexed: 10/12/2023]
Abstract
Interferons (IFNs) play crucial roles in antiviral defenses. Despite using the same Janus-activated kinase (JAK)-signal transducer and activator of transcription (STAT) signaling cascade, type I and III IFN receptors differ in the magnitude and dynamics of their signaling in terms of STAT phosphorylation, gene transcription, and antiviral responses. These differences are not due to ligand-binding affinity and receptor abundance. Here, we investigated the ability of the intracellular domains (ICDs) of IFN receptors to differentiate between type I and III IFN signaling. We engineered synthetic, heterodimeric type I and III IFN receptors that were stably expressed at similar amounts in human cells and responded to a common ligand. We found that our synthetic type I IFN receptors stimulated STAT phosphorylation and gene expression to greater extents than did the corresponding type III IFN receptors. Furthermore, we identified short "box motifs" within ICDs that bind to JAK1 that were sufficient to encode differences between the type I and III IFN receptors. Together, our results indicate that specific regions within the ICDs of IFN receptor subunits encode different downstream signaling strengths that enable type I and III IFN receptors to produce distinct signaling outcomes.
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Affiliation(s)
- Emily V. Mesev
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Aaron E. Lin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Emma G. Guare
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Brigitte L. Heller
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Florian Douam
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis Sigler Center for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Jared E. Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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8
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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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9
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Tsutsumi N, Masoumi Z, James SC, Tucker JA, Winkelmann H, Grey W, Picton LK, Moss L, Wilson SC, Caveney NA, Jude KM, Gati C, Piehler J, Hitchcock IS, Garcia KC. Structure of the thrombopoietin-MPL receptor complex is a blueprint for biasing hematopoiesis. Cell 2023; 186:4189-4203.e22. [PMID: 37633268 PMCID: PMC10528194 DOI: 10.1016/j.cell.2023.07.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Thrombopoietin (THPO or TPO) is an essential cytokine for hematopoietic stem cell (HSC) maintenance and megakaryocyte differentiation. Here, we report the 3.4 Å resolution cryoelectron microscopy structure of the extracellular TPO-TPO receptor (TpoR or MPL) signaling complex, revealing the basis for homodimeric MPL activation and providing a structural rationalization for genetic loss-of-function thrombocytopenia mutations. The structure guided the engineering of TPO variants (TPOmod) with a spectrum of signaling activities, from neutral antagonists to partial- and super-agonists. Partial agonist TPOmod decoupled JAK/STAT from ERK/AKT/CREB activation, driving a bias for megakaryopoiesis and platelet production without causing significant HSC expansion in mice and showing superior maintenance of human HSCs in vitro. These data demonstrate the functional uncoupling of the two primary roles of TPO, highlighting the potential utility of TPOmod in hematology research and clinical HSC transplantation.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan.
| | - Zahra Masoumi
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Sophie C James
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Julie A Tucker
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hauke Winkelmann
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - William Grey
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Lora K Picton
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lucie Moss
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Steven C Wilson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nathanael A Caveney
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelius Gati
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jacob Piehler
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - Ian S Hitchcock
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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10
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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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11
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Govindappa PK, Begom M, Gupta Y, Elfar JC, Rawat M, Elfar W. A critical role for erythropoietin on vagus nerve Schwann cells in intestinal motility. BMC Biotechnol 2023; 23:12. [PMID: 37127673 PMCID: PMC10152589 DOI: 10.1186/s12896-023-00781-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Dysmotility and postoperative ileus (POI) are frequent major clinical problems post-abdominal surgery. Erythropoietin (EPO) is a multifunctional tissue-protective cytokine that promotes recovery of the intestine in various injury models. While EPO receptors (EPOR) are present in vagal Schwann cells, the role of EPOR in POI recovery is unknown because of the lack of EPOR antagonists or Schwann-cell specific EPOR knockout animals. This study was designed to explore the effect of EPO via EPOR in vagal nerve Schwann cells in a mouse model of POI. RESULTS The structural features of EPOR and its activation by EPO-mediated dimerization were understood using structural analysis. Later, using the Cre-loxP system, we developed a myelin protein zero (Mpz) promoter-driven knockout mouse model of Schwann cell EPOR (MpzCre-EPORflox/flox / Mpz-EPOR-KO) confirmed using PCR and qRT-PCR techniques. We then measured the intestinal transit time (ITT) at baseline and after induction of POI with and without EPO treatment. Although we have previously shown that EPO accelerates functional recovery in POI in wild type mice, EPO treatment did not improve functional recovery of ITT in POI of Mpz-EPOR-KO mice. CONCLUSIONS To the best of our knowledge, this is the first pre-clinical study to demonstrate a novel mouse model of EPOR specific knock out on Schwan cells with an effect in the gut. We also showed novel beneficial effects of EPO through vagus nerve Schwann cell-EPOR in intestinal dysmotility. Our findings suggest that EPO-EPOR signaling in the vagus nerve after POI is important for the functional recovery of ITT.
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Affiliation(s)
- Prem Kumar Govindappa
- Department of Orthopaedics and Sports Medicine, University of Arizona College of Medicine, Tucson, AZ, 85724, USA
| | - Mosammat Begom
- Department of Medicine, The Penn State University College of Medicine, Hershey, PA, 17033, USA
| | - Yash Gupta
- Department of Medicine, The Penn State University College of Medicine, Hershey, PA, 17033, USA
| | - John C Elfar
- Department of Orthopaedics and Sports Medicine, University of Arizona College of Medicine, Tucson, AZ, 85724, USA
| | - Manmeet Rawat
- Department of Medicine, The Penn State University College of Medicine, Hershey, PA, 17033, USA.
| | - Walaa Elfar
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, AZ, 85724, USA.
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Kittur FS, Hung CY, Li PA, Sane DC, Xie J. Asialo-rhuEPO as a Potential Neuroprotectant for Ischemic Stroke Treatment. Pharmaceuticals (Basel) 2023; 16:610. [PMID: 37111367 PMCID: PMC10143832 DOI: 10.3390/ph16040610] [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: 03/28/2023] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Neuroprotective drugs to protect the brain against cerebral ischemia and reperfusion (I/R) injury are urgently needed. Mammalian cell-produced recombinant human erythropoietin (rhuEPOM) has been demonstrated to have excellent neuroprotective functions in preclinical studies, but its neuroprotective properties could not be consistently translated in clinical trials. The clinical failure of rhuEPOM was thought to be mainly due to its erythropoietic activity-associated side effects. To exploit its tissue-protective property, various EPO derivatives with tissue-protective function only have been developed. Among them, asialo-rhuEPO, lacking terminal sialic acid residues, was shown to be neuroprotective but non-erythropoietic. Asialo-rhuEPO can be prepared by enzymatic removal of sialic acid residues from rhuEPOM (asialo-rhuEPOE) or by expressing human EPO gene in glycoengineered transgenic plants (asialo-rhuEPOP). Both types of asialo-rhuEPO, like rhuEPOM, displayed excellent neuroprotective effects by regulating multiple cellular pathways in cerebral I/R animal models. In this review, we describe the structure and properties of EPO and asialo-rhuEPO, summarize the progress on neuroprotective studies of asialo-rhuEPO and rhuEPOM, discuss potential reasons for the clinical failure of rhuEPOM with acute ischemic stroke patients, and advocate future studies needed to develop asialo-rhuEPO as a multimodal neuroprotectant for ischemic stroke treatment.
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Affiliation(s)
- Farooqahmed S. Kittur
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute & Technology Enterprise, North Carolina Central University, Durham, NC 27707, USA; (C.-Y.H.); (P.A.L.)
| | - Chiu-Yueh Hung
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute & Technology Enterprise, North Carolina Central University, Durham, NC 27707, USA; (C.-Y.H.); (P.A.L.)
| | - P. Andy Li
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute & Technology Enterprise, North Carolina Central University, Durham, NC 27707, USA; (C.-Y.H.); (P.A.L.)
| | - David C. Sane
- Carilion Clinic and Virginia Tech Carilion School of Medicine, Roanoke, VA 24014, USA;
| | - Jiahua Xie
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute & Technology Enterprise, North Carolina Central University, Durham, NC 27707, USA; (C.-Y.H.); (P.A.L.)
