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Duncan-Lowey J, Crabill E, Jarret A, Reed SCO, Roy CR. The Coxiella burnetii effector EmcB is a deubiquitinase that inhibits RIG-I signaling. Proc Natl Acad Sci U S A 2023; 120:e2217602120. [PMID: 36893270 PMCID: PMC10089202 DOI: 10.1073/pnas.2217602120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/25/2023] [Indexed: 03/11/2023] Open
Abstract
Eukaryotes have cytosolic surveillance systems to detect invading microorganisms and initiate protective immune responses. In turn, host-adapted pathogens have evolved strategies to modulate these surveillance systems, which can promote dissemination and persistence in the host. The obligate intracellular pathogen Coxiella burnetii infects mammalian hosts without activating many innate immune sensors. The Defect in Organelle Trafficking/Intracellular Multiplication (Dot/Icm) protein secretion system is necessary for C. burnetii to establish a vacuolar niche inside of host cells, which sequesters these bacteria in a specialized organelle that could evade host surveillance systems. However, bacterial secretion systems often introduce agonists of immune sensors into the host cytosol during infection. For instance, nucleic acids are introduced to the host cytosol by the Dot/Icm system of Legionella pneumophila, which results in type I interferon production. Despite host infection requiring a homologous Dot/Icm system, C. burnetii does not induce type I interferon production during infection. Here, it was found that type I interferons are detrimental to C. burnetii infection and that C. burnetii blocks type I interferon production mediated by retionic acid inducible gene I (RIG-I) signaling. Two Dot/Icm effector proteins, EmcA and EmcB, are required for C. burnetii inhibition of RIG-I signaling. EmcB is sufficient to block RIG-I signaling and is a ubiquitin-specific cysteine protease capable of deconjugating ubiquitin chains from RIG-I that are necessary for signaling. EmcB preferentially cleaves K63-linked ubiquitin chains of three or more monomers, which represent ubiquitin chains that potently activate RIG-I signaling. Identification of a deubiquitinase encoded by C. burnetii provides insights into how a host-adapted pathogen antagonizes immune surveillance.
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Affiliation(s)
- Jeffrey Duncan-Lowey
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06536
| | - Emerson Crabill
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06536
- Department of Biology, Angelo State University, San Angelo, TX76909
| | - Abigail Jarret
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06536
| | - Shawna C. O. Reed
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06536
| | - Craig R. Roy
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06536
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2
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Sijben HJ, Dall’ Acqua L, Liu R, Jarret A, Christodoulaki E, Onstein S, Wolf G, Verburgt SJ, Le Dévédec SE, Wiedmer T, Superti-Furga G, IJzerman AP, Heitman LH. Impedance-Based Phenotypic Readout of Transporter Function: A Case for Glutamate Transporters. Front Pharmacol 2022; 13:872335. [PMID: 35677430 PMCID: PMC9169222 DOI: 10.3389/fphar.2022.872335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/29/2022] [Indexed: 11/18/2022] Open
Abstract
Excitatory amino acid transporters (EAAT/SLC1) mediate Na+-dependent uptake of extracellular glutamate and are potential drug targets for neurological disorders. Conventional methods to assess glutamate transport in vitro are based on radiolabels, fluorescent dyes or electrophysiology, which potentially compromise the cell’s physiology and are generally less suited for primary drug screens. Here, we describe a novel label-free method to assess human EAAT function in living cells, i.e., without the use of chemical modifications to the substrate or cellular environment. In adherent HEK293 cells overexpressing EAAT1, stimulation with glutamate or aspartate induced cell spreading, which was detected in real-time using an impedance-based biosensor. This change in cell morphology was prevented in the presence of the Na+/K+-ATPase inhibitor ouabain and EAAT inhibitors, which suggests the substrate-induced response was ion-dependent and transporter-specific. A mechanistic explanation for the phenotypic response was substantiated by actin cytoskeleton remodeling and changes in the intracellular levels of the osmolyte taurine, which suggests that the response involves cell swelling. In addition, substrate-induced cellular responses were observed for cells expressing other EAAT subtypes, as well as in a breast cancer cell line (MDA-MB-468) with endogenous EAAT1 expression. These findings allowed the development of a label-free high-throughput screening assay, which could be beneficial in early drug discovery for EAATs and holds potential for the study of other transport proteins that modulate cell shape.
