201
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Rafeld HL, Kolanus W, van Driel IR, Hartland EL. Interferon-induced GTPases orchestrate host cell-autonomous defence against bacterial pathogens. Biochem Soc Trans 2021; 49:1287-1297. [PMID: 34003245 PMCID: PMC8286824 DOI: 10.1042/bst20200900] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 01/08/2023]
Abstract
Interferon (IFN)-induced guanosine triphosphate hydrolysing enzymes (GTPases) have been identified as cornerstones of IFN-mediated cell-autonomous defence. Upon IFN stimulation, these GTPases are highly expressed in various host cells, where they orchestrate anti-microbial activities against a diverse range of pathogens such as bacteria, protozoan and viruses. IFN-induced GTPases have been shown to interact with various host pathways and proteins mediating pathogen control via inflammasome activation, destabilising pathogen compartments and membranes, orchestrating destruction via autophagy and the production of reactive oxygen species as well as inhibiting pathogen mobility. In this mini-review, we provide an update on how the IFN-induced GTPases target pathogens and mediate host defence, emphasising findings on protection against bacterial pathogens.
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Affiliation(s)
- Heike L. Rafeld
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Life and Medical Sciences Institute (LIMES), Molecular Immunology and Cell Biology, University of Bonn, Bonn, Germany
| | - Waldemar Kolanus
- Life and Medical Sciences Institute (LIMES), Molecular Immunology and Cell Biology, University of Bonn, Bonn, Germany
| | - Ian R. van Driel
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth L. Hartland
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
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202
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Martorell-Marugán J, López-Domínguez R, García-Moreno A, Toro-Domínguez D, Villatoro-García JA, Barturen G, Martín-Gómez A, Troule K, Gómez-López G, Al-Shahrour F, González-Rumayor V, Peña-Chilet M, Dopazo J, Sáez-Rodríguez J, Alarcón-Riquelme ME, Carmona-Sáez P. A comprehensive database for integrated analysis of omics data in autoimmune diseases. BMC Bioinformatics 2021; 22:343. [PMID: 34167460 PMCID: PMC8223391 DOI: 10.1186/s12859-021-04268-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 06/14/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Autoimmune diseases are heterogeneous pathologies with difficult diagnosis and few therapeutic options. In the last decade, several omics studies have provided significant insights into the molecular mechanisms of these diseases. Nevertheless, data from different cohorts and pathologies are stored independently in public repositories and a unified resource is imperative to assist researchers in this field. RESULTS Here, we present Autoimmune Diseases Explorer ( https://adex.genyo.es ), a database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most common autoimmune diseases. The database provides, in an easy-to-use environment, advanced data analysis and statistical methods for exploring omics datasets, including meta-analysis, differential expression or pathway analysis. CONCLUSIONS This is the first omics database focused on autoimmune diseases. This resource incorporates homogeneously processed data to facilitate integrative analyses among studies.
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Affiliation(s)
- Jordi Martorell-Marugán
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Atrys Health S.A., Barcelona, Spain
| | - Raúl López-Domínguez
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
| | - Adrián García-Moreno
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
| | - Daniel Toro-Domínguez
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Genetics of Complex Diseases, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
| | - Juan Antonio Villatoro-García
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Department of Statistics, University of Granada, 18071, Granada, Spain
| | - Guillermo Barturen
- Genetics of Complex Diseases, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
| | - Adoración Martín-Gómez
- Nephrology Units, AADEA: Asociación Andaluza de Enfermedades Autoinmunes, Hospital de Poniente, 04700, Almería, Spain
| | - Kevin Troule
- Bioinformatics Unit, Spanish National Cancer Center, CNIO, Madrid, Spain
| | | | - Fátima Al-Shahrour
- Bioinformatics Unit, Spanish National Cancer Center, CNIO, Madrid, Spain
| | | | - María Peña-Chilet
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocío, 41013, Seville, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Seville, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocío, 41013, Seville, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Seville, Spain
- INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, 42013, Seville, Spain
| | - Julio Sáez-Rodríguez
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, 52074, Aachen, Germany
- European Molecular Biology Laboratory-The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
- Institute for Computational Biomedicine, Bioquant Heidelberg, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, 69120, Heidelberg, Germany
| | - Marta E Alarcón-Riquelme
- Genetics of Complex Diseases, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Unit of Chronic Inflammatory Diseases, Institute of Environmental Medicine, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Pedro Carmona-Sáez
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain.
- Department of Statistics, University of Granada, 18071, Granada, Spain.
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203
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Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Becker ME, Pratt D, Churas C, Rosenthal SB, Liu S, Weston S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Curry HM, Oom AL, Miorin L, Rodriguez-Frandsen A, Zheng F, Wu C, Xiong Y, Urbanowski M, Shaw ML, Chang MW, Benner C, Hope TJ, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. Functional landscape of SARS-CoV-2 cellular restriction. Mol Cell 2021; 81:2656-2668.e8. [PMID: 33930332 PMCID: PMC8043580 DOI: 10.1016/j.molcel.2021.04.008] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/01/2021] [Accepted: 04/07/2021] [Indexed: 12/21/2022]
Abstract
A deficient interferon (IFN) response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been implicated as a determinant of severe coronavirus disease 2019 (COVID-19). To identify the molecular effectors that govern IFN control of SARS-CoV-2 infection, we conducted a large-scale gain-of-function analysis that evaluated the impact of human IFN-stimulated genes (ISGs) on viral replication. A limited subset of ISGs were found to control viral infection, including endosomal factors inhibiting viral entry, RNA binding proteins suppressing viral RNA synthesis, and a highly enriched cluster of endoplasmic reticulum (ER)/Golgi-resident ISGs inhibiting viral assembly/egress. These included broad-acting antiviral ISGs and eight ISGs that specifically inhibited SARS-CoV-2 and SARS-CoV-1 replication. Among the broad-acting ISGs was BST2/tetherin, which impeded viral release and is antagonized by SARS-CoV-2 Orf7a protein. Overall, these data illuminate a set of ISGs that underlie innate immune control of SARS-CoV-2/SARS-CoV-1 infection, which will facilitate the understanding of host determinants that impact disease severity and offer potential therapeutic strategies for COVID-19.
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Affiliation(s)
- Laura Martin-Sancho
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Mary K Lewinski
- Department of Medicine, University of California San Diego, and the VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Lars Pache
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Charlotte A Stoneham
- Department of Medicine, University of California San Diego, and the VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Xin Yin
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Mark E Becker
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Dexter Pratt
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Christopher Churas
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sara B Rosenthal
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sophie Liu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Paul D De Jesus
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Alan M O'Neill
- Department of Dermatology, University of California San Diego, La Jolla, CA 92093, USA
| | - Anshu P Gounder
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Courtney Nguyen
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Yuan Pu
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Heather M Curry
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Aaron L Oom
- Department of Medicine, University of California San Diego, and the VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA
| | - Ariel Rodriguez-Frandsen
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Fan Zheng
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Matthew Urbanowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA
| | - Megan L Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA; Department of Medical Biosciences, University of the Western Cape, Cape Town 7535, South Africa
| | - Max W Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Christopher Benner
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas J Hope
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA; The Tisch Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Judd F Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - John Guatelli
- Department of Medicine, University of California San Diego, and the VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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204
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Tecalco-Cruz AC, Macías-Silva M, Ramírez-Jarquín JO, Méndez-Ambrosio B. Identification of genes modulated by interferon gamma in breast cancer cells. Biochem Biophys Rep 2021; 27:101053. [PMID: 34189281 PMCID: PMC8220005 DOI: 10.1016/j.bbrep.2021.101053] [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: 04/16/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 11/04/2022] Open
Abstract
Interferon gamma (IFNγ) plays a context-dependent dual tumor-suppressor and pro-tumorigenic roles in cancer. IFNγ induces morphological changes in breast cancer (BC) cells with or without estrogen receptor alpha (ERα) expression. However, IFNγ-regulated genes in BC cells remain unexplored. Here, we performed a cDNA microarray analysis of MCF-7 (ERα+) and MDA-MB-231 (HER2-/PR-/ERα-) cells with and without IFNγ treatment. We identified specific IFNγ−modulated genes in each cell type, and a small group of genes regulated by IFNγ common in both cell types. IFNγ treatment for an extended time mainly repressed gene expression shared by both cell types. Nonetheless, some of these IFNγ-repressed genes were seemingly deregulated in human mammary tumor samples, along with decreased IFNGR1 (an IFNγ receptor) expression. Thus, IFNγ signaling-elicited anti-tumor activities may be mediated by the downregulation of main IFNγ target genes in BC; however, it may be deregulated by the tumor microenvironment in a tumor stage-dependent manner. Identification of new potential genes regulated by IFNγ in breast cancer cells. A small group of common genes is regulated by IFNγ in ERα- and ERα+ breast cancer cells. IFNγ treatment for a long time mainly represses gene expression in breast cancer cells. The tumor environment may lead to a decrease in IFNGR1 expression in mammary tumors.
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Affiliation(s)
- Angeles C Tecalco-Cruz
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Ciudad de México, Mexico
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205
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Vergara C, Valencia A, Thio CL, Goedert JJ, Mangia A, Piazzolla V, Johnson E, Kral AH, O’Brien TR, Mehta SH, Kirk GD, Kim AY, Lauer GM, Chung RT, Cox AL, Peters MG, Khakoo SI, Alric L, Cramp ME, Donfield SM, Edlin BR, Busch MP, Alexander G, Rosen HR, Murphy EL, Wojcik GL, Taub MA, Thomas DL, Duggal P. A Multiancestry Sex-Stratified Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus. J Infect Dis 2021; 223:2090-2098. [PMID: 33119750 PMCID: PMC8205624 DOI: 10.1093/infdis/jiaa677] [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: 07/27/2020] [Accepted: 10/28/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Spontaneous clearance of acute hepatitis C virus (HCV) infection is more common in women than in men, independent of known risk factors. METHODS To identify sex-specific genetic loci, we studied 4423 HCV-infected individuals (2903 male, 1520 female) of European, African, and Hispanic ancestry. We performed autosomal, and X chromosome sex-stratified and combined association analyses in each ancestry group. RESULTS A male-specific region near the adenosine diphosphate-ribosylation factor-like 5B (ARL5B) gene was identified. Individuals with the C allele of rs76398191 were about 30% more likely to have chronic HCV infection than individuals with the T allele (OR, 0.69; P = 1.98 × 10-07), and this was not seen in females. The ARL5B gene encodes an interferon-stimulated gene that inhibits immune response to double-stranded RNA viruses. We also identified suggestive associations near septin 6 and ribosomal protein L39 genes on the X chromosome. In box sexes, allele G of rs12852885 was associated with a 40% increase in HCV clearance compared with the A allele (OR, 1.4; P = 2.46 × 10-06). Septin 6 facilitates HCV replication via interaction with the HCV NS5b protein, and ribosomal protein L39 acts as an HCV core interactor. CONCLUSIONS These novel gene associations support differential mechanisms of HCV clearance between the sexes and provide biological targets for treatment or vaccine development.
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Affiliation(s)
- Candelaria Vergara
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
- Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alessandra Mangia
- Liver Unit IRCCS “Casa Sollievo della Sofferenza,” San Giovanni Rotondo, Italy
| | - Valeria Piazzolla
- Liver Unit IRCCS “Casa Sollievo della Sofferenza,” San Giovanni Rotondo, Italy
| | - Eric Johnson
- RTI International, Research Triangle Park, North Carolina, USA
| | - Alex H Kral
- RTI International, Research Triangle Park, North Carolina, USA
| | - Thomas R O’Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Gregory D Kirk
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea L Cox
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Marion G Peters
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, California, USA
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Laurent Alric
- Department of Internal Medicine and Digestive Diseases, CHU Rangueil, UMR 152 IRD, Toulouse 3 University, France
| | | | | | - Brian R Edlin
- SUNY Downstate College of Medicine, Brooklyn, New York, USA
| | - Michael P Busch
- University of California and Vitalant Research Institute, San Francisco, California, USA
| | - Graeme Alexander
- UCL Institute for Liver and Digestive Health, Royal Free Hospital, Hampstead, London, United Kingdom
| | | | - Edward L Murphy
- University of California and Vitalant Research Institute, San Francisco, California, USA
| | - Genevieve L Wojcik
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Margaret A Taub
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Priya Duggal
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
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206
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Hafler D, Sumida T, Dulberg S, Schupp J, Stillwell H, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A, Kuchroo V. Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells. RESEARCH SQUARE 2021:rs.3.rs-133494. [PMID: 34127967 PMCID: PMC8202434 DOI: 10.21203/rs.3.rs-133494/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
While inhibition of T cell co-inhibitory receptors has revolutionized cancer therapy, the mechanisms governing their expression on human T cells have not been elucidated. Type 1 interferon (IFN-I) modulates T cell immunity in viral infection, autoimmunity, and cancer, and may facilitate induction of T cell exhaustion in chronic viral infection. Here we show that IFN-I regulates co-inhibitory receptor expression on human T cells, inducing PD-1/TIM-3/LAG-3 while surprisingly inhibiting TIGIT expression. High-temporal-resolution mRNA profiling of IFN-I responses enabled the construction of dynamic transcriptional regulatory networks uncovering three temporal transcriptional waves. Perturbation of key transcription factors on human primary T cells revealed unique regulators that control expression of co-inhibitory receptors. We found that the dynamic IFN-I response in vitro closely mirrored T cell features with IFN-I linked acute SARS-CoV-2 infection in human, with high LAG3 and decreased TIGIT expression. Finally, our gene regulatory network identified SP140 as a key regulator for differential LAG3 and TIGIT expression, which were validated at the level of protein expression. The construction of IFN-I regulatory networks with identification of unique transcription factors controlling co-inhibitory receptor expression may provide targets for enhancement of immunotherapy in cancer, infectious diseases, and autoimmunity.