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13
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Zhou Y, Stevis PE, Cao J, Saotome K, Wu J, Glatman Zaretsky A, Haxhinasto S, Yancopoulos GD, Murphy AJ, Sleeman MW, Olson WC, Franklin MC. Structural insights into the assembly of gp130 family cytokine signaling complexes. SCIENCE ADVANCES 2023; 9:eade4395. [PMID: 36930708 PMCID: PMC10022904 DOI: 10.1126/sciadv.ade4395] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
The interleukin-6 (IL-6) family cytokines signal through gp130 receptor homodimerization or heterodimerization with a second signaling receptor and play crucial roles in various cellular processes. We determined cryo-electron microscopy structures of five signaling complexes of this family, containing full receptor ectodomains bound to their respective ligands ciliary neurotrophic factor, cardiotrophin-like cytokine factor 1 (CLCF1), leukemia inhibitory factor, IL-27, and IL-6. Our structures collectively reveal similarities and differences in the assembly of these complexes. The acute bends at both signaling receptors in all complexes bring the membrane-proximal domains to a ~30 angstrom range but with distinct distances and orientations. We also reveal how CLCF1 engages its secretion chaperone cytokine receptor-like factor 1. Our data provide valuable insights for therapeutically targeting gp130-mediated signaling.
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Affiliation(s)
- Yi Zhou
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | | | - Jing Cao
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Kei Saotome
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Jiaxi Wu
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
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Kilic F. The nature of the binding between insulin receptor and serotonin transporter in placenta (review). Placenta 2023; 133:40-44. [PMID: 36796293 DOI: 10.1016/j.placenta.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023]
Abstract
The interplay between the insulin receptor (IR) and serotonin transporter (SERT) allows reciprocal regulation of each other's physiological roles to ensure appropriate responses to specific environmental and developmental signals. The studies reported herein provided substantial evidence of how insulin signaling influences the modification and trafficking of SERT to the plasma membrane via enabling its association with specific endoplasmic reticulum (ER) proteins. While insulin signaling is important for the modifications of SERT proteins, the fact that phosphorylation of IR was significantly down-regulated in the placenta of SERT knock out (KO) mice suggests that SERT also regulates IR. Further suggestive of SERT functional regulation of IR, SERT-KO mice developed obesity and glucose intolerance with symptoms similar to those of type 2 diabetes. The picture emerging from those studies proposes that the interplay between IR and SERT maintains conditions supportive of IR phosphorylation and regulates insulin signaling in placenta which ultimately enables the trafficking of SERT to the plasma membrane. IR-SERT association thus appears to play a protective metabolic role in placenta and is impaired under diabetic conditions. This review focuses on recent findings describing the functional and physical associations between IR and SERT in placental cells, and the dysregulation of this process in diabetes.
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Affiliation(s)
- Fusun Kilic
- Biology Department, Merced College, Merced, CA, USA.
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15
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Mravic M, He L, Kratochvil H, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.526773. [PMID: 36824741 PMCID: PMC9949092 DOI: 10.1101/2023.02.13.526773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom designed topologies.
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16
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Adams TM, Zhao P, Chapla D, Moremen KW, Wells L. Sequential in vitro enzymatic N-glycoprotein modification reveals site-specific rates of glycoenzyme processing. J Biol Chem 2022; 298:102474. [PMID: 36089065 PMCID: PMC9530959 DOI: 10.1016/j.jbc.2022.102474] [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: 07/25/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 12/01/2022] Open
Abstract
N-glycosylation is an essential eukaryotic posttranslational modification that affects various glycoprotein properties, including folding, solubility, protein–protein interactions, and half-life. N-glycans are processed in the secretory pathway to form varied ensembles of structures, and diversity at a single site on a glycoprotein is termed ‘microheterogeneity’. To understand the factors that influence glycan microheterogeneity, we hypothesized that local steric and electrostatic factors surrounding each site influence glycan availability for enzymatic modification. We tested this hypothesis via expression of reporter N-linked glycoproteins in N-acetylglucosaminyltransferase MGAT1-null HEK293 cells to produce immature Man5GlcNAc2 glycoforms (38 glycan sites total). These glycoproteins were then sequentially modified in vitro from high mannose to hybrid and on to biantennary, core-fucosylated, complex structures by a panel of N-glycosylation enzymes, and each reaction time course was quantified by LC-MS/MS. Substantial differences in rates of in vitro enzymatic modification were observed between glycan sites on the same protein, and differences in modification rates varied depending on the glycoenzyme being evaluated. In comparison, proteolytic digestion of the reporters prior to N-glycan processing eliminated differences in in vitro enzymatic modification. Furthermore, comparison of in vitro rates of enzymatic modification with the glycan structures found on the mature reporters expressed in WT cells correlated well with the enzymatic bottlenecks observed in vivo. These data suggest higher order local structures surrounding each glycosylation site contribute to the efficiency of modification both in vitro and in vivo to establish the spectrum of microheterogeneity in N-linked glycoproteins.
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Affiliation(s)
- Trevor M Adams
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Peng Zhao
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Digantkumar Chapla
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602.
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602.
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17
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Sathyanesan M, Newton SS. Antidepressant-like effects of trophic factor receptor signaling. Front Mol Neurosci 2022; 15:958797. [PMID: 36081576 PMCID: PMC9445421 DOI: 10.3389/fnmol.2022.958797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
A significant body of research has demonstrated that antidepressants regulate neurotrophic factors and that neurotrophins themselves are capable of independently producing antidepressant-like effects. While brain derived neurotrophic factor (BDNF) remains the best studied molecule in this context, there are several structurally diverse trophic factors that have shown comparable behavioral effects, including basic fibroblast growth factor (FGF-2), insulin-like growth factor 1 (IGF-1) and vascular endothelial growth factor (VEGF). In this review we discuss the structural and biochemical signaling aspects of these neurotrophic factors with antidepressant activity. We also include a discussion on a cytokine molecule erythropoietin (EPO), widely known and prescribed as a hormone to treat anemia but has recently been shown to function as a neurotrophic factor in the central nervous system (CNS).
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18
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Wang X, Sun Y, Wang Q, Liu F, Yang W, Sui X, Yang J, Zhang M, Wang S, Xiao Z, Luo Y, Wang Y, Zhu T. Potential Common Mechanisms of Cytotoxicity Induced by Amide Herbicides via TRPA1 Channel Activation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:7985. [PMID: 35805655 PMCID: PMC9266004 DOI: 10.3390/ijerph19137985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022]
Abstract
The “Multi-Threat Medical Countermeasure (MTMC)” strategy was proposed to develop a single drug with therapeutic efficacy against multiple pathologies or broad-spectrum protection against various toxins with common biochemical signals, molecular mediators, or cellular processes. This study demonstrated that cytotoxicity, expression of transient receptor potential cation channel subfamily A member 1 (TRPA1) mRNA, and intracellular calcium influx were increased in A549 cells exposed to amide herbicides (AHs), in which the order of cytotoxicity was metolachlor > acetochlor > propisochlor > alachlor > butachlor > propanil > pretilachlor, based on IC50 values of 430, 524, 564, 565, 619, 831, and 2333 μM, respectively. Inhibition/knockout of TRPA1 efficiently protected against cytotoxicity, decreased TRPA1 mRNA expression, and reduced calcium influx. The results suggested that the TRPA1 channel could be a key common target for AHs poisoning. The order of TRPA1 affinity for AHs was propanil > pretilachlor > metolachlor > (propiso/ala/aceto/butachlor), based on KD values of 16.2, 309, and 364 μM, respectively. The common molecular mechanisms of TRPA1-AHs interactions were clarified, including toxicity-effector groups (benzene ring, nitrogen/oxygen-containing functional groups, halogen) and residues involved in interactions (Lys787, Leu982). This work provides valuable information for the development of TRPA1 as a promising therapeutic target for broad-spectrum antitoxins.