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Affiliation(s)
- Hubert J. Sijben
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Laura Dall’ Acqua
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Rongfang Liu
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Abigail Jarret
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Eirini Christodoulaki
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Svenja Onstein
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Simone J. Verburgt
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Sylvia E. Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Laura H. Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
- Oncode Institute, Leiden, Netherlands
- *Correspondence: Laura H. Heitman,
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3
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Bielecki P, Riesenfeld SJ, Hütter JC, Triglia ET, Kowalczyk MS, Ricardo-Gonzalez RR, Lian M, Vesely MCA, Kroehling L, Xu H, Slyper M, Muus C, Ludwig LS, Christian E, Tao L, Kedaigle AJ, Steach HR, York AG, Skadow MH, Yaghoubi P, Dionne D, Jarret A, McGee HM, Porter CBM, Licona-Limón P, Bailis W, Jackson R, Gagliani N, Gasteiger G, Locksley RM, Regev A, Flavell RA. Skin-resident innate lymphoid cells converge on a pathogenic effector state. Nature 2021; 592:128-132. [PMID: 33536623 PMCID: PMC8336632 DOI: 10.1038/s41586-021-03188-w] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/24/2020] [Indexed: 01/30/2023]
Abstract
Tissue-resident innate lymphoid cells (ILCs) help sustain barrier function and respond to local signals. ILCs are traditionally classified as ILC1, ILC2 or ILC3 on the basis of their expression of specific transcription factors and cytokines1. In the skin, disease-specific production of ILC3-associated cytokines interleukin (IL)-17 and IL-22 in response to IL-23 signalling contributes to dermal inflammation in psoriasis. However, it is not known whether this response is initiated by pre-committed ILCs or by cell-state transitions. Here we show that the induction of psoriasis in mice by IL-23 or imiquimod reconfigures a spectrum of skin ILCs, which converge on a pathogenic ILC3-like state. Tissue-resident ILCs were necessary and sufficient, in the absence of circulatory ILCs, to drive pathology. Single-cell RNA-sequencing (scRNA-seq) profiles of skin ILCs along a time course of psoriatic inflammation formed a dense transcriptional continuum-even at steady state-reflecting fluid ILC states, including a naive or quiescent-like state and an ILC2 effector state. Upon disease induction, the continuum shifted rapidly to span a mixed, ILC3-like subset also expressing cytokines characteristic of ILC2s, which we inferred as arising through multiple trajectories. We confirmed the transition potential of quiescent-like and ILC2 states using in vitro experiments, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) and in vivo fate mapping. Our results highlight the range and flexibility of skin ILC responses, suggesting that immune activities primed in healthy tissues dynamically adapt to provocations and, left unchecked, drive pathological remodelling.
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Affiliation(s)
- Piotr Bielecki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA. .,Celsius Therapeutics, Cambridge, MA, USA.
| | - Samantha J. Riesenfeld
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA, Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Correspondence to: A.R , R.A.F , P.B , and S.J.R
| | - Jan-Christian Hütter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Elena Torlai Triglia
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Monika S. Kowalczyk
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Roberto R. Ricardo-Gonzalez
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA, Department of Medicine, Sandler Asthma Research Center University of California San Francisco, San Francisco, CA, USA
| | - Mi Lian
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Germany, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maria C. Amezcua Vesely
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, Howard Hughes Medical Institute
| | - Lina Kroehling
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hao Xu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Christoph Muus
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Leif S. Ludwig
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Elena Christian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Liming Tao
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Amanda J. Kedaigle
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Holly R. Steach
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Autumn G. York
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mathias H. Skadow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Parastou Yaghoubi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Abigail Jarret
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Heather M. McGee
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Sciences, La Jolla, CA 92037, USA
| | - Caroline B. M. Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Paula Licona-Limón
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City 04510
| | - Will Bailis
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, Division of Protective Immunity, Children’s Hospital of Philadelphia, 19104, Philadelphia, PA, USA., Department of Pathology and Laboratory Medicine, University of Pennsylvania, 19104, Philadelphia, PA, USA
| | - Ruaidhrí Jackson
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nicola Gagliani
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany, Department of Medicine, University Medical Center Hamburg-Eppendorf Hamburg-Eppendorf, 20246 Hamburg, Germany, Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institute and University Hospital, 17176 Stockholm, Sweden
| | - Georg Gasteiger
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Germany
| | - Richard M. Locksley
- Department of Medicine, Sandler Asthma Research Center University of California San Francisco, San Francisco, CA, USA, Howard Hughes Medical Institute
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Genentech, South San Francisco, CA, USA.