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Affiliation(s)
| | | | | | | | | | | | - Michela Comi
- Department of Immunobiology, Yale University School of Medicine; Department of Neurology, Yale University School of Medicine
| | | | - Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
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207
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Vandsemb EN, Rye MB, Steiro IJ, Elsaadi S, Rø TB, Slørdahl TS, Sponaas AM, Børset M, Abdollahi P. PRL-3 induces a positive signaling circuit between glycolysis and activation of STAT1/2. FEBS J 2021; 288:6700-6715. [PMID: 34092011 DOI: 10.1111/febs.16058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/28/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022]
Abstract
Multiple myeloma (MM) is an incurable hematologic malignancy resulting from the clonal expansion of plasma cells. MM cells are interacting with components of the bone marrow microenvironment such as cytokines to survive and proliferate. Phosphatase of regenerating liver (PRL)-3, a cytokine-induced oncogenic phosphatase, is highly expressed in myeloma patients and is a mediator of metabolic reprogramming of cancer cells. To find novel pathways and genes regulated by PRL-3, we characterized the global transcriptional response to PRL-3 overexpression in two MM cell lines. We used pathway enrichment analysis to identify pathways regulated by PRL-3. We further confirmed the hits from the enrichment analysis with in vitro experiments and investigated their function. We found that PRL-3 induced expression of genes belonging to the type 1 interferon (IFN-I) signaling pathway due to activation of signal transducer and activator of transcription (STAT) 1 and STAT2. This activation was independent of autocrine IFN-I secretion. The increase in STAT1 and STAT2 did not result in any of the common consequences of increased IFN-I or STAT1 signaling in cancer. Knockdown of STAT1/2 did not affect the viability of the cells, but decreased PRL-3-induced glycolysis. Interestingly, glucose metabolism contributed to the activation of STAT1 and STAT2 and expression of IFN-I-stimulated genes in PRL-3-overexpressing cells. In summary, we describe a novel signaling circuit where the key IFN-I-activated transcription factors STAT1 and STAT2 are important drivers of the increase in glycolysis induced by PRL-3. Subsequently, increased glycolysis regulates the IFN-I-stimulated genes by augmenting the activation of STAT1/2.
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Affiliation(s)
- Esten Nymoen Vandsemb
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Clinic of Surgery, St. Olavs University Hospital, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs University Hospital, Trondheim, Norway.,Biocore - Bioinformatics Core Facility, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ida Johnsen Steiro
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Samah Elsaadi
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs University Hospital, Trondheim, Norway
| | - Torstein Bade Rø
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Children's Clinic, St. Olavs University Hospital, Trondheim, Norway
| | - Tobias Schmidt Slørdahl
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Clinic of Medicine, St. Olavs University Hospital, Trondheim, Norway
| | - Anne-Marit Sponaas
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Magne Børset
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Immunology and Transfusion Medicine, St. Olavs University Hospital, Norway
| | - Pegah Abdollahi
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs University Hospital, Trondheim, Norway.,Clinic of Medicine, St. Olavs University Hospital, Trondheim, Norway
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López-Díez R, Egaña-Gorroño L, Senatus L, Shekhtman A, Ramasamy R, Schmidt AM. Diabetes and Cardiovascular Complications: The Epidemics Continue. Curr Cardiol Rep 2021; 23:74. [PMID: 34081211 PMCID: PMC8173334 DOI: 10.1007/s11886-021-01504-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW The cardiovascular complications of type 1 and 2 diabetes are major causes of morbidity and mortality. Extensive efforts have been made to maximize glycemic control; this strategy reduces certain manifestations of cardiovascular complications. There are drawbacks, however, as intensive glycemic control does not impart perennial protective benefits, and these efforts are not without potential adverse sequelae, such as hypoglycemic events. RECENT FINDINGS Here, the authors have focused on updates into key areas under study for mechanisms driving these cardiovascular disorders in diabetes, including roles for epigenetics and gene expression, interferon networks, and mitochondrial dysfunction. Updates on the cardioprotective roles of the new classes of hyperglycemia-targeting therapies, the sodium glucose transport protein 2 inhibitors and the agonists of the glucagon-like peptide 1 receptor system, are reviewed. In summary, insights from ongoing research and the cardioprotective benefits of the newer type 2 diabetes therapies are providing novel areas for therapeutic opportunities in diabetes and CVD.
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Affiliation(s)
- Raquel López-Díez
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, 435 East 30th Street, Science Building, Room 615, New York, NY 10016 USA
| | - Lander Egaña-Gorroño
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, 435 East 30th Street, Science Building, Room 615, New York, NY 10016 USA
| | - Laura Senatus
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, 435 East 30th Street, Science Building, Room 615, New York, NY 10016 USA
| | - Alexander Shekhtman
- Department of Chemistry, The State University of New York at Albany, Albany, NY USA
| | - Ravichandran Ramasamy
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, 435 East 30th Street, Science Building, Room 615, New York, NY 10016 USA
| | - Ann Marie Schmidt
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, 435 East 30th Street, Science Building, Room 615, New York, NY 10016 USA
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209
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Assassi S, Li N, Volkmann ER, Mayes MD, Rünger D, Ying J, Roth MD, Hinchcliff M, Khanna D, Frech T, Clements PJ, Furst DE, Goldin J, Bernstein EJ, Castelino FV, Domsic RT, Gordon JK, Hant FN, Shah AA, Shanmugam VK, Steen VD, Elashoff RM, Tashkin DP. Predictive Significance of Serum Interferon-Inducible Protein Score for Response to Treatment in Systemic Sclerosis-Related Interstitial Lung Disease. Arthritis Rheumatol 2021; 73:1005-1013. [PMID: 33350170 PMCID: PMC8169525 DOI: 10.1002/art.41627] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/15/2020] [Indexed: 01/15/2023]
Abstract
OBJECTIVE Response to immunosuppression is highly variable in systemic sclerosis (SSc)-related interstitial lung disease (ILD). This study was undertaken to determine whether a composite serum interferon (IFN)-inducible protein score exhibits predictive significance for the response to immunosuppression in SSc-ILD. METHODS Serum samples collected in the Scleroderma Lung Study II, a randomized controlled trial of mycophenolate mofetil (MMF) versus cyclophosphamide (CYC), were examined. Results were validated in an independent observational cohort receiving active treatment. A composite score of 6 IFN-inducible proteins IFNγ-inducible 10-kd protein, monokine induced by IFNγ, monocyte chemotactic protein 2, β2 -microglobulin, tumor necrosis factor receptor type II, and macrophage inflammatory protein 3β) was calculated, and its predictive significance for longitudinal forced vital capacity percent predicted measurements was evaluated. RESULTS Higher baseline IFN-inducible protein score predicted better response over 3 to 12 months in the MMF arm (point estimate = 0.41, P = 0.001) and CYC arm (point estimate = 0.91, P = 0.009). In contrast, higher baseline C-reactive protein (CRP) levels were predictive of a worse ILD course in both treatment arms. The predictive significance of the IFN-inducible protein score and CRP levels remained after adjustment for baseline demographic and clinical predictors. During the second year of treatment, in which patients in the CYC arm were switched to placebo, a higher IFN-inducible protein score at 12 months showed a trend toward predicting a worse ILD course (point estimate = -0.61, P = 0.068), while it remained predictive of better response to active immunosuppression in the MMF arm (point estimate = 0.28, P = 0.029). The predictive significance of baseline IFN-inducible protein score was replicated in the independent cohort (rs = 0.43, P = 0.028). CONCLUSION A higher IFN-inducible protein score in SSc-ILD is predictive of better response to immunosuppression and could potentially be used to identify patients who may derive the most benefit from MMF or CYC.
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Affiliation(s)
- Shervin Assassi
- Department of Medicine, Division of Rheumatology, The University of Texas Health Science Center at Houston, USA
| | - Ning Li
- Department of Internal Medicine , University of California Los Angeles, USA
| | - Elizabeth R. Volkmann
- Department of Medicine, Division of Rheumatology, University of California Los Angeles, USA
| | - Maureen D. Mayes
- Department of Medicine, Division of Rheumatology, The University of Texas Health Science Center at Houston, USA
| | - Dennis Rünger
- Department of Internal Medicine , University of California Los Angeles, USA
| | - Jun Ying
- Department of Medicine, Division of Rheumatology, The University of Texas Health Science Center at Houston, USA
| | - Michael D. Roth
- Department of Medicine, Division of Pulmonary and Critical Care, University of California Los Angeles, USA
| | | | - Dinesh Khanna
- Department of Medicine, Division of Rheumatology, University of Michigan Ann Arbor, USA
| | - Tracy Frech
- Department of Medicine, Division of Rheumatology, University of Utah, USA
| | - Philip J. Clements
- Department of Medicine, Division of Rheumatology, University of California Los Angeles, USA
| | - Daniel E. Furst
- Department of Medicine, Division of Rheumatology, University of California Los Angeles, USA
| | - Jonathan Goldin
- Department of Radiological Sciences, University of California Los Angeles, USA
| | - Elana J. Bernstein
- Department of Medicine, Division of Rheumatology, Columbia University, USA
| | - Flavia V. Castelino
- Department of Medicine, Division of Rheumatology, Massachusetts General Hospital, Harvard University, USA
| | - Robyn T. Domsic
- Department of Medicine, Division of Rheumatology, Pittsburgh University, USA
| | - Jessica K. Gordon
- Department of Medicine, Division of Rheumatology, Hospital for Special Surgery, USA
| | - Faye N. Hant
- Department of Medicine, Division of Rheumatology, Medical University of South Carolina, USA
| | - Ami A. Shah
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, USA
| | | | - Virginia D. Steen
- Department of Medicine, Division of Rheumatology, Georgetown University, USA
| | - Robert M. Elashoff
- Department of Internal Medicine , University of California Los Angeles, USA
| | - Donald P. Tashkin
- Department of Medicine, Division of Pulmonary and Critical Care, University of California Los Angeles, USA
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210
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Komov L, Melamed Kadosh D, Barnea E, Admon A. The Effect of Interferons on Presentation of Defective Ribosomal Products as HLA Peptides. Mol Cell Proteomics 2021; 20:100105. [PMID: 34087483 PMCID: PMC8724922 DOI: 10.1016/j.mcpro.2021.100105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/15/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
A subset of class I major histocompatibility complex (MHC)-bound peptides is produced from immature proteins that are rapidly degraded after synthesis. These defective ribosomal products (DRiPs) have been implicated in early alert of the immune system about impending infections. Interferons are important cytokines, produced in response to viral infection, that modulate cellular metabolism and gene expression patterns, increase the presentation of MHC molecules, and induce rapid degradation of proteins and cell-surface presentation of their derived MHC peptides, thereby contributing to the battle against pathogen infections. This study evaluated the role of interferons in the induction of rapid degradation of DRiPs to modulate the repertoire of DRiP-derived MHC peptides. Cultured human breast cancer cells were treated with interferons, and the rates of synthesis and degradation of cellular protein and their degradation products were determined by LC-MS/MS analysis, following the rates of incorporation of heavy stable isotope–labeled amino acids (dynamic stable isotope labeling by amino acids in cell culture, dynamic SILAC) at several time points after the interferon application. Large numbers of MHC peptides that incorporated the heavy amino acids faster than their source proteins indicated that DRiP peptides were abundant in the MHC peptidome; interferon treatment increased by about twofold their relative proportions in the peptidome. Such typical DRiP-derived MHC peptides were from the surplus subunits of the proteasome and ribosome, which are degraded because of the transition to immunoproteasomes and a new composition of ribosomes incorporating protein subunits that are induced by the interferon. We conclude that degradation of surplus subunits induced by the interferon is a major source for DRiP–MHC peptides, a phenomenon relevant to coping with viral infections, where a rapid presentation of MHC peptides derived from excess viral proteins may help alert the immune system about the impending infection. Degradation products of surplus subunits are often presented as HLA peptides. Interferons increase degradation and presentation of such defective products. Dynamic SILAC facilitates identification of such HLA peptides. This cellular pathway provides alert to the immune system about viral infections.
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Affiliation(s)
- Liran Komov
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Eilon Barnea
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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211
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Nodari A, Scambi I, Peroni D, Calabria E, Benati D, Mannucci S, Manfredi M, Frontini A, Visonà S, Bozzato A, Sbarbati A, Schena F, Marengo E, Krampera M, Galiè M. Interferon regulatory factor 7 impairs cellular metabolism in aging adipose-derived stromal cells. J Cell Sci 2021; 134:jcs256230. [PMID: 34096605 DOI: 10.1242/jcs.256230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/26/2021] [Indexed: 11/20/2022] Open
Abstract
Dysregulated immunity and widespread metabolic dysfunctions are the most relevant hallmarks of the passing of time over the course of adult life, and their combination at midlife is strongly related to increased vulnerability to diseases; however, the causal connection between them remains largely unclear. By combining multi-omics and functional analyses of adipose-derived stromal cells established from young (1 month) and midlife (12 months) mice, we show that an increase in expression of interferon regulatory factor 7 (IRF7) during adult life drives major metabolic changes, which include impaired mitochondrial function, altered amino acid biogenesis and reduced expression of genes involved in branched-chain amino acid (BCAA) degradation. Our results draw a new paradigm of aging as the 'sterile' activation of a cell-autonomous pathway of self-defense and identify a crucial mediator of this pathway, IRF7, as driver of metabolic dysfunction with age.