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Affiliation(s)
- Xiaoning Wang
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110819, China;
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Yangyang Sun
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Qian Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Fengying Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Weijie Yang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Xin Sui
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Jun Yang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Minmin Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Shuai Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Zhenyu Xiao
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Yuan Luo
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Yongan Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.S.); (Q.W.); (F.L.); (W.Y.); (X.S.); (J.Y.); (M.Z.); (S.W.); (Z.X.); (Y.W.)
| | - Tong Zhu
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110819, China;
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Bhukhai K, Fouquet G, Rittavee Y, Tanhuad N, Lakmuang C, Borwornpinyo S, Anurathapan U, Suksamrarn A, Piyachaturawat P, Chairoungdua A, Hermine O, Hongeng S. Enhancing Erythropoiesis by a Phytoestrogen Diarylheptanoid from Curcuma comosa. Biomedicines 2022; 10:biomedicines10061427. [PMID: 35740448 PMCID: PMC9219836 DOI: 10.3390/biomedicines10061427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/16/2022] Open
Abstract
Erythropoietin (Epo) is widely used for the treatment of anemia; however, non-hematopoietic effects and cancer risk limit its clinical applications. Therefore, alternative molecules to improve erythropoiesis in anemia patients are urgently needed. Here, we investigated the potential effects of a phytoestrogen diarylheptanoid (3R)-1,7-diphenyl-(4E,6E)-4,6-heptadien-3-ol, (ASPP 049) isolated from Curcuma comosa on promoting erythropoiesis. Treatment with C. comosa extract improved anemia symptoms demonstrated by increasing red blood cell numbers, hematocrit, and hemoglobin content in anemic mice. In addition, ASPP 049, the major compound isolated from C. comosa, enhanced the suboptimal Epo dosages to improve erythroid cell differentiation from hematopoietic stem cells, which was inhibited by the estrogen receptor (ER) antagonist, ICI 182,780. Moreover, the ASPP 049-activated Epo-Epo receptor (EpoR) complex subsequently induced phosphorylation of EpoR-mediated erythropoiesis pathways: STAT5, MAPK/ERK, and PI3K/AKT in Epo-sensitive UT-7 cells. Taken together, these results suggest that C. comosa extract and ASPP 049 increased erythropoiesis through ER- and EpoR-mediated signaling cascades. Our findings provide insight into the specific interaction between a phytoestrogen diarylheptanoid and Epo-EpoR in a hematopoietic system for the potential treatment of anemia.
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Affiliation(s)
- Kanit Bhukhai
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.T.); (P.P.); (A.C.)
- Correspondence: (K.B.); (S.H.); Tel.: +66-22015614 (K.B.); +66-22011495 (S.H.)
| | - Guillemette Fouquet
- Institut Hospitalo-Universitaire Imagine, Université Sorbonne Paris Cité, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, 75015 Paris, France; (G.F.); (O.H.)
- INSERM U1163 and CNRS ERL8254, Université Paris Descartes, Faculté de Médecine, Hôpital Necker, 75015 Paris, France
| | - Yutthana Rittavee
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Nopmullee Tanhuad
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.T.); (P.P.); (A.C.)
| | - Chaiyaporn Lakmuang
- Department of Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Suparerk Borwornpinyo
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
- Excellent Center for Drug Discovery, Mahidol University, Bangkok 10400, Thailand
| | - Usanarat Anurathapan
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Apichart Suksamrarn
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand;
| | - Pawinee Piyachaturawat
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.T.); (P.P.); (A.C.)
| | - Arthit Chairoungdua
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.T.); (P.P.); (A.C.)
- Excellent Center for Drug Discovery, Mahidol University, Bangkok 10400, Thailand
| | - Olivier Hermine
- Institut Hospitalo-Universitaire Imagine, Université Sorbonne Paris Cité, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, 75015 Paris, France; (G.F.); (O.H.)
- INSERM U1163 and CNRS ERL8254, Université Paris Descartes, Faculté de Médecine, Hôpital Necker, 75015 Paris, France
- Laboratory of Excellence GReX, 75015 Paris, France
- Service d’Hématologie Clinique Adultes, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, 75015 Paris, France
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Correspondence: (K.B.); (S.H.); Tel.: +66-22015614 (K.B.); +66-22011495 (S.H.)
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20
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Skokowa J, Hernandez Alvarez B, Coles M, Ritter M, Nasri M, Haaf J, Aghaallaei N, Xu Y, Mir P, Krahl AC, Rogers KW, Maksymenko K, Bajoghli B, Welte K, Lupas AN, Müller P, ElGamacy M. A topological refactoring design strategy yields highly stable granulopoietic proteins. Nat Commun 2022; 13:2948. [PMID: 35618709 PMCID: PMC9135769 DOI: 10.1038/s41467-022-30157-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 04/19/2022] [Indexed: 11/09/2022] Open
Abstract
Protein therapeutics frequently face major challenges, including complicated production, instability, poor solubility, and aggregation. De novo protein design can readily address these challenges. Here, we demonstrate the utility of a topological refactoring strategy to design novel granulopoietic proteins starting from the granulocyte-colony stimulating factor (G-CSF) structure. We change a protein fold by rearranging the sequence and optimising it towards the new fold. Testing four designs, we obtain two that possess nanomolar activity, the most active of which is highly thermostable and protease-resistant, and matches its designed structure to atomic accuracy. While the designs possess starkly different sequence and structure from the native G-CSF, they show specific activity in differentiating primary human haematopoietic stem cells into mature neutrophils. The designs also show significant and specific activity in vivo. Our topological refactoring approach is largely independent of sequence or structural context, and is therefore applicable to a wide range of protein targets. Skokowa et al. reconstruct the fold of a granulopoietic cytokine, resulting in de novo, hyperstable, highly active proteins with therapeutic potential for treating several neutropenia disorders.
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Affiliation(s)
- Julia Skokowa
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany.
| | | | - Murray Coles
- Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Malte Ritter
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Masoud Nasri
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Jérémy Haaf
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Narges Aghaallaei
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Yun Xu
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Perihan Mir
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Ann-Christin Krahl
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Katherine W Rogers
- Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany.,Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kateryna Maksymenko
- Max Planck Institute for Biology, 72076, Tübingen, Germany.,Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany
| | - Baubak Bajoghli
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Karl Welte
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Andrei N Lupas
- Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany.,Department of Biology, University of Konstanz, 78464, Konstanz, Germany
| | - Mohammad ElGamacy
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany. .,Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany. .,Heliopolis Biotechnology Ltd, Cambridge, CB24 9RX, UK. .,Max Planck Institute for Biology, 72076, Tübingen, Germany.
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21
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PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions? Biomolecules 2022; 12:biom12020178. [PMID: 35204680 PMCID: PMC8961561 DOI: 10.3390/biom12020178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 01/25/2023] Open
Abstract
In a previous study, we have shown that PEPscan can provide a cheap and rapid means to identify candidate interfering peptides (IPs), i.e., peptides able to disrupt a target protein-protein interaction. PEPscan was shown to be effective in identifying a limited number of candidate IPs specific to the target interaction. Here, we investigate the results of 14 new PEPscan experiments for protein complexes of known 3D structures. We show that for almost all complexes, PEPscan is able to identify candidate IPs that are located at the protein-protein interface. The information it provides about the binding site seems, however, too ambiguous to be exploited in a simple manner to assist the modeling of protein complexes. Moreover, these candidates are associated with false positives. For these, we suggest they could correspond to non-specific binders, which leaves room for further optimization of the PEPscan protocol. Another unexpected advance comes from the observation of the applicability of PEPscan for polysaccharides and labeled peptides, suggesting that PEPscan could become a large spectrum approach to investigate protein-binder interactions, the binder not necessarily being a protein.
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22
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Gou P, Zhang W, Giraudier S. Insights into the Potential Mechanisms of JAK2V617F Somatic Mutation Contributing Distinct Phenotypes in Myeloproliferative Neoplasms. Int J Mol Sci 2022; 23:ijms23031013. [PMID: 35162937 PMCID: PMC8835324 DOI: 10.3390/ijms23031013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 12/19/2022] Open
Abstract
Myeloproliferative neoplasms (MPN) are a group of blood cancers in which the bone marrow (BM) produces an overabundance of erythrocyte, white blood cells, or platelets. Philadelphia chromosome-negative MPN has three subtypes, including polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). The over proliferation of blood cells is often associated with somatic mutations, such as JAK2, CALR, and MPL. JAK2V617F is present in 95% of PV and 50–60% of ET and PMF. Based on current molecular dynamics simulations of full JAK2 and the crystal structure of individual domains, it suggests that JAK2 maintains basal activity through self-inhibition, whereas other domains and linkers directly/indirectly enhance this self-inhibited state. Nevertheless, the JAK2V617F mutation is not the only determinant of MPN phenotype, as many normal individuals carry the JAK2V617F mutation without a disease phenotype. Here we review the major MPN phenotypes, JAK-STAT pathways, and mechanisms of development based on structural biology, while also describing the impact of other contributing factors such as gene mutation allele burden, JAK-STAT-related signaling pathways, epigenetic modifications, immune responses, and lifestyle on different MPN phenotypes. The cross-linking of these elements constitutes a complex network of interactions and generates differences in individual and cellular contexts that determine the phenotypic development of MPN.