| | - Richard A. Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA, Howard Hughes Medical Institute, Correspondence to: A.R , R.A.F , P.B , and S.J.R
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4
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Jarret A, Jackson R, Duizer C, Healy ME, Zhao J, Rone JM, Bielecki P, Sefik E, Roulis M, Rice T, Sivanathan KN, Zhou T, Solis AG, Honcharova-Biletska H, Vélez K, Hartner S, Low JS, Qu R, de Zoete MR, Palm NW, Ring AM, Weber A, Moor AE, Kluger Y, Nowarski R, Flavell RA. Enteric Nervous System-Derived IL-18 Orchestrates Mucosal Barrier Immunity. Cell 2020; 180:813-814. [PMID: 32084342 DOI: 10.1016/j.cell.2020.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Jarret A, Jackson R, Duizer C, Healy ME, Zhao J, Rone JM, Bielecki P, Sefik E, Roulis M, Rice T, Sivanathan KN, Zhou T, Solis AG, Honcharova-Biletska H, Vélez K, Hartner S, Low JS, Qu R, de Zoete MR, Palm NW, Ring AM, Weber A, Moor AE, Kluger Y, Nowarski R, Flavell RA. Enteric Nervous System-Derived IL-18 Orchestrates Mucosal Barrier Immunity. Cell 2020; 180:50-63.e12. [PMID: 31923399 PMCID: PMC7339937 DOI: 10.1016/j.cell.2019.12.016] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 11/01/2019] [Accepted: 12/12/2019] [Indexed: 12/18/2022]
Abstract
Mucosal barrier immunity is essential for the maintenance of the commensal microflora and combating invasive bacterial infection. Although immune and epithelial cells are thought to be the canonical orchestrators of this complex equilibrium, here, we show that the enteric nervous system (ENS) plays an essential and non-redundant role in governing the antimicrobial protein (AMP) response. Using confocal microscopy and single-molecule fluorescence in situ mRNA hybridization (smFISH) studies, we observed that intestinal neurons produce the pleiotropic cytokine IL-18. Strikingly, deletion of IL-18 from the enteric neurons alone, but not immune or epithelial cells, rendered mice susceptible to invasive Salmonella typhimurium (S.t.) infection. Mechanistically, unbiased RNA sequencing and single-cell sequencing revealed that enteric neuronal IL-18 is specifically required for homeostatic goblet cell AMP production. Together, we show that neuron-derived IL-18 signaling controls tissue-wide intestinal immunity and has profound consequences on the mucosal barrier and invasive bacterial killing.