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Affiliation(s)
- Alice Nodari
- Department of Neuroscience, Biomedicine and Movement, Section of Anatomy and Histology, University of Verona, 37134 Verona, Italy
| | - Ilaria Scambi
- Department of Neuroscience, Biomedicine and Movement, Section of Anatomy and Histology, University of Verona, 37134 Verona, Italy
| | - Daniele Peroni
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Elisa Calabria
- Department of Neuroscience, Biomedicine and Movement, Section of Anatomy and Histology, University of Verona, 37134 Verona, Italy
| | - Donatella Benati
- Department of Neuroscience, Biomedicine and Movement, Section of Anatomy and Histology, University of Verona, 37134 Verona, Italy
| | - Silvia Mannucci
- Department of Neuroscience, Biomedicine and Movement, Section of Anatomy and Histology, University of Verona, 37134 Verona, Italy
| | - Marcello Manfredi
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, 28100 Alessandria, Italy
- Center for Translational Research on Autoimmune and Allergic Disease - CAAD, University of Piemonte Orientale, 28100 Novara, Italy
| | - Andrea Frontini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 20121 Ancona, Italy
| | - Silvia Visonà
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Andrea Bozzato
- Department of Biomedical Sciences and Biotechnology, University of Brescia, 25123 Brescia, Italy
| | - Andrea Sbarbati
- Department of Neuroscience, Biomedicine and Movement, Section of Anatomy and Histology, University of Verona, 37134 Verona, Italy
| | - Federico Schena
- Department of Neuroscience, Biomedicine and Movement, Section of Anatomy and Histology, University of Verona, 37134 Verona, Italy
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, 28100 Alessandria, Italy
- Center for Translational Research on Autoimmune and Allergic Disease - CAAD, University of Piemonte Orientale, 28100 Novara, Italy
| | - Mauro Krampera
- Department of Medicine, Section of Hematology, Stem Cell Research Laboratory, University of Verona, 37134 Verona, Italy
| | - Mirco Galiè
- Department of Neuroscience, Biomedicine and Movement, Section of Anatomy and Histology, University of Verona, 37134 Verona, Italy
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212
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Freire PP, Marques AH, Baiocchi GC, Schimke LF, Fonseca DL, Salgado RC, Filgueiras IS, Napoleao SM, Plaça DR, Akashi KT, Hirata TDC, El Khawanky N, Giil LM, Cabral-Miranda G, Carvalho RF, Ferreira LCS, Condino-Neto A, Nakaya HI, Jurisica I, Ochs HD, Camara NOS, Calich VLG, Cabral-Marques O. The relationship between cytokine and neutrophil gene network distinguishes SARS-CoV-2-infected patients by sex and age. JCI Insight 2021; 6:147535. [PMID: 34027897 PMCID: PMC8262322 DOI: 10.1172/jci.insight.147535] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/07/2021] [Indexed: 01/11/2023] Open
Abstract
The fact that the COVID-19 fatality rate varies by sex and age is poorly understood. Notably, the outcome of SARS-CoV-2 infections mostly depends on the control of cytokine storm and the increasingly recognized pathological role of uncontrolled neutrophil activation. Here, we used an integrative approach with publicly available RNA-Seq data sets of nasopharyngeal swabs and peripheral blood leukocytes from patients with SARS-CoV-2, according to sex and age. Female and young patients infected by SARS-CoV-2 exhibited a larger number of differentially expressed genes (DEGs) compared with male and elderly patients, indicating a stronger immune modulation. Among them, we found an association between upregulated cytokine/chemokine- and downregulated neutrophil-related DEGs. This was correlated with a closer relationship between female and young subjects, while the relationship between male and elderly patients was closer still. The association between these cytokine/chemokines and neutrophil DEGs is marked by a strongly correlated interferome network. Here, female patients exhibited reduced transcriptional levels of key proinflammatory/neutrophil-related genes, such as CXCL8 receptors (CXCR1 and CXCR2), IL-1β, S100A9, ITGAM, and DBNL, compared with male patients. These genes are well known to be protective against inflammatory damage. Therefore, our work suggests specific immune-regulatory pathways associated with sex and age of patients infected with SARS-CoV-2 and provides a possible association between inverse modulation of cytokine/chemokine and neutrophil transcriptional signatures.
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Affiliation(s)
- Paula P Freire
- Department of Immunology, Institute of Biomedical Sciences, and
| | | | | | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, and
| | | | | | | | | | - Desirée R Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Karen T Akashi
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thiago Dominguez Crespo Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nadia El Khawanky
- Department of Hematology and Oncology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lasse M Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | | | - Robson F Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, São Paulo
| | - Luis Carlos S Ferreira
- Vaccine Development Laboratory, Institute of Biomedical Sciences, Department of Microbiology, University of São Paulo, São Paulo, Brazil
| | | | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, and Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, Washington
| | | | | | - Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, and.,Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Network of Immunity in Infection, Malignancy, and Autoimmunity, Universal Scientific Education and Research Network, São Paulo, Brazil
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213
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Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, Tang Z, Pope SD, Song E, Vogels CBF, Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF. Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface. MED 2021; 2:591-610.e10. [PMID: 33969332 PMCID: PMC8084634 DOI: 10.1016/j.medj.2021.04.016] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Pregnant women are at increased risk for severe outcomes from coronavirus disease 2019 (COVID-19), but the pathophysiology underlying this increased morbidity and its potential effect on the developing fetus is not well understood. METHODS We assessed placental histology, ACE2 expression, and viral and immune dynamics at the term placenta in pregnant women with and without respiratory severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. FINDINGS The majority (13 of 15) of placentas analyzed had no detectable viral RNA. ACE2 was detected by immunohistochemistry in syncytiotrophoblast cells of the normal placenta during early pregnancy but was rarely seen in healthy placentas at full term, suggesting that low ACE2 expression may protect the term placenta from viral infection. Using immortalized cell lines and primary isolated placental cells, we found that cytotrophoblasts, the trophoblast stem cells and precursors to syncytiotrophoblasts, rather than syncytiotrophoblasts or Hofbauer cells, are most vulnerable to SARS-CoV-2 infection in vitro. To better understand potential immune mechanisms shielding placental cells from infection in vivo, we performed bulk and single-cell transcriptomics analyses and found that the maternal-fetal interface of SARS-CoV-2-infected women exhibited robust immune responses, including increased activation of natural killer (NK) and T cells, increased expression of interferon-related genes, as well as markers associated with pregnancy complications such as preeclampsia. CONCLUSIONS SARS-CoV-2 infection in late pregnancy is associated with immune activation at the maternal-fetal interface even in the absence of detectable local viral invasion. FUNDING NIH (T32GM007205, F30HD093350, K23MH118999, R01AI157488, U01DA040588) and Fast Grant funding support from Emergent Ventures at the Mercatus Center.
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Affiliation(s)
- Alice Lu-Culligan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Arun R Chavan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Pavithra Vijayakumar
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Lina Irshaid
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Edward M Courchaine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Kristin M Milano
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Zhonghua Tang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Scott D Pope
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - William J Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Katherine H Campbell
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Santos Bermejo
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jessica M Toothaker
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hannah J Lee
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - John Fournier
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Adam J Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Liza Konnikova
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Raffaella Morotti
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Seth Guller
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Harvey J Kliman
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Shelli F Farhadian
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
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214
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STAT1 gain-of-function heterozygous cell models reveal diverse interferon-signature gene transcriptional responses. NPJ Genom Med 2021; 6:34. [PMID: 33990617 PMCID: PMC8121859 DOI: 10.1038/s41525-021-00196-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/05/2021] [Indexed: 12/12/2022] Open
Abstract
Signal transducer and activator of transcription 1 (STAT1) gain-of-function (GOF) is an autosomal dominant immune disorder marked by wide infectious predisposition, autoimmunity, vascular disease, and malignancy. Its molecular hallmark, elevated phospho-STAT1 (pSTAT1) following interferon (IFN) stimulation, is seen consistently in all patients and may not fully account for the broad phenotypic spectrum associated with this disorder. While over 100 mutations have been implicated in STAT1 GOF, genotype-phenotype correlation remains limited, and current overexpression models may be of limited use in gene expression studies. We generated heterozygous mutants in diploid HAP1 cells using CRISPR/Cas9 base-editing, targeting the endogenous STAT1 gene. Our models recapitulated the molecular phenotype of elevated pSTAT1, and were used to characterize the expression of five IFN-stimulated genes under a number of conditions. At baseline, transcriptional polarization was evident among mutants compared with wild type, and this was maintained following prolonged serum starvation. This suggests a possible role for unphosphorylated STAT1 in the pathogenesis of STAT1 GOF. Following stimulation with IFNα or IFNγ, differential patterns of gene expression emerged among mutants, including both gain and loss of transcriptional function. This work highlights the importance of modeling heterozygous conditions, and in particular transcription factor-related disorders, in a manner which accurately reflects patient genotype and molecular signature. Furthermore, we propose a complex and multifactorial transcriptional profile associated with various STAT1 mutations, adding to global efforts in establishing STAT1 GOF genotype-phenotype correlation and enhancing our understanding of disease pathogenesis.
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215
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Diaz-San Segundo F, Medina GN, Azzinaro P, Gutkoska J, Mogulothu A, Attreed SE, Lombardi KR, Shields J, Hudock TA, de Los Santos T. Use of Protein Pegylation to Prolong the Antiviral Effect of IFN Against FMDV. Front Microbiol 2021; 12:668890. [PMID: 34025625 PMCID: PMC8131870 DOI: 10.3389/fmicb.2021.668890] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/09/2021] [Indexed: 12/12/2022] Open
Abstract
Interferons (IFNs) are considered the first line of defense against viral diseases. Due to their ability to modulate immune responses, they have become an attractive therapeutic option to control virus infections. In fact, like many other viruses, foot-and-mouth disease virus (FMDV), the most contagious pathogen of cloven-hoofed animals, is highly sensitive to the action of IFNs. Previous studies demonstrated that type I, II, and III IFNs, expressed using a replication defective human adenovirus 5 (Ad5) vector, can effectively block FMDV replication in vitro and can protect animals when challenged 1 day after Ad5-IFN treatment, in some cases providing sterile immunity. Rapidly spreading foot-and-mouth disease (FMD) is currently controlled with vaccination, although development of a protective adaptive immune response takes 5–7 days. Therefore, an optimal strategy to control FMD outbreaks is to block virus replication and spread through sustained IFN activity while the vaccine-stimulated adaptive immune response is developed. Challenges with methods of delivery and/or with the relative short IFN protein half-life in vivo, have halted the development of such approach to effectively control FMD in the animal host. One strategy to chemically improve drug pharmacodynamics is the use of pegylation. In this proof-of-concept study, we demonstrate that pegylated recombinant porcine (po)IFNα displays strong and long-lasting antiviral activity against FMDV in vitro and in vivo, completely protecting swine against FMD for at least five days after a single dose. These results highlight the potential of this biotherapeutics to use in combination with vaccines to fully control FMD in the field.
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Affiliation(s)
| | - Gisselle N Medina
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY, United States.,Kansas State University College of Veterinary Medicine, Manhattan, KS, United States
| | - Paul Azzinaro
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY, United States
| | - Joseph Gutkoska
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY, United States
| | - Aishwarya Mogulothu
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY, United States.,Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, United States
| | - Sarah E Attreed
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY, United States.,ORISE-PIADC Research Participation Program, Oak Ridge, TN, United States
| | | | - Jacob Shields
- Elanco Animal Health, Inc., Greenfield, IN, United States
| | | | - Teresa de Los Santos
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY, United States
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216
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Wigle TJ, Ren Y, Molina JR, Blackwell DJ, Schenkel LB, Swinger KK, Kuplast-Barr K, Majer CR, Church WD, Lu AZ, Mo J, Abo R, Cheung A, Dorsey BW, Niepel M, Perl NR, Vasbinder MM, Keilhack H, Kuntz KW. Targeted Degradation of PARP14 Using a Heterobifunctional Small Molecule. Chembiochem 2021; 22:2107-2110. [PMID: 33838082 DOI: 10.1002/cbic.202100047] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/07/2021] [Indexed: 01/07/2023]
Abstract
PARP14 is an interferon-stimulated gene that is overexpressed in multiple tumor types, influencing pro-tumor macrophage polarization as well as suppressing the antitumor inflammation response by modulating IFN-γ and IL-4 signaling. PARP14 is a 203 kDa protein that possesses a catalytic domain responsible for the transfer of mono-ADP-ribose to its substrates. PARP14 also contains three macrodomains and a WWE domain which are binding modules for mono-ADP-ribose and poly-ADP-ribose, respectively, in addition to two RNA recognition motifs. Catalytic inhibitors of PARP14 have been shown to reverse IL-4 driven pro-tumor gene expression in macrophages, however it is not clear what roles the non-enzymatic biomolecular recognition motifs play in PARP14-driven immunology and inflammation. To further understand this, we have discovered a heterobifunctional small molecule designed based on a catalytic inhibitor of PARP14 that binds in the enzyme's NAD+ -binding site and recruits cereblon to ubiquitinate it and selectively target it for degradation.
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Affiliation(s)
- Tim J Wigle
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Yue Ren
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Jennifer R Molina
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | | | - Laurie B Schenkel
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Kerren K Swinger
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Kristy Kuplast-Barr
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Christina R Majer
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - W David Church
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Alvin Z Lu
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Jason Mo
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Ryan Abo
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Anne Cheung
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Bryan W Dorsey
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Mario Niepel
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Nicholas R Perl
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Melissa M Vasbinder
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Heike Keilhack
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
| | - Kevin W Kuntz
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA
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217
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Kveštak D, Juranić Lisnić V, Lisnić B, Tomac J, Golemac M, Brizić I, Indenbirken D, Cokarić Brdovčak M, Bernardini G, Krstanović F, Rožmanić C, Grundhoff A, Krmpotić A, Britt WJ, Jonjić S. NK/ILC1 cells mediate neuroinflammation and brain pathology following congenital CMV infection. J Exp Med 2021; 218:e20201503. [PMID: 33630019 PMCID: PMC7918636 DOI: 10.1084/jem.20201503] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/11/2020] [Accepted: 01/29/2021] [Indexed: 12/31/2022] Open
Abstract
Congenital human cytomegalovirus (cHCMV) infection of the brain is associated with a wide range of neurocognitive sequelae. Using infection of newborn mice with mouse cytomegalovirus (MCMV) as a reliable model that recapitulates many aspects of cHCMV infection, including disseminated infection, CNS infection, altered neurodevelopment, and sensorineural hearing loss, we have previously shown that mitigation of inflammation prevented alterations in cerebellar development, suggesting that host inflammatory factors are key drivers of neurodevelopmental defects. Here, we show that MCMV infection causes a dramatic increase in the expression of the microglia-derived chemokines CXCL9/CXCL10, which recruit NK and ILC1 cells into the brain in a CXCR3-dependent manner. Surprisingly, brain-infiltrating innate immune cells not only were unable to control virus infection in the brain but also orchestrated pathological inflammatory responses, which lead to delays in cerebellar morphogenesis. Our results identify NK and ILC1 cells as the major mediators of immunopathology in response to virus infection in the developing CNS, which can be prevented by anti-IFN-γ antibodies.