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Affiliation(s)
- Panhong Gou
- Laboratoire UMRS-1131, Ecole doctorale 561, Université de Paris, 75010 Paris, France
- INSERM UMR-S1131, Hôpital Saint-Louis, 75010 Paris, France
- Correspondence: (P.G.); (S.G.)
| | - Wenchao Zhang
- BFA, UMR 8251, CNRS, Université de Paris, 75013 Paris, France;
| | - Stephane Giraudier
- Laboratoire UMRS-1131, Ecole doctorale 561, Université de Paris, 75010 Paris, France
- INSERM UMR-S1131, Hôpital Saint-Louis, 75010 Paris, France
- Service de Biologie Cellulaire, Hôpital Saint-Louis, AP-HP, 75010 Paris, France
- Correspondence: (P.G.); (S.G.)
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23
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Erythropoietin Interacts with Specific S100 Proteins. Biomolecules 2022; 12:biom12010120. [PMID: 35053268 PMCID: PMC8773746 DOI: 10.3390/biom12010120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 02/06/2023] Open
Abstract
Erythropoietin (EPO) is a clinically significant four-helical cytokine, exhibiting erythropoietic, cytoprotective, immunomodulatory, and cancer-promoting activities. Despite vast knowledge on its signaling pathways and physiological effects, extracellular factors regulating EPO activity remain underexplored. Here we show by surface plasmon resonance spectroscopy, that among eighteen members of Ca2+-binding proteins of the S100 protein family studied, only S100A2, S100A6 and S100P proteins specifically recognize EPO with equilibrium dissociation constants ranging from 81 nM to 0.5 µM. The interactions occur exclusively under calcium excess. Bioinformatics analysis showed that the EPO-S100 interactions could be relevant to progression of neoplastic diseases, including cancer, and other diseases. The detailed knowledge of distinct physiological effects of the EPO-S100 interactions could favor development of more efficient clinical implications of EPO. Summing up our data with previous findings, we conclude that S100 proteins are potentially able to directly affect functional activities of specific members of all families of four-helical cytokines, and cytokines of other structural superfamilies.
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24
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Cho B, Yoo SJ, Kim SY, Lee CH, Lee YI, Lee SR, Moon C. Second-generation non-hematopoietic erythropoietin-derived peptide for neuroprotection. Redox Biol 2021; 49:102223. [PMID: 34953452 PMCID: PMC8715119 DOI: 10.1016/j.redox.2021.102223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 12/25/2022] Open
Abstract
Erythropoietin (EPO) is a well-known erythropoietic cytokine having a tissue-protective effect in various tissues against hypoxic stress, including the brain. Thus, its recombinants may function as neuroprotective compounds. However, despite considerable neuroprotective effects, the EPO-based therapeutic approach has side effects, including hyper-erythropoietic and tumorigenic effects. Therefore, some modified forms and derivatives of EPO have been proposed to minimize the side effects. In this study, we generated divergently modified new peptide analogs derived from helix C of EPO, with several amino acid replacements that interact with erythropoietin receptors (EPORs). This modification resulted in unique binding potency to EPOR. Unlike recombinant EPO, among the peptides, ML1-h3 exhibited a potent neuroprotective effect against oxidative stress without additional induction of cell-proliferation, owing to a differential activating mode of EPOR signaling. Furthermore, it inhibited neuronal death and brain injury under hypoxic stress in vitro and in an in vivo ischemic brain injury model. Therefore, the divergent modification of EPO-derivatives for affinity to EPOR could provide a basis for a more advanced and optimal neuroprotective strategy. Short peptides derived from helix C of EPO have a neuroprotective effect. Divergent modification of EPO-derived peptides has a differential affinity to EPOR. ML1 and its analogs have differential cell protective and proliferative effects. ML1-h3 protects neurons by suppressing in vitro oxidative stress. ML1-h3 mitigates brain injury in the in vivo mouse ischemic model without hematopoietic effect.
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Affiliation(s)
- Bongki Cho
- Department of Brain & Cognitive Sciences, Graduate School, DGIST, Daegu, 42988, South Korea; Convergence Research Advanced Centre for Olfaction, DGIST, Daegu, 42988, South Korea; Division of Biotechnology, DGIST, Daegu, 42988, South Korea
| | - Seung-Jun Yoo
- Department of Brain & Cognitive Sciences, Graduate School, DGIST, Daegu, 42988, South Korea; Convergence Research Advanced Centre for Olfaction, DGIST, Daegu, 42988, South Korea
| | - So Yeon Kim
- Department of Brain & Cognitive Sciences, Graduate School, DGIST, Daegu, 42988, South Korea; Convergence Research Advanced Centre for Olfaction, DGIST, Daegu, 42988, South Korea
| | - Chang-Hun Lee
- Department of New Biology, DGIST, Daegu, 42988, South Korea; New Biology Research Center, DGIST, Daegu, 42988, South Korea
| | - Yun-Il Lee
- Division of Biotechnology, DGIST, Daegu, 42988, South Korea
| | - Seong-Ryong Lee
- Department of Pharmacology and ODR Center, Brain Research Institute, School of Medicine, Keimyung University, Daegu, 42601, South Korea.
| | - Cheil Moon
- Department of Brain & Cognitive Sciences, Graduate School, DGIST, Daegu, 42988, South Korea; Convergence Research Advanced Centre for Olfaction, DGIST, Daegu, 42988, South Korea.
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25
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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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26
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Newton SS, Sathyanesan M. Erythropoietin and Non-Erythropoietic Derivatives in Cognition. Front Pharmacol 2021; 12:728725. [PMID: 34552490 PMCID: PMC8450392 DOI: 10.3389/fphar.2021.728725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/19/2021] [Indexed: 01/04/2023] Open
Abstract
Cognitive deficits are widespread in psychiatric disorders, including major depression and schizophrenia. These deficits are known to contribute significantly to the accompanying functional impairment. Progress in the development of targeted treatments of cognitive deficits has been limited and there exists a major unmet need to develop more efficacious treatments. Erythropoietin (Epo) has shown promising procognitive effects in psychiatric disorders, providing support for a neurotrophic drug development approach. Several preclinical studies with non-erythropoietic derivatives have demonstrated that the modulation of behavior is independent of erythropoiesis. In this review, we examine the molecular, cellular and cognitive actions of Epo and non-erythropoietic molecular derivatives by focusing on their neurotrophic, synaptic, myelin plasticity, anti-inflammatory and neurogenic mechanisms in the brain. We also discuss the role of receptor signaling in Epo and non-erythropoietic EPO-mimetic molecules in their procognitive 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, United States.,Sioux Falls VA Healthcare System, Sioux Falls, SD, United States
| | - Monica Sathyanesan
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States.,Sioux Falls VA Healthcare System, Sioux Falls, SD, United States
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27
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Minakata S, Manabe S, Inai Y, Ikezaki M, Nishitsuji K, Ito Y, Ihara Y. Protein C-Mannosylation and C-Mannosyl Tryptophan in Chemical Biology and Medicine. Molecules 2021; 26:molecules26175258. [PMID: 34500691 PMCID: PMC8433626 DOI: 10.3390/molecules26175258] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/25/2022] Open
Abstract
C-Mannosylation is a post-translational modification of proteins in the endoplasmic reticulum. Monomeric α-mannose is attached to specific Trp residues at the first Trp in the Trp-x-x-Trp/Cys (W-x-x-W/C) motif of substrate proteins, by the action of C-mannosyltransferases, DPY19-related gene products. The acceptor substrate proteins are included in the thrombospondin type I repeat (TSR) superfamily, cytokine receptor type I family, and others. Previous studies demonstrated that C-mannosylation plays critical roles in the folding, sorting, and/or secretion of substrate proteins. A C-mannosylation-defective gene mutation was identified in humans as the disease-associated variant affecting a C-mannosylation motif of W-x-x-W of ADAMTSL1, which suggests the involvement of defects in protein C-mannosylation in human diseases such as developmental glaucoma, myopia, and/or retinal defects. On the other hand, monomeric C-mannosyl Trp (C-Man-Trp), a deduced degradation product of C-mannosylated proteins, occurs in cells and extracellular fluids. Several studies showed that the level of C-Man-Trp is upregulated in blood of patients with renal dysfunction, suggesting that the metabolism of C-Man-Trp may be involved in human kidney diseases. Together, protein C-mannosylation is considered to play important roles in the biosynthesis and functions of substrate proteins, and the altered regulation of protein C-manosylation may be involved in the pathophysiology of human diseases. In this review, we consider the biochemical and biomedical knowledge of protein C-mannosylation and C-Man-Trp, and introduce recent studies concerning their significance in biology and medicine.