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Affiliation(s)
- Abigail Jarret
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ruaidhrí Jackson
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Coco Duizer
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Marc E Healy
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich 8091, Switzerland; Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Joseph M Rone
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Piotr Bielecki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Manolis Roulis
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Tyler Rice
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kisha N Sivanathan
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ting Zhou
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Angel G Solis
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hanna Honcharova-Biletska
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Karelia Vélez
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Saskia Hartner
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; University of Vienna, Universitätsring 1, Wien 1010, Austria
| | - Jun Siong Low
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rihao Qu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Marcel R de Zoete
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Noah W Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Aaron M Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich 8091, Switzerland; Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Andreas E Moor
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Yuval Kluger
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA; Applied Mathematics Program, Yale University, New Haven, CT 06511, USA
| | - Roni Nowarski
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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6
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Jackson R, Kroehling L, Khitun A, Bailis W, Jarret A, York AG, Khan OM, Brewer JR, Skadow MH, Duizer C, Harman CCD, Chang L, Bielecki P, Solis AG, Steach HR, Slavoff S, Flavell RA. The translation of non-canonical open reading frames controls mucosal immunity. Nature 2018; 564:434-438. [PMID: 30542152 PMCID: PMC6939389 DOI: 10.1038/s41586-018-0794-7] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 10/17/2018] [Indexed: 11/09/2022]
Abstract
The annotation of the mammalian protein-coding genome is incomplete. Arbitrary size restriction of open reading frames (ORFs) and the absolute requirement for a methionine codon as the sole initiator of translation have constrained the identification of potentially important transcripts with non-canonical protein-coding potential1,2. Here, using unbiased transcriptomic approaches in macrophages that respond to bacterial infection, we show that ribosomes associate with a large number of RNAs that were previously annotated as 'non-protein coding'. Although the idea that such non-canonical ORFs can encode functional proteins is controversial3,4, we identify a range of short and non-ATG-initiated ORFs that can generate stable and spatially distinct proteins. Notably, we show that the translation of a new ORF 'hidden' within the long non-coding RNA Aw112010 is essential for the orchestration of mucosal immunity during both bacterial infection and colitis. This work expands our interpretation of the protein-coding genome and demonstrates that proteinaceous products generated from non-canonical ORFs are crucial for the immune response in vivo. We therefore propose that the misannotation of non-canonical ORF-containing genes as non-coding RNAs may obscure the essential role of a multitude of previously undiscovered protein-coding genes in immunity and disease.
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Affiliation(s)
- Ruaidhrí Jackson
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Lina Kroehling
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Will Bailis
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Abigail Jarret
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Autumn G York
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Omair M Khan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - J Richard Brewer
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Mathias H Skadow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Coco Duizer
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Christian C D Harman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Lelina Chang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Piotr Bielecki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Angel G Solis
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Holly R Steach
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Sarah Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.
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7
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Jarret A, McFarland AP, Horner SM, Kell A, Schwerk J, Hong M, Badil S, Joslyn RC, Baker DP, Carrington M, Hagedorn CH, Gale M, Savan R. Hepatitis-C-virus-induced microRNAs dampen interferon-mediated antiviral signaling. Nat Med 2016; 22:1475-1481. [PMID: 27841874 PMCID: PMC5551900 DOI: 10.1038/nm.4211] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/15/2016] [Indexed: 12/12/2022]
Abstract
Hepatitis C virus (HCV) infects 200 million people globally, and 60-80% of cases persist as a chronic infection that will progress to cirrhosis and liver cancer in 2-10% of patients. We recently demonstrated that HCV induces aberrant expression of two host microRNAs (miRNAs), miR-208b and miR-499a-5p, encoded by myosin genes in infected hepatocytes. These miRNAs, along with AU-rich-element-mediated decay, suppress IFNL2 and IFNL3, members of the type III interferon (IFN) gene family, to support viral persistence. In this study, we show that miR-208b and miR-499a-5p also dampen type I IFN signaling in HCV-infected hepatocytes by directly down-regulating expression of the type I IFN receptor chain, IFNAR1. Inhibition of these miRNAs by using miRNA inhibitors during HCV infection increased expression of IFNAR1. Additionally, inhibition rescued the antiviral response to exogenous type I IFN, as measured by a marked increase in IFN-stimulated genes and a decrease in HCV load. Treatment of HCV-infected hepatocytes with type I IFN increased expression of myosins over HCV infection alone. Since these miRNAs can suppress type III IFN family members, these data collectively define a novel cross-regulation between type I and III IFNs during HCV infection.