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MESH Headings
- Animals
- Animals, Newborn
- Brain/immunology
- Brain/pathology
- Brain/virology
- Chemokine CXCL10/genetics
- Chemokine CXCL10/immunology
- Chemokine CXCL10/metabolism
- Chemokine CXCL9/genetics
- Chemokine CXCL9/immunology
- Chemokine CXCL9/metabolism
- Cytomegalovirus/immunology
- Cytomegalovirus/physiology
- Cytomegalovirus Infections/immunology
- Cytomegalovirus Infections/virology
- Gene Expression Regulation/immunology
- Humans
- Immunity, Innate/immunology
- Inflammation/genetics
- Inflammation/immunology
- Inflammation/virology
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lymphocytes/immunology
- Lymphocytes/metabolism
- Mice, 129 Strain
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Knockout
- Microglia/immunology
- Microglia/metabolism
- Microglia/virology
- Receptors, CXCR3/genetics
- Receptors, CXCR3/immunology
- Receptors, CXCR3/metabolism
- Mice
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Affiliation(s)
- Daria Kveštak
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Vanda Juranić Lisnić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Berislav Lisnić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Jelena Tomac
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Mijo Golemac
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ilija Brizić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Giovanni Bernardini
- Department of Molecular Medicine, Faculty of Pharmacy and Medicine, University of Rome “Sapienza”, Rome, Italy
| | - Fran Krstanović
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Carmen Rožmanić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Astrid Krmpotić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - William J. Britt
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Stipan Jonjić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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218
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Rothamel K, Arcos S, Kim B, Reasoner C, Lisy S, Mukherjee N, Ascano M. ELAVL1 primarily couples mRNA stability with the 3' UTRs of interferon-stimulated genes. Cell Rep 2021; 35:109178. [PMID: 34038724 PMCID: PMC8225249 DOI: 10.1016/j.celrep.2021.109178] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/13/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
Upon pathogen detection, the innate immune system triggers signaling events leading to upregulation of pro-inflammatory and anti-microbial mRNA transcripts. RNA-binding proteins (RBPs) interact with these critical mRNAs and regulate their fates at the post-transcriptional level. One such RBP is ELAVL1. Although significant progress has been made in understanding how embryonic lethal vision-like protein 1 (ELAVL1) regulates mRNAs, its target repertoire and binding distribution within an immunological context remain poorly understood. We overlap four high-throughput approaches to define its context-dependent targets and determine its regulatory impact during immune activation. ELAVL1 transitions from binding overwhelmingly intronic sites to 3′ UTR sites upon immune stimulation of cells, binding previously and newly expressed mRNAs. We find that ELAVL1 mediates the RNA stability of genes that regulate pathways essential to pathogen sensing and cytokine production. Our findings reveal the importance of examining RBP regulatory impact under dynamic transcriptomic events to understand their post-transcriptional regulatory roles within specific biological circuitries. Rothamel et al. show that upon immune activation, the RNA-binding protein ELAVL1 accumulates in the cytoplasm and redistributes from introns to mRNA 3′ UTRs. 3′ UTR binding confers enrichment and transcript stability. Many top-ranking transcripts are interferon-stimulated genes (ISGs), indicating that ELAVL1 is a positive regulator of an innate immune response.
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Affiliation(s)
- Katherine Rothamel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Sarah Arcos
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Byungil Kim
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Clara Reasoner
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Samantha Lisy
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Manuel Ascano
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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219
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Sprenger HG, MacVicar T, Bahat A, Fiedler KU, Hermans S, Ehrentraut D, Ried K, Milenkovic D, Bonekamp N, Larsson NG, Nolte H, Giavalisco P, Langer T. Cellular pyrimidine imbalance triggers mitochondrial DNA-dependent innate immunity. Nat Metab 2021; 3:636-650. [PMID: 33903774 PMCID: PMC8144018 DOI: 10.1038/s42255-021-00385-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022]
Abstract
Cytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. Here, we show that mtDNA-dependent immune signalling via the cyclic GMP-AMP synthase‒stimulator of interferon genes‒TANK-binding kinase 1 (cGAS-STING-TBK1) pathway is under metabolic control and is induced by cellular pyrimidine deficiency. The mitochondrial protease YME1L preserves pyrimidine pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC25A33. Deficiency of YME1L causes inflammation in mouse retinas and in cultured cells. It drives the release of mtDNA and a cGAS-STING-TBK1-dependent inflammatory response, which requires SLC25A33 and is suppressed upon replenishment of cellular pyrimidine pools. Overexpression of SLC25A33 is sufficient to induce immune signalling by mtDNA. Similarly, depletion of cytosolic nucleotides upon inhibition of de novo pyrimidine synthesis triggers mtDNA-dependent immune responses in wild-type cells. Our results thus identify mtDNA release and innate immune signalling as a metabolic response to cellular pyrimidine deficiencies.
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Affiliation(s)
- Hans-Georg Sprenger
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thomas MacVicar
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Amir Bahat
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Kai Uwe Fiedler
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Steffen Hermans
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Katharina Ried
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Nina Bonekamp
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nils-Göran Larsson
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Thomas Langer
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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220
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Mori T, Kataoka H, Into T. Effect of Myd88 deficiency on gene expression profiling in salivary glands of female non-obese diabetic (NOD) mice. J Oral Biosci 2021; 63:192-198. [PMID: 33933610 DOI: 10.1016/j.job.2021.04.003] [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: 03/23/2021] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES Sjögren's syndrome (SS) is a chronic autoimmune disease characterized by inflammatory lesions in the salivary and lacrimal glands, which are caused by distinct lymphocytic infiltrates. Female non-obese diabetic (NOD) mice spontaneously develop inflammatory lesions of the salivary glands with SS-like pathological features. Previous studies have shown that MyD88, a crucial adaptor protein that activates innate immune signaling, affects lymphocytic infiltration, but its detailed role remains unclear. In this study, we investigated the role of MyD88 through gene expression profiling in the early phase of pathogenesis in the salivary glands of female NOD mice. METHODS Submandibular glands collected from 10-week-old female wild-type and Myd88-deficient NOD mice were used for RNA preparation, followed by microarray analysis. The microarray dataset was analyzed to identify Myd88-dependent differentially expressed genes (DEGs). Data generated were used for GO enrichment, KEGG pathway, STRING database, and INTERFEROME database analyses. RESULTS Myd88 deficiency was found to affect 230 DEGs, including SS-associated genes, such as Cxcl9 and Bpifa2. Most of the DEGs were identified as being involved in immunological processes. KEGG pathway analysis indicated that the DEGs were putatively involved in autoimmune diseases, such as systemic lupus erythematosus and rheumatoid arthritis. Furthermore, the DEGs included 149 interferon (IFN)-regulated genes. CONCLUSIONS MyD88 is involved in the expression of specific genes associated with IFN-associated immunopathological processes in the salivary glands of NOD mice. Our findings are important for understanding the role of MyD88-dependent innate immune signaling in SS manifestation.
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Affiliation(s)
- Taiki Mori
- Department of Oral Microbiology, Division of Oral Infection Health Sciences, Asahi University School of Dentistry, 1851 Hozumi, Mizuho, Gifu, 501-0296, Japan
| | - Hideo Kataoka
- Department of Oral Microbiology, Division of Oral Infection Health Sciences, Asahi University School of Dentistry, 1851 Hozumi, Mizuho, Gifu, 501-0296, Japan
| | - Takeshi Into
- Department of Oral Microbiology, Division of Oral Infection Health Sciences, Asahi University School of Dentistry, 1851 Hozumi, Mizuho, Gifu, 501-0296, Japan.
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221
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Stearrett N, Dawson T, Rahnavard A, Bachali P, Bendall ML, Zeng C, Caricchio R, Pérez-Losada M, Grammer AC, Lipsky PE, Crandall KA. Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression. Front Immunol 2021; 12:661437. [PMID: 33986751 PMCID: PMC8112243 DOI: 10.3389/fimmu.2021.661437] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/12/2021] [Indexed: 11/20/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by the production of autoantibodies predominantly to nuclear material. Many aspects of disease pathology are mediated by the deposition of nucleic acid containing immune complexes, which also induce the type 1interferon response, a characteristic feature of SLE. Notably, SLE is remarkably heterogeneous, with a variety of organs involved in different individuals, who also show variation in disease severity related to their ancestries. Here, we probed one potential contribution to disease heterogeneity as well as a possible source of immunoreactive nucleic acids by exploring the expression of human endogenous retroviruses (HERVs). We investigated the expression of HERVs in SLE and their potential relationship to SLE features and the expression of biochemical pathways, including the interferon gene signature (IGS). Towards this goal, we analyzed available and new RNA-Seq data from two independent whole blood studies using Telescope. We identified 481 locus specific HERV encoding regions that are differentially expressed between case and control individuals with only 14% overlap of differentially expressed HERVs between these two datasets. We identified significant differences between differentially expressed HERVs and non-differentially expressed HERVs between the two datasets. We also characterized the host differentially expressed genes and tested their association with the differentially expressed HERVs. We found that differentially expressed HERVs were significantly more physically proximal to host differentially expressed genes than non-differentially expressed HERVs. Finally, we capitalized on locus specific resolution of HERV mapping to identify key molecular pathways impacted by differential HERV expression in people with SLE.
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Affiliation(s)
- Nathaniel Stearrett
- Computational Biology Institute, George Washington University, Washington, DC, United States
| | - Tyson Dawson
- Computational Biology Institute, George Washington University, Washington, DC, United States
| | - Ali Rahnavard
- Computational Biology Institute, George Washington University, Washington, DC, United States
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Prathyusha Bachali
- RILITE Research Institute and AMPEL BioSolutions, Charlottesville, VA, United States
| | - Matthew L. Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Chen Zeng
- Department of Physics, The George Washington University, Washington, DC, United States
| | - Roberto Caricchio
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Marcos Pérez-Losada
- Computational Biology Institute, George Washington University, Washington, DC, United States
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Amrie C. Grammer
- RILITE Research Institute and AMPEL BioSolutions, Charlottesville, VA, United States
| | - Peter E. Lipsky
- RILITE Research Institute and AMPEL BioSolutions, Charlottesville, VA, United States
| | - Keith A. Crandall
- Computational Biology Institute, George Washington University, Washington, DC, United States
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
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222
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Judd EN, Gilchrist AR, Meyerson NR, Sawyer SL. Positive natural selection in primate genes of the type I interferon response. BMC Ecol Evol 2021; 21:65. [PMID: 33902453 PMCID: PMC8074226 DOI: 10.1186/s12862-021-01783-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/29/2021] [Indexed: 12/28/2022] Open
Abstract
Background The Type I interferon response is an important first-line defense against viruses. In turn, viruses antagonize (i.e., degrade, mis-localize, etc.) many proteins in interferon pathways. Thus, hosts and viruses are locked in an evolutionary arms race for dominance of the Type I interferon pathway. As a result, many genes in interferon pathways have experienced positive natural selection in favor of new allelic forms that can better recognize viruses or escape viral antagonists. Here, we performed a holistic analysis of selective pressures acting on genes in the Type I interferon family. We initially hypothesized that the genes responsible for inducing the production of interferon would be antagonized more heavily by viruses than genes that are turned on as a result of interferon. Our logic was that viruses would have greater effect if they worked upstream of the production of interferon molecules because, once interferon is produced, hundreds of interferon-stimulated proteins would activate and the virus would need to counteract them one-by-one.
Results We curated multiple sequence alignments of primate orthologs for 131 genes active in interferon production and signaling (herein, “induction” genes), 100 interferon-stimulated genes, and 100 randomly chosen genes. We analyzed each multiple sequence alignment for the signatures of recurrent positive selection. Counter to our hypothesis, we found the interferon-stimulated genes, and not interferon induction genes, are evolving significantly more rapidly than a random set of genes. Interferon induction genes evolve in a way that is indistinguishable from a matched set of random genes (22% and 18% of genes bear signatures of positive selection, respectively). In contrast, interferon-stimulated genes evolve differently, with 33% of genes evolving under positive selection and containing a significantly higher fraction of codons that have experienced selection for recurrent replacement of the encoded amino acid. Conclusion Viruses may antagonize individual products of the interferon response more often than trying to neutralize the system altogether.
Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01783-z.
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Affiliation(s)
- Elena N Judd
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA
| | - Alison R Gilchrist
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA
| | - Nicholas R Meyerson
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA
| | - Sara L Sawyer
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA.
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223
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Ryan FJ, Carr JM, Furtado JM, Ma Y, Ashander LM, Simões M, Oliver GF, Granado GB, Dawson AC, Michael MZ, Appukuttan B, Lynn DJ, Smith JR. Zika Virus Infection of Human Iris Pigment Epithelial Cells. Front Immunol 2021; 12:644153. [PMID: 33968035 PMCID: PMC8100333 DOI: 10.3389/fimmu.2021.644153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
During recent Zika epidemics, adults infected with Zika virus (ZIKV) have developed organ-specific inflammatory complications. The most serious Zika-associated inflammatory eye disease is uveitis, which is commonly anterior in type, affecting both eyes and responding to corticosteroid eye drops. Mechanisms of Zika-associated anterior uveitis are unknown, but ZIKV has been identified in the aqueous humor of affected individuals. The iris pigment epithelium is a target cell population in viral anterior uveitis, and it acts to maintain immune privilege within the anterior eye. Interactions between ZIKV and human iris pigment epithelial cells were investigated with infectivity assays and RNA-sequencing. Primary cell isolates were prepared from eyes of 20 cadaveric donors, and infected for 24 hours with PRVABC59 strain ZIKV or incubated uninfected as control. Cytoimmunofluorescence, RT-qPCR on total cellular RNA, and focus-forming assays of culture supernatant showed cell isolates were permissive to infection, and supported replication and release of infectious ZIKV. To explore molecular responses of cell isolates to ZIKV infection at the whole transcriptome level, RNA was sequenced on the Illumina NextSeq 500 platform, and results were aligned to the human GRCh38 genome. Multidimensional scaling showed clear separation between transcriptomes of infected and uninfected cell isolates. Differential expression analysis indicated a vigorous molecular response of the cell to ZIKV: 7,935 genes were differentially expressed between ZIKV-infected and uninfected cells (FDR < 0.05), and 99% of 613 genes that changed at least two-fold were up-regulated. Reactome and KEGG pathway and Gene Ontology enrichment analyses indicated strong activation of viral recognition and defense, in addition to biosynthesis processes. A CHAT network included 6275 molecular nodes and 24 contextual hubs in the cell response to ZIKV infection. Receptor-interacting serine/threonine kinase 1 (RIPK1) was the most significantly connected contextual hub. Correlation of gene expression with read counts assigned to the ZIKV genome identified a negative correlation between interferon signaling and viral load across isolates. This work represents the first investigation of mechanisms of Zika-associated anterior uveitis using an in vitro human cell model. The results suggest the iris pigment epithelium mounts a molecular response that limits intraocular pathology in most individuals.