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Affiliation(s)
- Shiho Minakata
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Shino Manabe
- Pharmaceutical Department, The Institute of Medicinal Chemistry, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan;
- Research Center for Pharmaceutical Development, Graduate School of Pharmaceutical Science & Faculty of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Sendai, Miyagi 980-8578, Japan
| | - Yoko Inai
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Midori Ikezaki
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Kazuchika Nishitsuji
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Yukishige Ito
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan;
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshito Ihara
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
- Correspondence: ; Tel.: +81-73-441-0628
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28
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Asimakopoulos B, Tiptiri-Kourpeti A, Metalinou C. Erythropoitein Increases In Vitro Motility and Vitality of Human Spermatozoa. In Vivo 2021; 35:2669-2673. [PMID: 34410955 DOI: 10.21873/invivo.12550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/01/2021] [Accepted: 07/13/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Erythropoietin and its receptor are expressed in the male reproductive system. Initial studies have shown that erythropoietin affects the motility of spermatozoa. The aim of the present study was to investigate the in vitro effect of erythropoietin in the motility and vitality of human spermatozoa. MATERIALS AND METHODS Forty-three semen samples, obtained after 2-4 days of abstinence from sex, were analyzed and processed using density gradient centrifugation. Aliquots containing one million of spermatozoa were treated with either erythropoietin, at concentrations of 10 and 100 mIU/μl or standard culture medium for one hour. RESULTS Progressive motility and vitality of spermatozoa significantly increased following treatment with erythropoietin. The effect was not dose-dependent. CONCLUSION The supplementation of culture medium with erythropoietin improves sperm processing in terms of vitality and motility. Future research should focus on the effects of erythropoietin on sperm capacitation as well as on the signal transduction pathways activated by erythropoietin and its receptor in spermatozoa.
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Affiliation(s)
- Byron Asimakopoulos
- Laboratory of Physiology, Faculty of Medicine, School of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Aggeliki Tiptiri-Kourpeti
- Laboratory of Physiology, Faculty of Medicine, School of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Chryssa Metalinou
- Laboratory of Physiology, Faculty of Medicine, School of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
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29
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Hitchcock IS, Hafer M, Sangkhae V, Tucker JA. The thrombopoietin receptor: revisiting the master regulator of platelet production. Platelets 2021; 32:770-778. [PMID: 34097561 PMCID: PMC8292222 DOI: 10.1080/09537104.2021.1925102] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/25/2022]
Abstract
Thrombopoietin (TPO) and its receptor, MPL, are the primary regulators of platelet production and critical for hematopoietic stem cell (HSC) maintenance. Since TPO was first cloned in 1994, the physiological and pathological roles of TPO and MPL have been well characterized, culminating in the first MPL agonists being approved for the treatment of chronic immune thrombocytopenia in 2008. Dysregulation of the TPO-MPL signaling axis contributes to the pathogenesis of hematological disorders: decreased expression or function results in severe thrombocytopenia progressing to bone marrow failure, while hyperactivation of MPL signaling, either by mutations in the receptor or associated Janus kinase 2 (JAK2), results in pathological myeloproliferation. Despite its importance, it was only recently that the long-running debate over the mechanism by which TPO binding activates MPL has been resolved. This review will cover key aspects of TPO and MPL structure and function and their importance in receptor activation, discuss how these are altered in hematological disorders and consider how a greater understanding could lead to the development of better-targeted and more efficacious therapies.
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Affiliation(s)
- Ian S. Hitchcock
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Maximillian Hafer
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Veena Sangkhae
- Center for Iron Disorders, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Julie A. Tucker
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
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30
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Vittori DC, Chamorro ME, Hernández YV, Maltaneri RE, Nesse AB. Erythropoietin and derivatives: Potential beneficial effects on the brain. J Neurochem 2021; 158:1032-1057. [PMID: 34278579 DOI: 10.1111/jnc.15475] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/24/2021] [Accepted: 07/14/2021] [Indexed: 12/16/2022]
Abstract
Erythropoietin (Epo), the main erythropoiesis-stimulating factor widely prescribed to overcome anemia, is also known nowadays for its cytoprotective action on non-hematopoietic tissues. In this context, Epo showed not only its ability to cross the blood-brain barrier, but also its expression in the brain of mammals. In clinical trials, recombinant Epo treatment has been shown to stimulate neurogenesis; improve cognition; and activate antiapoptotic, antioxidant, and anti-inflammatory signaling pathways. These mechanisms, proposed to characterize a neuroprotective property, opened new perspectives on the Epo pharmacological potencies. However, many questions arise about a possible physiological role of Epo in the central nervous system (CNS) and the factors or environmental conditions that induce its expression. Although Epo may be considered a strong candidate to be used against neuronal damage, long-term treatments, particularly when high Epo doses are needed, may induce thromboembolic complications associated with increases in hematocrit and blood viscosity. To avoid these adverse effects, different Epo analogs without erythropoietic activity but maintaining neuroprotection ability are currently being investigated. Carbamylated erythropoietin, as well as alternative molecules like Epo fusion proteins and partial peptides of Epo, seems to match this profile. This review will focus on the discussion of experimental evidence reported in recent years linking erythropoietin and CNS function through investigations aimed at finding benefits in the treatment of neurodegenerative diseases. In addition, it will review the proposed mechanisms for novel derivatives which may clarify and, eventually, improve the neuroprotective action of Epo.
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Affiliation(s)
- Daniela C Vittori
- Department of Biological Chemistry, National Scientific and Technical Research Council, Institute of Biological Chemistry (IQUIBICEN), School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
| | - María E Chamorro
- Department of Biological Chemistry, National Scientific and Technical Research Council, Institute of Biological Chemistry (IQUIBICEN), School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
| | - Yender V Hernández
- Department of Biological Chemistry, National Scientific and Technical Research Council, Institute of Biological Chemistry (IQUIBICEN), School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
| | - Romina E Maltaneri
- Department of Biological Chemistry, National Scientific and Technical Research Council, Institute of Biological Chemistry (IQUIBICEN), School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
| | - Alcira B Nesse
- Department of Biological Chemistry, National Scientific and Technical Research Council, Institute of Biological Chemistry (IQUIBICEN), School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
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31
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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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Yachnin BJ, Mulligan VK, Khare SD, Bailey-Kellogg C. MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform. J Chem Inf Model 2021; 61:2368-2382. [PMID: 33900750 PMCID: PMC8225355 DOI: 10.1021/acs.jcim.1c00056] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As non-"self" macromolecules, biotherapeutics can trigger an immune response that can reduce drug efficacy, require patients to be taken off therapy, or even cause life-threatening reactions. To enable the flexible and facile design of protein biotherapeutics while reducing the prevalence of T-cell epitopes that drive immune recognition, we have integrated into the Rosetta protein design suite a new scoring term that allows design protocols to account for predicted or experimentally identified epitopes in the optimized objective function. This flexible scoring term can be used in any Rosetta design trajectory, can be targeted to specific regions of a protein, and can be readily extended to work with a variety of epitope predictors. By performing extensive design runs with varied design parameter choices for three case study proteins as well as a larger diverse benchmark, we show that the incorporation of this scoring term enables the effective exploration of an alternative, deimmunized sequence space to discover diverse proteins that are potentially highly deimmunized while retaining physical and chemical qualities similar to those yielded by equivalent nondeimmunizing sequence design protocols.