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Affiliation(s)
- Abigail Jarret
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Adelle P McFarland
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Stacy M Horner
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Alison Kell
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Johannes Schwerk
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - MeeAe Hong
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Samantha Badil
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Rochelle C Joslyn
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | | | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research-Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts, USA
| | - Curt H Hagedorn
- Department of Medicine and Genetics Program, University of Arkansas for Medical Sciences, and The Central Arkansas Veterans Healthcare System, Little Rock, Arkansas, USA
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, Washington, USA
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8
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Hong M, Schwerk J, Lim C, Kell A, Jarret A, Pangallo J, Loo YM, Liu S, Hagedorn CH, Gale M, Savan R. Interferon lambda 4 expression is suppressed by the host during viral infection. J Exp Med 2016; 213:2539-2552. [PMID: 27799623 PMCID: PMC5110018 DOI: 10.1084/jem.20160437] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/10/2016] [Accepted: 10/04/2016] [Indexed: 01/21/2023] Open
Abstract
Interferon (IFN) lambdas are critical antiviral effectors in hepatic and mucosal infections. Although IFNλ1, IFNλ2, and IFNλ3 act antiviral, genetic association studies have shown that expression of the recently discovered IFNL4 is detrimental to hepatitis C virus (HCV) infection through a yet unknown mechanism. Intriguingly, human IFNL4 harbors a genetic variant that introduces a premature stop codon. We performed a molecular and biochemical characterization of IFNλ4 to determine its role and regulation of expression. We found that IFNλ4 exhibits similar antiviral activity to IFNλ3 without negatively affecting antiviral IFN activity or cell survival. We show that humans deploy several mechanisms to limit expression of functional IFNλ4 through noncoding splice variants and nonfunctional protein isoforms. Furthermore, protein-coding IFNL4 mRNA are not loaded onto polyribosomes and lack a strong polyadenylation signal, resulting in poor translation efficiency. This study provides mechanistic evidence that humans suppress IFNλ4 expression, suggesting that immune function is dependent on other IFNL family members.
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Affiliation(s)
- MeeAe Hong
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Johannes Schwerk
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Chrissie Lim
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Alison Kell
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Abigail Jarret
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Joseph Pangallo
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Yueh-Ming Loo
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Shuanghu Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112
| | - Curt H Hagedorn
- Department of Medicine, University of Arkansas for Medical Sciences and the Central Arkansas Veterans Healthcare System, Little Rock, AR 72205
- Genetics Program, University of Arkansas for Medical Sciences and the Central Arkansas Veterans Healthcare System, Little Rock, AR 72205
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, WA 98109
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9
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Schwerk J, Thomas K, Aarreberg L, Jarret A, Hong M, Savan R. Post-transcriptional regulation of interferon lambda during viral infection (IRM5P.640). The Journal of Immunology 2015. [DOI: 10.4049/jimmunol.194.supp.59.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Interferon lambda (IFN-λ) has gained increasing attention recently as an important mediator of antiviral protection in hepatitis C virus (HCV) infection. Similar to many cytokines, we have shown that expression of IFNL is regulated on a post-transcriptional level. Interestingly, single nucleotide polymorphisms (SNPs) within the IFNL genes dictate the outcome of acute HCV infection and serve as a prognostic marker for therapy of chronic HCV infection. Previously, we demonstrated that a functional SNP (rs4803217) within the 3'-untranslated region (UTR) of IFNL3 affects transcript stability and correlates with HCV clearance (G/G) or persistence (T/T) in infected patients and this is mediated by miRNAs and AU-rich elements. In our current study we have identified RNA-binding protein(s) (RBPs) that differentially regulate IFNL3 variants. We identified RBP candidates by carrying out mass spectrometry analysis on both variants of IFNL3 mRNA. We found that these candidates exclusively interact with the IFNL3 (T/T) mRNA. Intriguingly, gene expression of one candidate RBP is strongly induced upon stimulation of cells with HCV RNA or viral PAMP. Collectively, our data suggest that IFNL3 mRNA is post-transcriptionally regulated by miRNA and RBP-mediated mechanisms and that HCV potentially hijacks these regulatory mechanisms to suppress host antiviral responses.