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Affiliation(s)
- Feargal J Ryan
- Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
| | - Jillian M Carr
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - João M Furtado
- Ophthalmology Division, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Yuefang Ma
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Liam M Ashander
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Milena Simões
- Ophthalmology Division, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Genevieve F Oliver
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - G Bracho Granado
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Abby C Dawson
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Michael Z Michael
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Binoy Appukuttan
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - David J Lynn
- Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Justine R Smith
- Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
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Padariya M, Sznarkowska A, Kote S, Gómez-Herranz M, Mikac S, Pilch M, Alfaro J, Fahraeus R, Hupp T, Kalathiya U. Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes. Biomolecules 2021; 11:622. [PMID: 33922087 PMCID: PMC8143464 DOI: 10.3390/biom11050622] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Interferon (IFN)-related DNA damage resistant signature (IRDS) genes are a subgroup of interferon-stimulated genes (ISGs) found upregulated in different cancer types, which promotes resistance to DNA damaging chemotherapy and radiotherapy. Along with briefly discussing IFNs and signalling in this review, we highlighted how different IRDS genes are affected by viruses. On the contrary, different strategies adopted to suppress a set of IRDS genes (STAT1, IRF7, OAS family, and BST2) to induce (chemo- and radiotherapy) sensitivity were deliberated. Significant biological pathways that comprise these genes were classified, along with their frequently associated genes (IFIT1/3, IFITM1, IRF7, ISG15, MX1/2 and OAS1/3/L). Major upstream regulators from the IRDS genes were identified, and different IFN types regulating these genes were outlined. Functional interfaces of IRDS proteins with DNA/RNA/ATP/GTP/NADP biomolecules featured a well-defined pharmacophore model for STAT1/IRF7-dsDNA and OAS1/OAS3/IFIH1-dsRNA complexes, as well as for the genes binding to GDP or NADP+. The Lys amino acid was found commonly interacting with the ATP phosphate group from OAS1/EIF2AK2/IFIH1 genes. Considering the premise that targeting IRDS genes mediated resistance offers an efficient strategy to resensitize tumour cells and enhances the outcome of anti-cancer treatment, this review can add some novel insights to the field.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Alicja Sznarkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Maria Gómez-Herranz
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Sara Mikac
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Magdalena Pilch
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Javier Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- Department of Medical Biosciences, Building 6M, Umeå University, 901 85 Umeå, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zlutykopec 7, 65653 Brno, Czech Republic
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
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225
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Wilmes S, Jeffrey PA, Martinez-Fabregas J, Hafer M, Fyfe PK, Pohler E, Gaggero S, López-García M, Lythe G, Taylor C, Guerrier T, Launay D, Mitra S, Piehler J, Molina-París C, Moraga I. Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses. eLife 2021; 10:66014. [PMID: 33871355 PMCID: PMC8099432 DOI: 10.7554/elife.66014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/18/2021] [Indexed: 12/29/2022] Open
Abstract
Cytokines elicit pleiotropic and non-redundant activities despite strong overlap in their usage of receptors, JAKs and STATs molecules. We use IL-6 and IL-27 to ask how two cytokines activating the same signaling pathway have different biological roles. We found that IL-27 induces more sustained STAT1 phosphorylation than IL-6, with the two cytokines inducing comparable levels of STAT3 phosphorylation. Mathematical and statistical modeling of IL-6 and IL-27 signaling identified STAT3 binding to GP130, and STAT1 binding to IL-27Rα, as the main dynamical processes contributing to sustained pSTAT1 levels by IL-27. Mutation of Tyr613 on IL-27Rα decreased IL-27-induced STAT1 phosphorylation by 80% but had limited effect on STAT3 phosphorgylation. Strong receptor/STAT coupling by IL-27 initiated a unique gene expression program, which required sustained STAT1 phosphorylation and IRF1 expression and was enriched in classical Interferon Stimulated Genes. Interestingly, the STAT/receptor coupling exhibited by IL-6/IL-27 was altered in patients with systemic lupus erythematosus (SLE). IL-6/IL-27 induced a more potent STAT1 activation in SLE patients than in healthy controls, which correlated with higher STAT1 expression in these patients. Partial inhibition of JAK activation by sub-saturating doses of Tofacitinib specifically lowered the levels of STAT1 activation by IL-6. Our data show that receptor and STATs concentrations critically contribute to shape cytokine responses and generate functional pleiotropy in health and disease.
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Affiliation(s)
- Stephan Wilmes
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Polly-Anne Jeffrey
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Jonathan Martinez-Fabregas
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Maximillian Hafer
- Department of Biology and Centre of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Paul K Fyfe
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Elizabeth Pohler
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Silvia Gaggero
- Université de Lille, INSERM UMR1277 CNRS UMR9020-CANTHER and Institut pour la Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Martín López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Charles Taylor
- Department of Statistics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Thomas Guerrier
- Univ. Lille, Univ. LilleInserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - David Launay
- Univ. Lille, Univ. LilleInserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Suman Mitra
- Université de Lille, INSERM UMR1277 CNRS UMR9020-CANTHER and Institut pour la Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Jacob Piehler
- Department of Biology and Centre of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom.,T-6 Theoretical Division, Los Alamos National Laboratory, Los Alamos, United States
| | - Ignacio Moraga
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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226
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Björk A, Richardsdotter Andersson E, Imgenberg-Kreuz J, Thorlacius GE, Mofors J, Syvänen AC, Kvarnström M, Nordmark G, Wahren-Herlenius M. Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren's syndrome. RMD Open 2021; 6:rmdopen-2019-000995. [PMID: 31958277 PMCID: PMC7046975 DOI: 10.1136/rmdopen-2019-000995] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/30/2019] [Accepted: 11/13/2019] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVE Standard assessment of interferon (IFN) system activity in systemic rheumatic diseases depends on the availability of RNA samples. In this study, we describe and evaluate alternative methods using plasma, serum and DNA samples, exemplified in the IFN-driven disease primary Sjögren's syndrome (pSS). METHODS Patients with pSS seropositive or negative for anti-SSA/SSB and controls were included. Protein-based IFN (pIFN) scores were calculated from levels of PD-1, CXCL9 and CXCL10. DNA methylation-based (DNAm) IFN scores were calculated from DNAm levels at RSAD2, IFIT1 and IFI44L . Scores were compared with mRNA-based IFN scores measured by quantitative PCR (qPCR), Nanostring or RNA sequencing (RNAseq). RESULTS mRNA-based IFN scores displayed strong correlations between B cells and monocytes (r=0.93 and 0.95, p<0.0001) and between qPCR and Nanostring measurements (r=0.92 and 0.92, p<0.0001). The pIFN score in plasma and serum was higher in patients compared with controls (p<0.0001) and correlated well with mRNA-based IFN scores (r=0.62-0.79, p<0.0001), as well as with each other (r=0.94, p<0.0001). Concordance of classification as 'high' or 'low' IFN signature between the pIFN score and mRNA-based IFN scores ranged from 79.5% to 88.6%, and the pIFN score was effective at classifying patients and controls (area under the curve, AUC=0.89-0.93, p<0.0001). The DNAm IFN score showed strong correlation to the RNAseq IFN score (r=0.84, p<0.0001) and performed well in classifying patients and controls (AUC=0.96, p<0.0001). CONCLUSIONS We describe novel methods of assessing IFN system activity in plasma, serum or DNA samples, which may prove particularly valuable in studies where RNA samples are not available.
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Affiliation(s)
- Albin Björk
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Juliana Imgenberg-Kreuz
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gudny Ella Thorlacius
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Johannes Mofors
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marika Kvarnström
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gunnel Nordmark
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marie Wahren-Herlenius
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
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227
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Olsson N, Heberling ML, Zhang L, Jhunjhunwala S, Phung QT, Lin S, Anania VG, Lill JR, Elias JE. An Integrated Genomic, Proteomic, and Immunopeptidomic Approach to Discover Treatment-Induced Neoantigens. Front Immunol 2021; 12:662443. [PMID: 33936100 PMCID: PMC8082494 DOI: 10.3389/fimmu.2021.662443] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
All nucleated mammalian cells express major histocompatibility complex (MHC) proteins that present peptides on cell surfaces for immune surveillance. These MHC-presented peptides (pMHC) are necessary for directing T-cell responses against cells harboring non-self antigens derived from pathogens or from somatic mutations. Alterations in tumor-specific antigen repertoires - particularly novel MHC presentation of mutation-bearing peptides (neoantigens) - can be potent targets of anti-tumor immune responses. Here we employed an integrated genomic and proteomic antigen discovery strategy aimed at measuring how interferon gamma (IFN-γ) alters antigen presentation, using a human lymphoma cell line, GRANTA-519. IFN-γ treatment resulted in 126 differentially expressed proteins (2% of all quantified proteins), which included components of antigen presentation machinery and interferon signaling pathways, and MHC molecules themselves. In addition, several proteasome subunits were found to be modulated, consistent with previous reports of immunoproteasome induction by IFN-γ exposure. This finding suggests that a modest proteomic response to IFN-γ could create larger alteration to cells' antigen/epitope repertoires. Accordingly, MHC immunoprecipitation followed by mass spectrometric analysis of eluted peptide repertoires revealed exclusive signatures of IFN-γ induction, with 951 unique peptides reproducibly presented by MHC-I and 582 presented by MHC-II. Furthermore, an additional set of pMHCs including several candidate neoantigens, distinguished control and the IFN-γ samples by their altered relative abundances. Accordingly, we developed a classification system to distinguish peptides which are differentially presented due to altered expression from novel peptides resulting from changes in antigen processing. Taken together, these data demonstrate that IFN-γ can re-shape antigen repertoires by identity and by abundance. Extending this approach to models with greater clinical relevance could help develop strategies by which immunopeptide repertoires are intentionally reshaped to improve endogenous or vaccine-induced anti-tumor immune responses and potentially anti-viral immune responses.
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Affiliation(s)
- Niclas Olsson
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA, United States
| | - Marlene L. Heberling
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA, United States
| | - Lichao Zhang
- Mass Spectrometry Platform, Chan Zuckerberg Biohub, Stanford, CA, United States
| | - Suchit Jhunjhunwala
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, United States
| | - Qui T. Phung
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, United States
- Department of OMNI Biomarker Development, Genentech, South San Francisco, CA, United States
| | - Sarah Lin
- Mass Spectrometry Platform, Chan Zuckerberg Biohub, Stanford, CA, United States
| | - Veronica G. Anania
- Department of OMNI Biomarker Development, Genentech, South San Francisco, CA, United States
| | - Jennie R. Lill
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, United States
| | - Joshua E. Elias
- Mass Spectrometry Platform, Chan Zuckerberg Biohub, Stanford, CA, United States
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228
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Jackson SE, Chen KC, Groves IJ, Sedikides GX, Gandhi A, Houldcroft CJ, Poole EL, Montanuy I, Mason GM, Okecha G, Reeves MB, Sinclair JH, Wills MR. Latent Cytomegalovirus-Driven Recruitment of Activated CD4+ T Cells Promotes Virus Reactivation. Front Immunol 2021; 12:657945. [PMID: 33912186 PMCID: PMC8072157 DOI: 10.3389/fimmu.2021.657945] [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: 01/24/2021] [Accepted: 03/19/2021] [Indexed: 12/15/2022] Open
Abstract
Human cytomegalovirus (HCMV) infection is not cleared by the initial immune response but persists for the lifetime of the host, in part due to its ability to establish a latent infection in cells of the myeloid lineage. HCMV has been shown to manipulate the secretion of cellular proteins during both lytic and latent infection; with changes caused by latent infection mainly investigated in CD34+ progenitor cells. Whilst CD34+ cells are generally bone marrow resident, their derivative CD14+ monocytes migrate to the periphery where they briefly circulate until extravasation into tissue sites. We have analyzed the effect of HCMV latent infection on the secretome of CD14+ monocytes, identifying an upregulation of both CCL8 and CXCL10 chemokines in the CD14+ latency-associated secretome. Unlike CD34+ cells, the CD14+ latency-associated secretome did not induce migration of resting immune cell subsets but did induce migration of activated NK and T cells expressing CXCR3 in a CXCL10 dependent manner. As reported in CD34+ latent infection, the CD14+ latency-associated secretome also suppressed the anti-viral activity of stimulated CD4+ T cells. Surprisingly, however, co-culture of activated autologous CD4+ T cells with latently infected monocytes resulted in reactivation of HCMV at levels comparable to those observed using M-CSF and IL-1β cytokines. We propose that these events represent a potential strategy to enable HCMV reactivation and local dissemination of the virus at peripheral tissue sites.