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Affiliation(s)
- Brahm J. Yachnin
- Department of Chemistry and Chemical Biology and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Vikram Khipple Mulligan
- Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY, 10010, USA
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
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Venkatesan A, Geng J, Kandarpa M, Wijeyesakere SJ, Bhide A, Talpaz M, Pogozheva ID, Raghavan M. Mechanism of mutant calreticulin-mediated activation of the thrombopoietin receptor in cancers. J Cell Biol 2021; 220:212031. [PMID: 33909030 PMCID: PMC8085772 DOI: 10.1083/jcb.202009179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/10/2021] [Accepted: 03/17/2021] [Indexed: 12/21/2022] Open
Abstract
Myeloproliferative neoplasms (MPNs) are frequently driven by mutations within the C-terminal domain (C-domain) of calreticulin (CRT). CRTDel52 and CRTIns5 are recurrent mutations. Oncogenic transformation requires both mutated CRT and the thrombopoietin receptor (Mpl), but the molecular mechanism of CRT-mediated constitutive activation of Mpl is unknown. We show that the acquired C-domain of CRTDel52 mediates both Mpl binding and disulfide-linked CRTDel52 dimerization. Cysteine mutations within the novel C-domain (C400A and C404A) and the conserved N-terminal domain (N-domain; C163A) of CRTDel52 are required to reduce disulfide-mediated dimers and multimers of CRTDel52. Based on these data and published structures of CRT oligomers, we identify an N-domain dimerization interface relevant to both WT CRT and CRTDel52. Elimination of disulfide bonds and ionic interactions at both N-domain and C-domain dimerization interfaces is required to abrogate the ability of CRTDel52 to mediate cell proliferation via Mpl. Thus, MPNs exploit a natural dimerization interface of CRT combined with C-domain gain of function to achieve cell transformation.
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Affiliation(s)
- Arunkumar Venkatesan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
| | - Jie Geng
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
| | - Malathi Kandarpa
- Department of Internal Medicine/Division of Hematology/Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | | | - Ashwini Bhide
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
| | - Moshe Talpaz
- Department of Internal Medicine/Division of Hematology/Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
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Prestegard JH. A perspective on the PDB's impact on the field of glycobiology. J Biol Chem 2021; 296:100556. [PMID: 33744289 PMCID: PMC8058564 DOI: 10.1016/j.jbc.2021.100556] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Structures deposited in the Protein Data Bank (PDB) facilitate our understanding of many biological processes including those that fall under the general category of glycobiology. However, structure-based studies of how glycans affect protein structure, how they are synthesized, and how they regulate other biological processes remain challenging. Despite the abundant presence of glycans on proteins and the dense layers of glycans that surround most of our cells, structures containing glycans are underrepresented in the PDB. There are sound reasons for this, including difficulties in producing proteins with well-defined glycosylation and the tendency of mobile and heterogeneous glycans to inhibit crystallization. Nevertheless, the structures we do find in the PDB, even some of the earliest deposited structures, have had an impact on our understanding of function. I highlight a few examples in this review and point to some promises for the future. Promises include new structures from methodologies, such as cryo-EM, that are less affected by the presence of glycans and experiment-aided computational methods that build on existing structures to provide insight into the many ways glycans affect biological function.
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Affiliation(s)
- James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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35
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Comprehensive multi-omics analysis of G6PC3 deficiency-related congenital neutropenia with inflammatory bowel disease. iScience 2021; 24:102214. [PMID: 33748703 PMCID: PMC7960940 DOI: 10.1016/j.isci.2021.102214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/29/2020] [Accepted: 02/17/2021] [Indexed: 11/26/2022] Open
Abstract
Autosomal recessive mutations in G6PC3 cause isolated and syndromic congenital neutropenia which includes congenital heart disease and atypical inflammatory bowel disease (IBD). In a highly consanguineous pedigree with novel mutations in G6PC3 and MPL, we performed comprehensive multi-omics analyses. Structural analysis of variant G6PC3 and MPL proteins suggests a damaging effect. A distinct molecular cytokine profile (cytokinome) in the affected proband with IBD was detected. Liquid chromatography-mass spectrometry-based proteomics analysis of the G6PC3-deficient plasma samples identified 460 distinct proteins including 75 upregulated and 73 downregulated proteins. Specifically, the transcription factor GATA4 and LST1 were downregulated while platelet factor 4 (PF4) was upregulated. GATA4 and PF4 have been linked to congenital heart disease and IBD respectively, while LST1 may have perturbed a variety of essential cell functions as it is required for normal cell-cell communication. Together, these studies provide potentially novel insights into the pathogenesis of syndromic congenital G6PC3 deficiency. Multi-omics approaches identify unique signatures Whole-exome sequencing reveals distinct cytokine profiles Expression of GATA4, PF4, and LST1 is dysregulated
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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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Chauhan P, Nair A, Patidar A, Dandapat J, Sarkar A, Saha B. A primer on cytokines. Cytokine 2021; 145:155458. [PMID: 33581983 DOI: 10.1016/j.cyto.2021.155458] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/19/2022]
Abstract
Cytokines are pleiotropic polypeptides that control the development of and responses mediated by immune cells. Cytokine classification predominantly relies on [1] the target receptor(s), [2] the primary structural features of the extracellular domains of their receptors, and [3] their receptor composition. Functionally, cytokines are either pro-inflammatory or anti-inflammatory, hematopoietic colony-stimulating factors, developmental and would healing maintaining immune homeostasis. When the balance in C can form complex networks amongst themselves that may affect the homeostasis and diseases. Cytokines can affect resistance and susceptibility for many diseases and their availability in the host cytokine production and interaction is disturbed, immunopathogenesis sets in. Therefore, cytokine-targeting bispecific, and chimeric antibodies form a significant mode of immnuo-therapeutics Although the field has grown deep and wide, many areas of cytokine biology remain unknown. Here, we have reviewed these cytokines along with the organization, signaling, and functions through respective cytokine-receptor-families. Being part of the special issue on the Role of Cytokines in Leishmaniasis, this review is intended to be used as an organized primer on cytokines and not a resource for detailed discussion- for which a two-volume Handbook of cytokines is available- on each of the cytokines. Priming the readers on cytokines, we next brief the role of cytokines in Leishmaniasis. In the brief, we do not provide an account of each of the involved cytokines known to date, instead, we offer a temporal relationship between the cytokines and the progress of the infection towards the alternate outcomes- healing or non-healing- of the infection.
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Affiliation(s)
- Prashant Chauhan
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Arathi Nair
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Ashok Patidar
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Jagneshwar Dandapat
- P.G. Department of Biotechnology, Utkal University, Bhubaneswar 751004, India
| | - Arup Sarkar
- Trident Academy of Creative Technology, Bhubaneswar 751024, India
| | - Bhaskar Saha
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India; Trident Academy of Creative Technology, Bhubaneswar 751024, India; Department of Allied Health Sciences, BLDE (Deemed University), Vijayapura 562135, India.
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Choi YB, Dunn-Meynell AA, Marchese M, Blumberg BM, Gaindh D, Dowling PC, Lu W. Erythropoietin-derived peptide treatment reduced neurological deficit and neuropathological changes in a mouse model of tauopathy. Alzheimers Res Ther 2021; 13:32. [PMID: 33504364 PMCID: PMC7839226 DOI: 10.1186/s13195-020-00766-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 12/29/2020] [Indexed: 01/12/2023]
Abstract
BACKGROUND Prominent activation of microglial immune/inflammatory processes is a characteristic feature of brains of patients with tauopathies including Alzheimer's disease (AD), suggesting that neuroinflammation may be a critical factor in their pathogenesis. Strategies aimed at developing new therapeutics for tauopathies based on anti-inflammation or immunomodulation are likely to be promising avenues of research. We previously developed JM4-a 19'mer cyclic peptide derived from the first loop of human erythropoietin. This peptide possesses beneficial immune modulatory and tissue protective effects while lacking the undesirable side effects of full-length erythropoietin. In this preclinical study, we investigated the effect of chronic JM4 treatment on the PS19 mouse that carries the P301S mutant human tau gene, linked to a form of frontotemporal dementia. This transgenic mouse has been widely used as a model of tauopathies including AD and related dementias. METHODS Daily subcutaneous treatment of female PS19 mice with JM4 was initiated before disease onset and continued on for the animals' lifespan. The progression of neurological deficit and the lifespan of these mice were assessed. To evaluate the effect of JM4 treatment on cognition of these animals, the PS19 mice underwent Barnes maze test and elevated plus maze test. In addition, neuronal loss, phosphorylated tau aggregation, and microglial activation were assessed using immunohistochemistry of PS19 mouse brain sections. RESULTS JM4 treatment of PS19 mice initiated before disease onset reduced neurological deficit, prolonged lifespan, and rescued memory impairment. The beneficial effects of JM4 were accompanied by reductions in neuronal loss, phosphorylated tau aggregation, and microglial activation in the PS19 mouse brain. LIMITATIONS Use of a single dose of JM4 and female mice only. CONCLUSION JM4 is a potential novel therapeutic agent for the treatment of tauopathies including AD and related dementias.