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10
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McFarland AP, Horner SM, Jarret A, Joslyn RC, Bindewald E, Shapiro BA, Delker DA, Hagedorn CH, Carrington M, Gale M, Savan R. The favorable IFNL3 genotype escapes mRNA decay mediated by AU-rich elements and hepatitis C virus-induced microRNAs. Nat Immunol 2014; 15:72-9. [PMID: 24241692 PMCID: PMC4183367 DOI: 10.1038/ni.2758] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 09/24/2013] [Indexed: 12/12/2022]
Abstract
IFNL3, which encodes interferon-λ3 (IFN-λ3), has received considerable attention in the hepatitis C virus (HCV) field, as many independent genome-wide association studies have identified a strong association between polymorphisms near IFNL3 and clearance of HCV. However, the mechanism underlying this association has remained elusive. In this study, we report the identification of a functional polymorphism (rs4803217) in the 3' untranslated region (UTR) of IFNL3 mRNA that dictated transcript stability. We found that this polymorphism influenced AU-rich element (ARE)-mediated decay (AMD) of IFNL3 mRNA, as well as the binding of HCV-induced microRNAs during infection. Together these pathways mediated robust repression of the unfavorable IFNL3 polymorphism. Our data reveal a previously unknown mechanism by which HCV attenuates the antiviral response and indicate new potential therapeutic targets for HCV treatment.
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Affiliation(s)
- Adelle P McFarland
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Stacy M Horner
- 1] Department of Immunology, University of Washington, Seattle, Washington, USA. [2]
| | - Abigail Jarret
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Rochelle C Joslyn
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bruce A Shapiro
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, Maryland, USA
| | - Don A Delker
- Divison of Gastroenterology, Hepatology and Nutrition, School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Curt H Hagedorn
- 1] Divison of Gastroenterology, Hepatology and Nutrition, School of Medicine, University of Utah, Salt Lake City, Utah, USA. [2]
| | - Mary Carrington
- 1] Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation-Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA. [2] Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts, USA
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, Washington, USA
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11
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Steinhagen F, McFarland AP, Rodriguez LG, Tewary P, Jarret A, Savan R, Klinman DM. IRF-5 and NF-κB p50 co-regulate IFN-β and IL-6 expression in TLR9-stimulated human plasmacytoid dendritic cells. Eur J Immunol 2013; 43:1896-906. [PMID: 23616277 DOI: 10.1002/eji.201242792] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 03/27/2013] [Accepted: 04/18/2013] [Indexed: 11/12/2022]
Abstract
Synthetic oligonucleotides (ODN) expressing CpG motifs mimic the ability of bacterial DNA to trigger the innate immune system via TLR9. Plasmacytoid dendritic cells (pDCs) make a critical contribution to the ensuing immune response. This work examines the induction of antiviral (IFN-β) and pro-inflammatory (IL-6) cytokines by CpG-stimulated human pDCs and the human CAL-1 pDC cell line. Results show that interferon regulatory factor-5 (IRF-5) and NF-κB p50 are key co-regulators of IFN-β and IL-6 expression following TLR9-mediated activation of human pDCs. The nuclear accumulation of IRF-1 was also observed, but this was a late event that was dependant on type 1 IFN and unrelated to the initiation of gene expression. IRF-8 was identified as a novel negative regulator of gene activation in CpG-stimulated pDCs. As variants of IRF-5 and IRF-8 were recently found to correlate with susceptibility to certain autoimmune diseases, these findings are relevant to our understanding of the pharmacologic effects of "K" ODN and the role of TLR9 ligation under physiologic, pathologic, and therapeutic conditions.
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Affiliation(s)
- Folkert Steinhagen
- Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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12
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McFarland A, Steinhagen F, Rodriguez L, Tewary P, Jarret A, Savan R, Klinman D. IRF-5 and NF-κB p50 co-regulate IFN-β and IL-6 expression in TLR9-stimulated human plasmacytoid dendritic cells (P1363). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.63.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Robust production of type I interferon (IFN) by plasmacytoid dendritic cells (pDCs) occurs in response to Toll-like receptor 9 (TLR9) activation by unmethylated CpG dinucleotides present in bacterial and viral DNA. Previous work using different CpG oligodeoxynucleotides (ODN) revealed that CpG-A ODN but not CpG-B ODN robustly induce IFN-α production in pDCs. Although CpG-B ODN do not efficiently induce IFN-α, they are capable of highly inducing IFN-β. However, it is currently unclear what factors mediate CpG-B ODN induction of IFN-β in human pDCs. Using nuclear translocation, siRNA and proximity ligation assays, we demonstrate a requirement for both IRF-5 and NF-κB p50 in the induction of IFN-β and IL-6 by CpG-B ODN in human pDCs. The finding that CpG-B ODN activation of IRF-5 leads to IFN-β production in human pDCs may have clinical importance as IRF-5 has recently been identified as a major risk locus in systemic lupus erythematosus (SLE), a disease largely driven by aberrant type I IFN production by pDCs. Overall, this study provides new insights into the transcriptional regulation of IFN-β and IL-6 induced by CpG-B ODN in human pDCs and identifies a clinically important link between IRF-5 and IFN-β.