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Affiliation(s)
- Sarah E Jackson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Kevin C Chen
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Ian J Groves
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - George X Sedikides
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Amar Gandhi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Charlotte J Houldcroft
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Emma L Poole
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Inmaculada Montanuy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Gavin M Mason
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Georgina Okecha
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Matthew B Reeves
- Institute of Immunity & Transplantation, University College London (UCL), London, United Kingdom
| | - John H Sinclair
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Mark R Wills
- Cambridge Institute of Therapeutic Immunology and Infectious Disease and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
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229
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Bourn JR, Ruiz-Torres SJ, Hunt BG, Benight NM, Waltz SE. Tumor cell intrinsic RON signaling suppresses innate immune responses in breast cancer through inhibition of IRAK4 signaling. Cancer Lett 2021; 503:75-90. [PMID: 33508385 PMCID: PMC7981256 DOI: 10.1016/j.canlet.2021.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/11/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022]
Abstract
Increasing evidence suggests that cancer cells require both alterations in intrinsic cellular processes and the tumor microenvironment for tumor establishment, growth, and progression to metastatic disease. Despite this, knowledge of tumor-cell intrinsic molecular mechanisms controlling both tumor cell processes as well as the tumor microenvironment is limited. In this study, we provide evidence demonstrating the novel role of RON signaling in regulating breast cancer initiation, progression, and metastasis through modulation of tumor cell intrinsic processes and the tumor microenvironment. Using clinically relevant models of breast cancer, we show that RON signaling in the mammary epithelial tumor cells promotes tumor cell survival and proliferation as well as an immunopermissive microenvironment associated with decreased M1 macrophage, natural killer (NK) cell, and CD8+ T cell recruitment. Moreover, we demonstrate that RON signaling supports these phenotypes through novel mechanisms involving suppression of IRAK4 signaling and inhibition of type I Interferons. Our studies indicate that activation of RON signaling within breast cancer cells promotes tumor cell intrinsic growth and immune evasion which support breast cancer progression and highlight the role of targeting RON signaling as a potential therapeutic strategy against breast cancer.
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Affiliation(s)
- Jennifer R Bourn
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267-0521, USA
| | - Sasha J Ruiz-Torres
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267-0521, USA
| | - Brian G Hunt
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267-0521, USA
| | - Nancy M Benight
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267-0521, USA
| | - Susan E Waltz
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267-0521, USA; Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH, 45267, USA.
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230
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Farias Amorim C, O. Novais F, Nguyen BT, Nascimento MT, Lago J, Lago AS, Carvalho LP, Beiting DP, Scott P. Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature. PLoS Negl Trop Dis 2021; 15:e0009321. [PMID: 33793565 PMCID: PMC8043375 DOI: 10.1371/journal.pntd.0009321] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/13/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023] Open
Abstract
Cutaneous leishmaniasis is a localized infection controlled by CD4+ T cells that produce IFN-γ within lesions. Phagocytic cells recruited to lesions, such as monocytes, are then exposed to IFN-γ which triggers their ability to kill the intracellular parasites. Consistent with this, transcriptional analysis of patient lesions identified an interferon stimulated gene (ISG) signature. To determine whether localized L. braziliensis infection triggers a systemic immune response that may influence the disease, we performed RNA sequencing (RNA-seq) on the blood of L. braziliensis-infected patients and healthy controls. Functional enrichment analysis identified an ISG signature as the dominant transcriptional response in the blood of patients. This ISG signature was associated with an increase in monocyte- and macrophage-specific marker genes in the blood and elevated serum levels IFN-γ. A cytotoxicity signature, which is a dominant feature in the lesions, was also observed in the blood and correlated with an increased abundance of cytolytic cells. Thus, two transcriptional signatures present in lesions were found systemically, although with a substantially reduced number of differentially expressed genes (DEGs). Finally, we found that the number of DEGs and ISGs in leishmaniasis was similar to tuberculosis-another localized infection-but significantly less than observed in malaria. In contrast, the cytolytic signature and increased cytolytic cell abundance was not found in tuberculosis or malaria. Our results indicate that systemic signatures can reflect what is occurring in leishmanial lesions. Furthermore, the presence of an ISG signature in blood monocytes and macrophages suggests a mechanism to limit systemic spread of the parasite, as well as enhance parasite control by pre-activating cells prior to lesion entry.
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Affiliation(s)
- Camila Farias Amorim
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Fernanda O. Novais
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Ba T. Nguyen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Mauricio T. Nascimento
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz–Fiocruz, Salvador, Brazil
| | - Jamile Lago
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz–Fiocruz, Salvador, Brazil
| | - Alexsandro S. Lago
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz–Fiocruz, Salvador, Brazil
| | - Lucas P. Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz–Fiocruz, Salvador, Brazil
| | - Daniel P. Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Phillip Scott
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States of America
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231
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Analysis of human total antibody repertoires in TIF1γ autoantibody positive dermatomyositis. Commun Biol 2021; 4:419. [PMID: 33772100 PMCID: PMC7997983 DOI: 10.1038/s42003-021-01932-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
We investigate the accumulated microbial and autoantigen antibody repertoire in adult-onset dermatomyositis patients sero-positive for TIF1γ (TRIM33) autoantibodies. We use an untargeted high-throughput approach which combines immunoglobulin disease-specific epitope-enrichment and identification of microbial and human antigens. We observe antibodies recognizing a wider repertoire of microbial antigens in dermatomyositis. Antibodies recognizing viruses and Poxviridae family species are significantly enriched. The identified autoantibodies recognise a large portion of the human proteome, including interferon regulated proteins; these proteins cluster in specific biological processes. In addition to TRIM33, we identify autoantibodies against eleven further TRIM proteins, including TRIM21. Some of these TRIM proteins share epitope homology with specific viral species including poxviruses. Our data suggest antibody accumulation in dermatomyositis against an expanded diversity of microbial and human proteins and evidence of non-random targeting of specific signalling pathways. Our findings indicate that molecular mimicry and epitope spreading events may play a role in dermatomyositis pathogenesis. Megremis, Walker at al. identify immunogenic epitopes in dermatomyositis patients. They identify antibodies recognizing a wider diversity of microbial antigens including poxviruses, and autoantibodies recognizing a large portion of the human proteome. Shared epitope homology between viral and human proteins suggests that molecular mimicry and epitope spreading events may play a role in dermatomyositis pathogenesis.
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De novo histidine biosynthesis protects Mycobacterium tuberculosis from host IFN-γ mediated histidine starvation. Commun Biol 2021; 4:410. [PMID: 33767335 PMCID: PMC7994828 DOI: 10.1038/s42003-021-01926-4] [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: 03/20/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023] Open
Abstract
Intracellular pathogens including Mycobacterium tuberculosis (Mtb) have evolved with strategies to uptake amino acids from host cells to fulfil their metabolic requirements. However, Mtb also possesses de novo biosynthesis pathways for all the amino acids. This raises a pertinent question- how does Mtb meet its histidine requirements within an in vivo infection setting? Here, we present a mechanism in which the host, by up-regulating its histidine catabolizing enzymes through interferon gamma (IFN-γ) mediated signalling, exerts an immune response directed at starving the bacillus of intracellular free histidine. However, the wild-type Mtb evades this host immune response by biosynthesizing histidine de novo, whereas a histidine auxotroph fails to multiply. Notably, in an IFN-γ-/- mouse model, the auxotroph exhibits a similar extent of virulence as that of the wild-type. The results augment the current understanding of host-Mtb interactions and highlight the essentiality of Mtb histidine biosynthesis for its pathogenesis.
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233
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SARS-CoV-2 infection and smoking: What is the association? A brief review. Comput Struct Biotechnol J 2021; 19:1654-1660. [PMID: 33777332 PMCID: PMC7985684 DOI: 10.1016/j.csbj.2021.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/12/2021] [Accepted: 03/20/2021] [Indexed: 02/06/2023] Open
Abstract
The link between smoking and the expression of SARS-CoV-2 key entry genes is discussed. Smoking-related cardiac and respiratory diseases are risk factors for COVID-19. The impact of smoking on ACE-2 and TMPRSS2 receptors expression is controversial.
Susceptibility to severe illness from COVID-19 is anticipated to be associated with cigarette smoking as it aggravates the risk of cardiovascular and respiratory illness, including infections. This is particularly important with the advent of a new strain of coronaviruses, the severe acute respiratory syndrome coronavirus (SARS-CoV-2) that has led to the present pandemic, coronavirus disease 2019 (COVID-19). Although, the effects of smoking on COVID-19 are less described and controversial, we presume a link between smoking and COVID-19. Smoking has been shown to enhance the expression of the angiotensin-converting enzyme-2 (ACE-2) and transmembrane serine protease 2 (TMPRSS2) key entry genes utilized by SARS-CoV-2 to infect cells and induce a ‘cytokine storm’, which further increases the severity of COVID-19 clinical course. Nevertheless, the impact of smoking on ACE-2 and TMPRSS2 receptors expression remains paradoxical. Thus, further research is necessary to unravel the association between smoking and COVID-19 and to pursue the development of potential novel therapies that are able to constrain the morbidity and mortality provoked by this infectious disease. Herein we present a brief overview of the current knowledge on the correlation between smoking and the expression of SARS-CoV-2 key entry genes, clinical manifestations, and disease progression.
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Key Words
- ACE2, angiotensin-converting enzyme-2
- ACEIs, Angiotensin‐converting enzyme inhibitors
- ADAM17, ADAM metallopeptidase domain 17
- ALCAM, activated leukocyte cell adhesion molecule
- ARBs, angiotensin receptor blockers
- ARDS, acute respiratory distress syndrome
- Ang, angiotensin
- BatCoV, bat coronavirus
- CLDN7, claudin 7
- COPD, chronic obstructive pulmonary disease
- COVID-19
- COVID-19, coronavirus disease 2019
- CTNNB1, catenin beta 1
- Coronavirus
- ERK, extracellular signal-regulated kinases
- HDAC6, histone deacetylase 6
- HIV-1, human immunodeficiency virus 1
- IFN, Interferons
- IPF, Idiopathic pulmonary fibrosis
- IR, Ionizing radiation
- JNK, c-Jun N-terminal kinase
- Lung disease
- MCN, mucin
- MERS, middle-East respiratory syndrome
- NO, nitric oxide
- Oral disease
- R0, R-nought
- RAS, renin-angiotensin
- RR, relative risk
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus
- Smoking
- TJP3, tight junction protein 3
- TMPRSS, transmembrane serine protease
- hrsACE2, human recombinant soluble ACE-2
- nAChR, α7 nicotinic acetylcholine receptor
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234
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Zika Virus Pathogenesis: A Battle for Immune Evasion. Vaccines (Basel) 2021; 9:vaccines9030294. [PMID: 33810028 PMCID: PMC8005041 DOI: 10.3390/vaccines9030294] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 12/13/2022] Open
Abstract
Zika virus (ZIKV) infection and its associated congenital and other neurological disorders, particularly microcephaly and other fetal developmental abnormalities, constitute a World Health Organization (WHO) Zika Virus Research Agenda within the WHO’s R&D Blueprint for Action to Prevent Epidemics, and continue to be a Public Health Emergency of International Concern (PHEIC) today. ZIKV pathogenicity is initiated by viral infection and propagation across multiple placental and fetal tissue barriers, and is critically strengthened by subverting host immunity. ZIKV immune evasion involves viral non-structural proteins, genomic and non-coding RNA and microRNA (miRNA) to modulate interferon (IFN) signaling and production, interfering with intracellular signal pathways and autophagy, and promoting cellular environment changes together with secretion of cellular components to escape innate and adaptive immunity and further infect privileged immune organs/tissues such as the placenta and eyes. This review includes a description of recent advances in the understanding of the mechanisms underlying ZIKV immune modulation and evasion that strongly condition viral pathogenesis, which would certainly contribute to the development of anti-ZIKV strategies, drugs, and vaccines.
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235
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Pérez-Pulido AJ, Asencio-Cortés G, Brokate-Llanos AM, Brea-Calvo G, Rodríguez-Griñolo R, Garzón A, Muñoz MJ. Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators. Brief Bioinform 2021; 22:1038-1052. [PMID: 33458747 PMCID: PMC7929451 DOI: 10.1093/bib/bbaa419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/11/2020] [Accepted: 12/19/2020] [Indexed: 11/14/2022] Open
Abstract
The current genomics era is bringing an unprecedented growth in the amount of gene expression data, only comparable to the exponential growth of sequences in databases during the last decades. This data allow the design of secondary analyses that take advantage of this information to create new knowledge. One of these feasible analyses is the evaluation of the expression level for a gene through a series of different conditions or cell types. Based on this idea, we have developed Automatic and Serial Analysis of CO-expression, which performs expression profiles for a given gene along hundreds of heterogeneous and normalized transcriptomics experiments and discover other genes that show either a similar or an inverse behavior. It might help to discover co-regulated genes, and common transcriptional regulators in any biological model. The present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an opportunity to test this novel approach due to the wealth of data that are being generated, which could be used for validating results. Thus, we have identified 35 host factors in the literature putatively involved in the infectious cycle of SARS-CoV viruses and searched for genes tightly co-expressed with them. We have found 1899 co-expressed genes whose assigned functions are strongly related to viral cycles. Moreover, this set of genes heavily overlaps with those identified by former laboratory high-throughput screenings (with P-value near 0). Our results reveal a series of common regulators, involved in immune and inflammatory responses that might be key virus targets to induce the coordinated expression of SARS-CoV-2 host factors.
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Affiliation(s)
- Antonio J Pérez-Pulido
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | | | - Ana M Brokate-Llanos
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Gloria Brea-Calvo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, 41013, Sevilla, Spain
- CIBERER, Instituto de Salud Carlos III, 28000, Madrid, Spain
| | - Rosario Rodríguez-Griñolo
- Dpto. de Economía, Métodos Cuantitativos e Historia Económica. Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Andrés Garzón
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Manuel J Muñoz
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
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236
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McKellar J, Rebendenne A, Wencker M, Moncorgé O, Goujon C. Mammalian and Avian Host Cell Influenza A Restriction Factors. Viruses 2021; 13:522. [PMID: 33810083 PMCID: PMC8005160 DOI: 10.3390/v13030522] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022] Open
Abstract
The threat of a new influenza pandemic is real. With past pandemics claiming millions of lives, finding new ways to combat this virus is essential. Host cells have developed a multi-modular system to detect incoming pathogens, a phenomenon called sensing. The signaling cascade triggered by sensing subsequently induces protection for themselves and their surrounding neighbors, termed interferon (IFN) response. This response induces the upregulation of hundreds of interferon-stimulated genes (ISGs), including antiviral effectors, establishing an antiviral state. As well as the antiviral proteins induced through the IFN system, cells also possess a so-called intrinsic immunity, constituted of antiviral proteins that are constitutively expressed, creating a first barrier preceding the induction of the interferon system. All these combined antiviral effectors inhibit the virus at various stages of the viral lifecycle, using a wide array of mechanisms. Here, we provide a review of mammalian and avian influenza A restriction factors, detailing their mechanism of action and in vivo relevance, when known. Understanding their mode of action might help pave the way for the development of new influenza treatments, which are absolutely required if we want to be prepared to face a new pandemic.