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Affiliation(s)
- Yun-Beom Choi
- Neurology Service, VA New Jersey Health Care System and Department of Neurology, Rutgers New Jersey Medical School, 385 Tremont Ave., East Orange, NJ 07018 USA
| | - Ambrose A. Dunn-Meynell
- Neurology Service, VA New Jersey Health Care System and Department of Pharmacology, Physiology, and Neuroscience, Rutgers New Jersey Medical School, 385 Tremont Ave., East Orange, NJ 07018 USA
| | - Michelle Marchese
- Neurology Service, VA New Jersey Health Care System, 385 Tremont Ave., East Orange, NJ 07018 USA
| | - Benjamin M. Blumberg
- Neurology Service, VA New Jersey Health Care System, 385 Tremont Ave., East Orange, NJ 07018 USA
| | - Deeya Gaindh
- Neurology Service, VA New Jersey Health Care System and Department of Neurology, Rutgers New Jersey Medical School, 385 Tremont Ave., East Orange, NJ 07018 USA
| | - Peter C. Dowling
- Neurology Service, VA New Jersey Health Care System and Department of Neurology, Rutgers New Jersey Medical School, 385 Tremont Ave., East Orange, NJ 07018 USA
- Neurology Service, VA New Jersey Health Care System and Department of Pharmacology, Physiology, and Neuroscience, Rutgers New Jersey Medical School, 385 Tremont Ave., East Orange, NJ 07018 USA
| | - Wei Lu
- Neurology Service, VA New Jersey Health Care System, 385 Tremont Ave., East Orange, NJ 07018 USA
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Wilson IA, Stanfield RL. 50 Years of structural immunology. J Biol Chem 2021; 296:100745. [PMID: 33957119 PMCID: PMC8163984 DOI: 10.1016/j.jbc.2021.100745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.
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MESH Headings
- Adaptive Immunity
- Allergy and Immunology/history
- Animals
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigen Presentation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Crystallography/history
- Crystallography/methods
- History, 20th Century
- History, 21st Century
- Humans
- Immunity, Innate
- Protein Folding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Cytokine/chemistry
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- V(D)J Recombination
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Affiliation(s)
- Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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Hernandez Alvarez B, Skokowa J, Coles M, Mir P, Nasri M, Maksymenko K, Weidmann L, Rogers KW, Welte K, Lupas AN, Müller P, ElGamacy M. Design of novel granulopoietic proteins by topological rescaffolding. PLoS Biol 2020; 18:e3000919. [PMID: 33351791 PMCID: PMC7755208 DOI: 10.1371/journal.pbio.3000919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 11/24/2020] [Indexed: 11/18/2022] Open
Abstract
Computational protein design is rapidly becoming more powerful, and improving the accuracy of computational methods would greatly streamline protein engineering by eliminating the need for empirical optimization in the laboratory. In this work, we set out to design novel granulopoietic agents using a rescaffolding strategy with the goal of achieving simpler and more stable proteins. All of the 4 experimentally tested designs were folded, monomeric, and stable, while the 2 determined structures agreed with the design models within less than 2.5 Å. Despite the lack of significant topological or sequence similarity to their natural granulopoietic counterpart, 2 designs bound to the granulocyte colony-stimulating factor (G-CSF) receptor and exhibited potent, but delayed, in vitro proliferative activity in a G-CSF-dependent cell line. Interestingly, the designs also induced proliferation and differentiation of primary human hematopoietic stem cells into mature granulocytes, highlighting the utility of our approach to develop highly active therapeutic leads purely based on computational design. De novo designed cytokines that activate the G-CSF receptor show that the receptor-binding information can be encoded onto stable, miniaturised protein scaffolds that possess potent granulopoietic activity; such novel proteins provide for ideal candidates for protein-based therapeutics.
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Affiliation(s)
| | - Julia Skokowa
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
- * E-mail: (JS); (ME)
| | - Murray Coles
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Perihan Mir
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
| | - Masoud Nasri
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
| | | | - Laura Weidmann
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Karl Welte
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
| | - Andrei N. Lupas
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Patrick Müller
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
- Friedrich Miescher Laboratory of the Max Planck Society Tübingen, Germany
| | - Mohammad ElGamacy
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
- Friedrich Miescher Laboratory of the Max Planck Society Tübingen, Germany
- Heliopolis Biotechnology Ltd., London, United Kingdom
- * E-mail: (JS); (ME)
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41
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Pekas NJ, Petersen JL, Sathyanesan M, Newton SS. Design and Development of a Behaviorally Active Recombinant Neurotrophic Factor. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:5393-5403. [PMID: 33304094 PMCID: PMC7723032 DOI: 10.2147/dddt.s274308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022]
Abstract
Introduction Carbamoylated erythropoietin (CEPO) is a chemically engineered, nonhematopoietic derivative of erythropoietin (EPO) that retains its antidepressant and pro-cognitive effects, which are attributed to the increased expression of neurotrophic factors like brain derived neurotrophic factor (BDNF), in the central nervous system. However, the chemical modification process which produces CEPO from erythropoietin (EPO) requires pure EPO as raw material, is challenging to scale-up and can also cause batch-to-batch variability. To address these key limitations while retaining its behavioral effects, we designed, expressed and analyzed a triple, glutamine, substitution recombinant mimetic of CEPO, named QPO. Methods and Materials We employ a combination of computational structural biology, molecular, cellular and behavioral assays to design, produce, purify and test QPO. Results QPO was shown to be a nonhematopoietic polypeptide with significant antidepressant-like and pro-cognitive behavioral effects in rodent assays while significantly upregulating BDNF expression in-vitro and in-vivo. The in-silico binding affinity analysis of QPO bound to the EPOR/EPOR homodimer receptor shows significantly decreased binding to Active Site 2, but not Active Site 1, of EPOR. Discussion The results of the behavioral and gene expression analysis imply that QPO is a successful CEPO mimetic protein and potentially acts via a similar neurotrophic mechanism, making it a drug development target for psychiatric disorders. The decreased binding to Active Site 2 could imply that this active site is not involved in neuroactive signaling and could allow the development of a functional innate repair receptor (IRR) model. Substituting the three glutamine substitution residues with arginine (RPO) resulted in the loss of behavioral activity, indicating the importance of glutamine residues at those positions.
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Affiliation(s)
- Nicholas J Pekas
- Department of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermilion, SD, USA
| | - Jason L Petersen
- Sioux Falls VA Health Care System, Sioux Falls, SD, USA.,Department of Internal Medicine, University of South Dakota Sanford School of Medicine, Vermillion, SD, USA
| | - Monica Sathyanesan
- Department of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermilion, SD, USA.,Sioux Falls VA Health Care System, Sioux Falls, SD, USA
| | - Samuel S Newton
- Department of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermilion, SD, USA.,Sioux Falls VA Health Care System, Sioux Falls, SD, USA
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Jankowski W, Lagassé HAD, Chang WC, McGill J, Jankowska KI, Gelinas AD, Janjic N, Sauna ZE. Modified aptamers as reagents to characterize recombinant human erythropoietin products. Sci Rep 2020; 10:18593. [PMID: 33122796 PMCID: PMC7596557 DOI: 10.1038/s41598-020-75713-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/14/2020] [Indexed: 11/08/2022] Open
Abstract
Reliable and reproducible monitoring of the conformational state of therapeutic protein products remains an unmet technological need. This need is amplified by the increasing number of biosimilars entering the drug development pipeline as many branded biologics are reaching the end of their market exclusivity period. Availability of methods to better characterize protein conformation may improve detection of counterfit and unlicensed therapeutic proteins. In this study, we report the use of a set of modified DNA aptamers with enhanced chemical diversity to probe the conformational state of 12 recombinant human erythropoietin (rHuEPO) therapeutic protein products; one FDA-licensed rHuEPO originator biological product, three rHuEPO products that are approved for marketing in the US or EU as biosimilars, and eight rHuEPO products that are not approved for marketing in the US or EU. We show that several of these modified aptamers are able to distinguish rHuEPO reference products or approved biosimilars from non-licensed rHuEPO products on the basis of differences in binding kinetics and equilibrium affinity constants. These reagents exhibit sensitivity to the conformational integrity of various forms of rHuEPO and as such represent powerful, simple-to-use analytical tools to monitor the conformational integrity of therapeutic-proteins during manufacture and to screen for and identify both substandard and counterfeit products.