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Affiliation(s)
- Adelle McFarland
- 1Department of Immunology, University of Washington, Seattle, WA
| | - Folkert Steinhagen
- 2Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- 5Department for Anaesthesiology and Intensive Care Medicine, University Hospital Bonn, Bonn, Germany
| | - Luis Rodriguez
- 3Laboratory of Proteomics and Analytical Technologies, SAIC Frederick Inc., Frederick, MD
| | - Poonam Tewary
- 4Laboratory of Molecular Immunoregulation, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Abigail Jarret
- 1Department of Immunology, University of Washington, Seattle, WA
| | - Ram Savan
- 1Department of Immunology, University of Washington, Seattle, WA
| | - Dennis Klinman
- 2Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Frederick, MD
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13
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Boza JJ, Dangin M, Moënnoz D, Montigon F, Vuichoud J, Jarret A, Pouteau E, Gremaud G, Oguey-Araymon S, Courtois D, Woupeyi A, Finot PA, Ballèvre O. Free and protein-bound glutamine have identical splanchnic extraction in healthy human volunteers. Am J Physiol Gastrointest Liver Physiol 2001; 281:G267-74. [PMID: 11408280 DOI: 10.1152/ajpgi.2001.281.1.g267] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The objectives of the present study were to determine the splanchnic extraction of glutamine after ingestion of glutamine-rich protein ((15)N-labeled oat proteins) and to compare it with that of free glutamine and to determine de novo glutamine synthesis before and after glutamine consumption. Eight healthy adults were infused intravenously in the postabsorptive state with L-[1-(13)C]glutamine (3 micromol x kg(-1) x h(-1)) and L-[1-(13)C]lysine (1.5 micromol x kg(-1) x h(-1)) for 8 h. Four hours after the beginning of the infusion, subjects consumed (every 20 min) a liquid formula providing either 2.5 g of protein from (15)N-labeled oat proteins or a mixture of free amino acids that mimicked the oat-amino acid profile and contained L-[2,5-(15)N(2)]glutamine and L-[2-(15)N]lysine. Splanchnic extraction of glutamine reached 62.5 +/- 5.0% and 66.7 +/- 3.9% after administration of (15)N-labeled oat proteins and the mixture of free amino acids, respectively. Lysine splanchnic extraction was also not different (40.9 +/- 11.9% and 34.9 +/- 10.6% for (15)N-labeled oat proteins and free amino acids, respectively). The main conclusion of the present study is that glutamine is equally bioavailable when given enterally as a free amino acid and when protein bound. Therefore, and taking into consideration the drawbacks of free glutamine supplementation of ready-to-use formulas for enteral nutrition, protein sources naturally rich in this amino acid are the best option for providing stable glutamine.
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Affiliation(s)
- J J Boza
- Nestlé Research Center, Vers-Chez-Les-Blanc, 1000 Lausanne 26, Switzerland
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Schenkel-Hulliger L, Maier R, Barthe PL, Desaulles PA, Jarret A, Riniker B, Rittel W, Sieber P. Biological activity of synthetic human corticotropin with revised amino acid sequence. Acta Endocrinol (Copenh) 1974; 75:24-32. [PMID: 4363844 DOI: 10.1530/acta.0.0750024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
ABSTRACT
The corticotrophic, melanotrophic and lipolytic activity of synthetic human corticotrophin of revised structure has been evaluated and compared with that of synthetic porcine ACTH (uncorrected structure). The amino acid sequence of the two peptides differs at 3 sites in the 25 to 31 region. The two peptides exihibit identical biological activities in in vitro and in vivo test systems in the rat.
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15
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Jarret A. The pentose phosphte pathway in human and animal skin. Br J Dermatol 1971; 84:545-53. [PMID: 5557510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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