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Affiliation(s)
- Joe McKellar
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Antoine Rebendenne
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Mélanie Wencker
- Centre International de Recherche en Infectiologie, INSERM/CNRS/UCBL1/ENS de Lyon, 69007 Lyon, France;
| | - Olivier Moncorgé
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Caroline Goujon
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
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237
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Mini-TrpRS is essential for IFNγ-induced monocyte-derived giant cell formation. Cytokine 2021; 142:155486. [PMID: 33721618 DOI: 10.1016/j.cyto.2021.155486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/07/2021] [Accepted: 02/24/2021] [Indexed: 11/24/2022]
Abstract
Truncated tryptophanyl-tRNA synthetase (mini-TrpRS), like any other aminoacyl-tRNA synthetases, canonically functions as a protein synthesis enzyme. Here we provide evidence for an additional signaling role of mini-TrpRS in the formation of monocyte-derived multinuclear giant cells (MGCs). Interferon-gamma (IFNγ) readily induced monocyte aggregation leading to MGC formation with paralleled marked upregulation of mini-TrpRS. Small interfering (si)RNA, targeting mini-TrpRS in the presence of IFNγ prevented monocyte aggregation. Moreover, blockade of mini-TrpRS, either by siRNA, or the cognate amino acid and decoy substrate D-Tryptophan to prevent mini-TrpRS signaling, resulted in a marked reduction in expression of the purinergic receptor P2X 7 (P2RX7) in monocytes activated by IFNγ. Our findings identify mini-TrpRS as a critical signaling molecule in a mechanism by which IFNγ initiates monocyte-derived giant cell formation.
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238
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Cai L, Liu H, Huang F, Fujimoto J, Girard L, Chen J, Li Y, Zhang YA, Deb D, Stastny V, Pozo K, Kuo CS, Jia G, Yang C, Zou W, Alomar A, Huffman K, Papari-Zareei M, Yang L, Drapkin B, Akbay EA, Shames DS, Wistuba II, Wang T, Johnson JE, Xiao G, DeBerardinis RJ, Minna JD, Xie Y, Gazdar AF. Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer. Commun Biol 2021; 4:314. [PMID: 33750914 PMCID: PMC7943563 DOI: 10.1038/s42003-021-01842-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/09/2021] [Indexed: 12/17/2022] Open
Abstract
Small cell lung cancer (SCLC) is classified as a high-grade neuroendocrine (NE) tumor, but a subset of SCLC has been termed “variant” due to the loss of NE characteristics. In this study, we computed NE scores for patient-derived SCLC cell lines and xenografts, as well as human tumors. We aligned NE properties with transcription factor-defined molecular subtypes. Then we investigated the different immune phenotypes associated with high and low NE scores. We found repression of immune response genes as a shared feature between classic SCLC and pulmonary neuroendocrine cells of the healthy lung. With loss of NE fate, variant SCLC tumors regain cell-autonomous immune gene expression and exhibit higher tumor-immune interactions. Pan-cancer analysis revealed this NE lineage-specific immune phenotype in other cancers. Additionally, we observed MHC I re-expression in SCLC upon development of chemoresistance. These findings may help guide the design of treatment regimens in SCLC. Ling Cai et al. used transcriptomic profiling data of healthy lung, patient-derived small cell lung cancer cell lines, xenografts, and primary tumors to examine a link between neuroendocrine (NE) signatures and immune gene expression. Their findings suggest that cell-autonomous immune gene repression is a shared feature between healthy and tumor cells of NE lineage and may influence tumor-immune cell interaction and response to immunotherapy.
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Affiliation(s)
- Ling Cai
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA. .,Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA. .,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Hongyu Liu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Fang Huang
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luc Girard
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jun Chen
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China.,Department of Lung Cancer Surgery, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Yongwen Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Yu-An Zhang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Dhruba Deb
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Victor Stastny
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Karine Pozo
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Christin S Kuo
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Gaoxiang Jia
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chendong Yang
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Wei Zou
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Adeeb Alomar
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kenneth Huffman
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Mahboubeh Papari-Zareei
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lin Yang
- Department of Pathology, National Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Benjamin Drapkin
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Esra A Akbay
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - David S Shames
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jane E Johnson
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ralph J DeBerardinis
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - John D Minna
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA. .,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA. .,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Adi F Gazdar
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
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239
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Type I IFNs facilitate innate immune control of the opportunistic bacteria Burkholderia cenocepacia in the macrophage cytosol. PLoS Pathog 2021; 17:e1009395. [PMID: 33684179 PMCID: PMC7971856 DOI: 10.1371/journal.ppat.1009395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 03/18/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
The mammalian immune system is constantly challenged by signals from both pathogenic and non-pathogenic microbes. Many of these non-pathogenic microbes have pathogenic potential if the immune system is compromised. The importance of type I interferons (IFNs) in orchestrating innate immune responses to pathogenic microbes has become clear in recent years. However, the control of opportunistic pathogens-and especially intracellular bacteria-by type I IFNs remains less appreciated. In this study, we use the opportunistic, Gram-negative bacterial pathogen Burkholderia cenocepacia (Bc) to show that type I IFNs are capable of limiting bacterial replication in macrophages, preventing illness in immunocompetent mice. Sustained type I IFN signaling through cytosolic receptors allows for increased expression of autophagy and linear ubiquitination mediators, which slows bacterial replication. Transcriptomic analyses and in vivo studies also show that LPS stimulation does not replicate the conditions of intracellular Gram-negative bacterial infection as it pertains to type I IFN stimulation or signaling. This study highlights the importance of type I IFNs in protection against opportunistic pathogens through innate immunity, without the need for damaging inflammatory responses.
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240
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Mezera MA, Li W, Wiltbank MC. Pregnancy-induced changes in the transcriptome of the bovine corpus luteum during and after embryonic interferon-tau secretion†. Biol Reprod 2021; 105:148-163. [PMID: 33690863 DOI: 10.1093/biolre/ioab034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/04/2021] [Accepted: 03/03/2021] [Indexed: 01/18/2023] Open
Abstract
Understanding luteal maintenance during early pregnancy is of substantial biological and practical importance. Characterizing effects of early pregnancy, however, has historically been confounded by use of controls with potential exposure to early Prostaglandin F2-alpha (PGF) pulses or differences in Corpus Luteum (CL) age. To avoid this, the present study utilized bihourly blood sampling to ensure control CL (n = 6) were of a similar age to CL from pregnant animals (n = 5), yet without exposure to PGF pulses. Additionally, CL from second month of pregnancy (n = 4) were analyzed to track fate of altered genes after cessation of embryonic interferon tau (IFNT) secretion. The major alteration in gene expression in first month of pregnancy occurred in interferon-stimulated genes (ISGs), with immune/interferon signaling pathways enriched in three independent over-representation analyses. Most ISGs decreased during second month of pregnancy, though, surprisingly, some ISGs remained elevated in the second month even after cessation of IFNT secretion. Investigation of luteolytic genes found few altered transcripts, in contrast to previous reports, likely due to removal of controls exposed to PGF pulses. An exception to this trend was decreased expression of transcription factor NR4A1. Beyond luteolytic genes and ISGs, over representation analyses highlighted the prevalence of altered genes within the extracellular matrix and regulation of Insulin-like growth factor (IGF) availability, confirming results of other studies independent of luteolytic genes. These results support the idea that CL maintenance in early pregnancy is related to lack of PGF exposure, although potential roles for CL expression of diverse ISGs and other pathways activated during early pregnancy remain undefined.
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Affiliation(s)
- Megan A Mezera
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA.,Endocrinology and Reproductive Physiology Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Wenli Li
- USDA Dairy Forage Research Center, Madison, WI, USA
| | - Milo C Wiltbank
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA.,Endocrinology and Reproductive Physiology Program, University of Wisconsin-Madison, Madison, WI, USA
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241
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Schenkel LB, Molina JR, Swinger KK, Abo R, Blackwell DJ, Lu AZ, Cheung AE, Church WD, Kunii K, Kuplast-Barr KG, Majer CR, Minissale E, Mo JR, Niepel M, Reik C, Ren Y, Vasbinder MM, Wigle TJ, Richon VM, Keilhack H, Kuntz KW. A potent and selective PARP14 inhibitor decreases protumor macrophage gene expression and elicits inflammatory responses in tumor explants. Cell Chem Biol 2021; 28:1158-1168.e13. [PMID: 33705687 DOI: 10.1016/j.chembiol.2021.02.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/18/2020] [Accepted: 02/11/2021] [Indexed: 11/28/2022]
Abstract
PARP14 has been implicated by genetic knockout studies to promote protumor macrophage polarization and suppress the antitumor inflammatory response due to its role in modulating interleukin-4 (IL-4) and interferon-γ signaling pathways. Here, we describe structure-based design efforts leading to the discovery of a potent and highly selective PARP14 chemical probe. RBN012759 inhibits PARP14 with a biochemical half-maximal inhibitory concentration of 0.003 μM, exhibits >300-fold selectivity over all PARP family members, and its profile enables further study of PARP14 biology and disease association both in vitro and in vivo. Inhibition of PARP14 with RBN012759 reverses IL-4-driven protumor gene expression in macrophages and induces an inflammatory mRNA signature similar to that induced by immune checkpoint inhibitor therapy in primary human tumor explants. These data support an immune suppressive role of PARP14 in tumors and suggest potential utility of PARP14 inhibitors in the treatment of cancer.
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Affiliation(s)
- Laurie B Schenkel
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; MOMA Therapeutics, Cambridge, MA 02142, USA
| | - Jennifer R Molina
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Kerren K Swinger
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; Xilio Therapeutics, Waltham, MA 02451, USA
| | - Ryan Abo
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; Obsidian Therapeutics, Cambridge, MA 02138, USA
| | - Danielle J Blackwell
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Alvin Z Lu
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Anne E Cheung
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; A2Empowerment, Arlington, MA 02474, USA
| | - W David Church
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Kaiko Kunii
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Kristy G Kuplast-Barr
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Christina R Majer
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Elena Minissale
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Jan-Rung Mo
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Mario Niepel
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Christopher Reik
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; Bain & Company, Boston, MA 02116, USA
| | - Yue Ren
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Melissa M Vasbinder
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Tim J Wigle
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Victoria M Richon
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Heike Keilhack
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Kevin W Kuntz
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA.
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Björk A, Da Silva Rodrigues R, Richardsdotter Andersson E, Ramírez Sepúlveda JI, Mofors J, Kvarnström M, Oke V, Svenungsson E, Gunnarsson I, Wahren-Herlenius M. Interferon activation status underlies higher antibody response to viral antigens in patients with systemic lupus erythematosus receiving no or light treatment. Rheumatology (Oxford) 2021; 60:1445-1455. [PMID: 33006609 DOI: 10.1093/rheumatology/keaa611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/21/2020] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Infections have been proposed as an environmental risk factor for autoimmune disease. Responses to microbial antigens may be studied in vivo during vaccination. We therefore followed patients with SLE and controls during split-virion influenza vaccination to quantify antibody responses against viral antigens and associated cellular and proteome parameters. METHODS Blood samples and clinical data were collected from female patients with SLE with no or HCQ and/or low-dose prednisolone treatment (n = 29) and age- and sex-matched healthy controls (n = 17). Vaccine-specific antibody titres were measured by ELISA and IFN-induced gene expression in monocytes by quantitative PCR. Serum proteins were measured by proximity extension assay and disease-associated symptoms were followed by questionnaires. RESULTS The vaccine-specific antibody response was significantly higher in patients compared with controls and titres of IgG targeting the viral proteins were higher in patients than controls at both 1 and 3 months after immunization. Clinical disease symptoms and autoantibody titres remained unchanged throughout the study. Notably, a positive pre-vaccination mRNA-based IFN score was associated with a significantly higher vaccine-specific antibody response and with a broader profile of autoantibody specificities. Screening of serum protein biomarkers revealed higher levels of IFN-regulated proteins in patients compared with controls and that levels of such proteins correlated with the vaccine-specific IgG response, with C-C motif chemokine ligand 3 exhibiting the strongest association. CONCLUSION Augmented antibody responses to viral antigens develop in patients with SLE on no or light treatment and associate with markers of type I IFN system activation at the RNA and protein levels.
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Affiliation(s)
- Albin Björk
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rui Da Silva Rodrigues
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Johannes Mofors
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marika Kvarnström
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Vilija Oke
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Elisabet Svenungsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Iva Gunnarsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.,Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
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243
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Lai HC, James A, Luff J, De Souza P, Quek H, Ho U, Lavin MF, Roberts TL. Regulation of RNA degradation pathways during the lipopolysaccharide response in Macrophages. J Leukoc Biol 2021; 109:593-603. [PMID: 32829531 DOI: 10.1002/jlb.2ab0420-151rr] [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: 06/25/2019] [Revised: 04/01/2020] [Accepted: 05/26/2020] [Indexed: 11/09/2022] Open
Abstract
The innate immune response to LPS is highly dynamic yet tightly regulated. The majority of studies of gene expression have focussed on transcription. However, it is also important to understand how post-transcriptional pathways are regulated in response to inflammatory stimuli as the rate of RNA degradation relative to new transcription is important for overall expression. RNA decay pathways include nonsense-mediated decay, the RNA decay exosome, P-body localized deadenylation, decapping and degradation, and AU-rich element targeted decay mediated by tristetraprolin. Here, bone marrow-derived Mϕs were treated with LPS over a time course of 0, 2, 6, and 24 h and the transcriptional profiles were analyzed by RNA sequencing. The data show that components of RNA degradation pathways are regulated during an LPS response. Processing body associated decapping enzyme DCP2 and regulatory subunit DCP1A, and 5' exonuclease XRN1 and sequence specific RNA decay pathways were upregulated. Nonsense mediated decay was also increased in response to LPS induced signaling, initially by increased activation and at later timepoints at the mRNA and protein levels. This leads to increased nonsense mediated decay efficiency across the 24 h following LPS treatment. These findings suggest that LPS activation of Mϕs results in targeted regulation of RNA degradation pathways in order to change how subsets of mRNAs are degraded during an inflammatory response.