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Affiliation(s)
- Wojciech Jankowski
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - H A Daniel Lagassé
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - William C Chang
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Joseph McGill
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Katarzyna I Jankowska
- Laboratory of Cellular Hematology, Division of Blood Components and Devices, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | | | | | - Zuben E Sauna
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
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43
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Araki D, Alvarado LJ, Huntsman HD, Smith RH, Larochelle A. IFN-γ directly inhibits the activity of erythropoietin in human erythroid progenitors. Blood Cells Mol Dis 2020; 85:102488. [PMID: 32889151 DOI: 10.1016/j.bcmd.2020.102488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Daisuke Araki
- National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Luigi J Alvarado
- National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Heather D Huntsman
- National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Richard H Smith
- National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Andre Larochelle
- National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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44
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45
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Gutierrez JM, Feizi A, Li S, Kallehauge TB, Hefzi H, Grav LM, Ley D, Baycin Hizal D, Betenbaugh MJ, Voldborg B, Faustrup Kildegaard H, Min Lee G, Palsson BO, Nielsen J, Lewis NE. Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion. Nat Commun 2020; 11:68. [PMID: 31896772 PMCID: PMC6940358 DOI: 10.1038/s41467-019-13867-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/22/2019] [Indexed: 01/08/2023] Open
Abstract
In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster ovary cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology.
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Affiliation(s)
- Jahir M Gutierrez
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Amir Feizi
- Department of Biology and Biological Engineering, Kemivägen 10, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Shangzhong Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Thomas B Kallehauge
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Hooman Hefzi
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Lise M Grav
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Daniel Ley
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Michael J Betenbaugh
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218-2686, USA
| | - Bjorn Voldborg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Helene Faustrup Kildegaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Gyun Min Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Kemivägen 10, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA.
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA.
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA.
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46
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Dmytriyeva O, Belmeguenai A, Bezin L, Soud K, Drucker Woldbye DP, Gøtzsche CR, Pankratova S. Short erythropoietin-derived peptide enhances memory, improves long-term potentiation, and counteracts amyloid beta–induced pathology. Neurobiol Aging 2019; 81:88-101. [DOI: 10.1016/j.neurobiolaging.2019.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 03/27/2019] [Accepted: 05/06/2019] [Indexed: 12/23/2022]
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Spangler JB, Moraga I, Jude KM, Savvides CS, Garcia KC. A strategy for the selection of monovalent antibodies that span protein dimer interfaces. J Biol Chem 2019; 294:13876-13886. [PMID: 31387945 PMCID: PMC6755802 DOI: 10.1074/jbc.ra119.009213] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/15/2019] [Indexed: 11/06/2022] Open
Abstract
Ligand-induced dimerization is the predominant mechanism through which secreted proteins activate cell surface receptors to transmit essential biological signals. Cytokines are a large class of soluble proteins that dimerize transmembrane receptors into precise signaling topologies, but there is a need for alternative, engineerable ligand scaffolds that specifically recognize and stabilize these protein interactions. Recombinant antibodies can potentially serve as robust and versatile platforms for cytokine complex stabilization, and their specificity allows for tunable modulation of dimerization equilibrium. Here, we devised an evolutionary strategy to isolate monovalent antibody fragments that bridge together two different receptor subunits in a cytokine-receptor complex, precisely as the receptors are disposed in their natural signaling orientations. To do this, we screened a naive antibody library against a stabilized ligand-receptor ternary complex that acted as a "molecular cast" of the natural receptor dimer conformation. Our selections elicited "stapler" single-chain variable fragments (scFvs) of antibodies that specifically engage the interleukin-4 receptor heterodimer. The 3.1 Å resolution crystal structure of one such stapler revealed that, as intended, this scFv recognizes a composite epitope between the two receptors as they are positioned in the complex. Extending our approach, we evolved a stapler scFv that specifically binds to and stabilizes the interface between the interleukin-2 cytokine and one of its receptor subunits, leading to a 15-fold enhancement in interaction affinity. This demonstration that scFvs can be selected to recognize epitopes that span protein interfaces presents new opportunities to engineer structurally defined antibodies for a broad range of research and therapeutic applications.
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Affiliation(s)
- Jamie B Spangler
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305 .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218
| | - Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Christina S Savvides
- Department of Biology, Stanford University School of Medicine, Stanford, California 94305
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305 .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
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48
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Morris R, Kershaw NJ, Babon JJ. The molecular details of cytokine signaling via the JAK/STAT pathway. Protein Sci 2019; 27:1984-2009. [PMID: 30267440 DOI: 10.1002/pro.3519] [Citation(s) in RCA: 476] [Impact Index Per Article: 95.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/24/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
Abstract
More than 50 cytokines signal via the JAK/STAT pathway to orchestrate hematopoiesis, induce inflammation and control the immune response. Cytokines are secreted glycoproteins that act as intercellular messengers, inducing proliferation, differentiation, growth, or apoptosis of their target cells. They act by binding to specific receptors on the surface of target cells and switching on a phosphotyrosine-based intracellular signaling cascade initiated by kinases then propagated and effected by SH2 domain-containing transcription factors. As cytokine signaling is proliferative and often inflammatory, it is tightly regulated in terms of both amplitude and duration. Here we review molecular details of the cytokine-induced signaling cascade and describe the architectures of the proteins involved, including the receptors, kinases, and transcription factors that initiate and propagate signaling and the regulatory proteins that control it.
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Affiliation(s)
- Rhiannon Morris
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3050, Victoria, Australia
| | - Nadia J Kershaw
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3050, Victoria, Australia
| | - Jeffrey J Babon
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3050, Victoria, Australia
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49
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Inhibition of tetrameric Patched1 by Sonic Hedgehog through an asymmetric paradigm. Nat Commun 2019; 10:2320. [PMID: 31127104 PMCID: PMC6534611 DOI: 10.1038/s41467-019-10234-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/28/2019] [Indexed: 12/16/2022] Open
Abstract
The Hedgehog (Hh) pathway controls embryonic development and postnatal tissue maintenance and regeneration. Inhibition of Hh receptor Patched (Ptch) by the Hh ligands relieves suppression of signaling cascades. Here, we report the cryo-EM structure of tetrameric Ptch1 in complex with the palmitoylated N-terminal signaling domain of human Sonic hedgehog (ShhNp) at a 4:2 stoichiometric ratio. The structure shows that four Ptch1 protomers are organized as a loose dimer of dimers. Each dimer binds to one ShhNp through two distinct inhibitory interfaces, one mainly through the N-terminal peptide and the palmitoyl moiety of ShhNp and the other through the Ca2+-mediated interface on ShhNp. Map comparison reveals that the cholesteryl moiety of native ShhN occupies a recently identified extracellular steroid binding pocket in Ptch1. Our structure elucidates the tetrameric assembly of Ptch1 and suggests an asymmetric mode of action of the Hh ligands for inhibiting the potential cholesterol transport activity of Ptch1. Hedgehog (Hh) controls embryonic development via interaction with its receptor Patched (Ptch). Here the authors report the cryo-EM structure of tetrameric Ptch1 in complex with the palmitoylated N-terminal signaling domain of human Sonic hedgehog (ShhNp) at a 4:2 stoichiometric ratio.
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50
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Mohan K, Ueda G, Kim AR, Jude KM, Fallas JA, Guo Y, Hafer M, Miao Y, Saxton RA, Piehler J, Sankaran VG, Baker D, Garcia KC. Topological control of cytokine receptor signaling induces differential effects in hematopoiesis. Science 2019; 364:eaav7532. [PMID: 31123111 PMCID: PMC7274355 DOI: 10.1126/science.aav7532] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
Abstract
Although tunable signaling by G protein-coupled receptors can be exploited through medicinal chemistry, a comparable pharmacological approach has been lacking for the modulation of signaling through dimeric receptors, such as those for cytokines. We present a strategy to modulate cytokine receptor signaling output by use of a series of designed C2-symmetric cytokine mimetics, based on the designed ankyrin repeat protein (DARPin) scaffold, that can systematically control erythropoietin receptor (EpoR) dimerization orientation and distance between monomers. We sampled a range of EpoR geometries by varying intermonomer angle and distance, corroborated by several ligand-EpoR complex crystal structures. Across the range, we observed full, partial, and biased agonism as well as stage-selective effects on hematopoiesis. This surrogate ligand strategy opens access to pharmacological modulation of therapeutically important cytokine and growth factor receptor systems.
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Affiliation(s)
- Kritika Mohan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ah Ram Kim
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jorge A Fallas
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Maximillian Hafer
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Yi Miao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert A Saxton
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
- Center for Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Vijay G Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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