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Affiliation(s)
- Hui-Chi Lai
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
- South West Sydney Clinical School, UNSW Australia, Liverpool, New South Wales, Australia
| | - Alexander James
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
| | - John Luff
- The University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Paul De Souza
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
- Medical Oncology Department, Liverpool Hospital, Liverpool, New South Wales, Australia
- School of Medicine, Western Sydney University, Macarthur, New South Wales, Australia
| | - Hazel Quek
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Uda Ho
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Martin F Lavin
- The University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Tara L Roberts
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
- South West Sydney Clinical School, UNSW Australia, Liverpool, New South Wales, Australia
- The University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
- School of Medicine, Western Sydney University, Macarthur, New South Wales, Australia
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244
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Bellocchi C, Ying J, Goldmuntz EA, Keyes-Elstein L, Varga J, Hinchcliff ME, Lyons MA, McSweeney P, Furst DE, Nash R, Crofford LJ, Welch B, Goldin JG, Pinckney A, Mayes MD, Sullivan KM, Assassi S. Large-Scale Characterization of Systemic Sclerosis Serum Protein Profile: Comparison to Peripheral Blood Cell Transcriptome and Correlations With Skin/Lung Fibrosis. Arthritis Rheumatol 2021; 73:660-670. [PMID: 33131208 DOI: 10.1002/art.41570] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To provide a large-scale assessment of serum protein dysregulation in diffuse cutaneous systemic sclerosis (dcSSc) and to investigate serum protein correlates of SSc fibrotic features. METHODS We investigated serum protein profiles of 66 participants with dcSSc at baseline who were enrolled in the Scleroderma: Cyclophosphamide or Transplant Trial and 66 age- and sex-matched healthy control subjects. A panel of 230 proteins, including several cytokines and chemokines, was investigated. Whole blood gene expression profiling in concomitantly collected samples was performed. RESULTS Among the participants with dcSSc, the mean disease duration was 2.3 years. All had interstitial lung disease (ILD), and none were being treated with immunosuppressive agents at baseline. Ninety proteins were differentially expressed in participants with dcSSc compared to healthy control subjects. Similar to previous global skin transcript results, hepatic fibrosis, granulocyte and agranulocyte adhesion, and diapedesis were the top overrepresented pathways. Eighteen proteins correlated with the modified Rodnan skin thickness score (MRSS). Soluble epidermal growth factor receptor was significantly down-regulated in dcSSc and showed the strongest negative correlation with the MRSS, being predictive of the score's course over time, whereas α1 -antichymotrypsin was significantly up-regulated in dcSSc and showed the strongest positive correlation with the MRSS. Furthermore, higher levels of cancer antigen 15-3 correlated with more severe ILD, based on findings of reduced forced vital capacity and higher scores of disease activity on high-resolution computed tomography. Only 14 genes showed significant differential expression in the same direction in serum protein and whole blood RNA gene expression analyses. CONCLUSION Diffuse cutaneous SSc has a distinct serum protein profile with prominent dysregulation of proteins related to fibrosis and immune cell adhesion/diapedesis. The differential expression for most serum proteins in SSc is likely to originate outside the peripheral blood cells.
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Affiliation(s)
- Chiara Bellocchi
- The University of Texas Health Science Center at Houston and McGovern Medical School, Houston, and Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Jun Ying
- The University of Texas Health Science Center at Houston and McGovern Medical School, Houston
| | - Ellen A Goldmuntz
- National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | | | - John Varga
- Northwestern University, Chicago, Illinois
| | | | - Marka A Lyons
- The University of Texas Health Science Center at Houston and McGovern Medical School, Houston
| | | | - Daniel E Furst
- University of California Los Angeles, University of Washington, Seattle, and University of Florence, Florence, Italy
| | | | | | - Beverly Welch
- National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | | | | | - Maureen D Mayes
- The University of Texas Health Science Center at Houston and McGovern Medical School, Houston
| | | | - Shervin Assassi
- The University of Texas Health Science Center at Houston and McGovern Medical School, Houston
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245
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Maire CL, Mohme M, Bockmayr M, Fita KD, Riecken K, Börnigen D, Alawi M, Failla A, Kolbe K, Zapf S, Holz M, Neumann K, Dührsen L, Lange T, Fehse B, Westphal M, Lamszus K. Glioma escape signature and clonal development under immune pressure. J Clin Invest 2021; 130:5257-5271. [PMID: 32603315 DOI: 10.1172/jci138760] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
Immunotherapeutic strategies are increasingly important in neuro-oncology, and the elucidation of escape mechanisms that lead to treatment resistance is crucial. We investigated the impact of immune pressure on the clonal dynamics and immune escape signature by comparing glioma growth in immunocompetent versus immunodeficient mice. Glioma-bearing WT and Pd-1-/- mice survived significantly longer than immunodeficient Pfp-/- Rag2-/- mice. While tumors in Pfp-/- Rag2-/- mice were highly polyclonal, immunoedited tumors in WT and Pd-1-/- mice displayed reduced clonality with emergence of immune escape clones. Tumor cells in WT mice were distinguished by an IFN-γ-mediated response signature with upregulation of genes involved in immunosuppression. Tumor-infiltrating stromal cells, which include macrophages/microglia, contributed even more strongly to the immunosuppressive signature than the actual tumor cells. The identified murine immune escape signature was reflected in human patients and correlated with poor survival. In conclusion, immune pressure profoundly shapes the clonal composition and gene regulation in malignant gliomas.
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Affiliation(s)
| | | | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt University Berlin and Berlin Institute of Health, Berlin, Germany
| | | | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation
| | | | | | | | | | | | | | | | | | - Tobias Lange
- Institutes of Anatomy, Experimental Morphology and Pathology, University Cancer Center Hamburg, Hamburg, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation
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Zangari T, Ortigoza MB, Lokken-Toyli KL, Weiser JN. Type I Interferon Signaling Is a Common Factor Driving Streptococcus pneumoniae and Influenza A Virus Shedding and Transmission. mBio 2021; 12:e03589-20. [PMID: 33593970 PMCID: PMC8545127 DOI: 10.1128/mbio.03589-20] [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: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 01/27/2023] Open
Abstract
The dynamics underlying respiratory contagion (the transmission of infectious agents from the airways) are poorly understood. We investigated host factors involved in the transmission of the leading respiratory pathogen Streptococcus pneumoniae Using an infant mouse model, we examined whether S. pneumoniae triggers inflammatory pathways shared by influenza A virus (IAV) to promote nasal secretions and shedding from the upper respiratory tract to facilitate transit to new hosts. Here, we show that amplification of the type I interferon (IFN-I) response is a critical host factor in this process, as shedding and transmission by both IAV and S. pneumoniae were decreased in pups lacking the common IFN-I receptor (Ifnar1-/- mice). Additionally, providing exogenous recombinant IFN-I to S. pneumoniae-infected pups was sufficient to increase bacterial shedding. The expression of IFN-stimulated genes (ISGs) was upregulated in S. pneumoniae-infected wild-type (WT) but not Ifnar1-/- mice, including genes involved in mucin type O-glycan biosynthesis; this correlated with an increase in secretions in S. pneumoniae- and IAV-infected WT compared to Ifnar1-/- pups. S. pneumoniae stimulation of ISGs was largely dependent on its pore-forming toxin, pneumolysin, and coinfection with IAV and S. pneumoniae resulted in synergistic increases in ISG expression. We conclude that the induction of IFN-I signaling appears to be a common factor driving viral and bacterial respiratory contagion.IMPORTANCE Respiratory tract infections are a leading cause of childhood mortality and, globally, Streptococcus pneumoniae is the leading cause of mortality due to pneumonia. Transmission of S. pneumoniae primarily occurs through direct contact with respiratory secretions, although the host and bacterial factors underlying transmission are poorly understood. We examined transmission dynamics of S. pneumoniae in an infant mouse model and here show that S. pneumoniae colonization of the upper respiratory tract stimulates host inflammatory pathways commonly associated with viral infections. Amplification of this response was shown to be a critical host factor driving shedding and transmission of both S. pneumoniae and influenza A virus, with infection stimulating expression of a wide variety of genes, including those involved in the biosynthesis of mucin, a major component of respiratory secretions. Our findings suggest a mechanism facilitating S. pneumoniae contagion that is shared by viral infection.
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Affiliation(s)
- Tonia Zangari
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Mila B Ortigoza
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, New York, USA
| | - Kristen L Lokken-Toyli
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jeffrey N Weiser
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
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Rivière E, Pascaud J, Virone A, Dupré A, Ly B, Paoletti A, Seror R, Tchitchek N, Mingueneau M, Smith N, Duffy D, Cassard L, Chaput N, Pengam S, Gauttier V, Poirier N, Mariette X, Nocturne G. Interleukin-7/Interferon Axis Drives T Cell and Salivary Gland Epithelial Cell Interactions in Sjögren's Syndrome. Arthritis Rheumatol 2021; 73:631-640. [PMID: 33058491 DOI: 10.1002/art.41558] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/08/2020] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Primary Sjögren's syndrome (SS) is characterized by a lymphocytic infiltration of salivary glands (SGs) and the presence of an interferon (IFN) signature. SG epithelial cells (SGECs) play an active role in primary SS pathophysiology. We undertook this study to examine the interactions between SGECs and T cells in primary SS and the role of the interleukin-7 (IL-7)/IFN axis. METHODS Primary cultured SGECs from control subjects and patients with primary SS were stimulated with poly(I-C), IFNα, or IFNγ. T cells were sorted from blood and stimulated with IL-7. CD25 expression was assessed by flow cytometry. SG explants were cultured for 4 days with anti-IL-7 receptor (IL-7R) antagonist antibody (OSE-127), and transcriptomic analysis was performed using the NanoString platform. RESULTS Serum IL-7 level was increased in patients with primary SS compared to controls and was associated with B cell biomarkers. IL7R expression was decreased in T cells from patients with primary SS compared to controls. SGECs stimulated with poly(I-C), IFNα, or IFNγ secreted IL-7. IL-7 stimulation increased the activation of T cells, as well as IFNγ secretion. Transcriptomic analysis of SG explants showed a correlation between IL7 and IFN expression. Finally, explants cultured with anti-IL-7R antibody showed decreased IFN-stimulated gene expression. CONCLUSION These results suggest the presence of an IL-7/IFNγ amplification loop involving SGECs and T cells in primary SS. IL-7 was secreted by SGECs stimulated with type I or type II IFN and, in turn, activated T cells that secrete type II IFN. An anti-IL-7R antibody decreased the IFN signature in T cells in primary SS and could be of therapeutic interest.
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Affiliation(s)
- Elodie Rivière
- Université Paris-Saclay, INSERM, CEA, Centre de Recherche en Immunologie des Infections Virales et des Maladies Auto-Immunes, Hôpital Bicêtre, AP-HP, Recherche et Développement, Arthritis Fondation Courtin, Paris, France
| | - Juliette Pascaud
- Université Paris-Saclay, INSERM, CEA, Centre de Recherche en Immunologie des Infections Virales et des Maladies Auto-Immunes, Hôpital Bicêtre, AP-HP, Paris, France
| | - Alexandre Virone
- Université Paris-Saclay, INSERM, CEA, Centre de Recherche en Immunologie des Infections Virales et des Maladies Auto-Immunes, Hôpital Bicêtre, AP-HP, Paris, France
| | - Anastasia Dupré
- Université Paris-Saclay, INSERM, CEA, Centre de Recherche en Immunologie des Infections Virales et des Maladies Auto-Immunes, Hôpital Bicêtre, AP-HP, Paris, France
| | - Bineta Ly
- Université Paris-Saclay, INSERM, CEA, Centre de Recherche en Immunologie des Infections Virales et des Maladies Auto-Immunes, Hôpital Bicêtre, AP-HP, Paris, France
| | - Audrey Paoletti
- Université Paris-Saclay, INSERM, CEA, Centre de Recherche en Immunologie des Infections Virales et des Maladies Auto-Immunes, Hôpital Bicêtre, AP-HP, Paris, France
| | - Raphaèle Seror
- Université Paris-Saclay, INSERM, CEA, Centre de Recherche en Immunologie des Infections Virales et des Maladies Auto-Immunes, Hôpital Bicêtre, AP-HP, Paris, France
| | - Nicolas Tchitchek
- Université Paris-Saclay, INSERM, CEA, Centre de Recherche en Immunologie des Infections Virales et des Maladies Auto-Immunes, Hôpital Bicêtre, AP-HP, Paris, France
| | | | - Nikaïa Smith
- Laboratoire d'Immunobiologie des Cellules Dendritiques, INSERM U1223, Institut Pasteur, Paris, France
| | - Darragh Duffy
- Laboratoire d'Immunobiologie des Cellules Dendritiques, INSERM U1223, Institut Pasteur, Paris, France
| | - Lydie Cassard
- Université Paris-Saclay, Institut Gustave Roussy, Analyse moléculaire, modélisation et imagerie de la maladie cancéreuse, Laboratoire d'Immunomonitoring en Oncologie, INSERM, CNRS, Paris, France
| | - Nathalie Chaput
- Université Paris-Saclay, Institut Gustave Roussy, Analyse moléculaire, modélisation et imagerie de la maladie cancéreuse, Laboratoire d'Immunomonitoring en Oncologie, INSERM, CNRS, Paris, France
| | | | | | | | - Xavier Mariette
- Université Paris-Saclay, INSERM, CEA, Centre de Recherche en Immunologie des Infections Virales et des Maladies Auto-Immunes, Hôpital Bicêtre, AP-HP, Paris, France
| | - Gaetane Nocturne
- Université Paris-Saclay, INSERM, CEA, Centre de Recherche en Immunologie des Infections Virales et des Maladies Auto-Immunes, Hôpital Bicêtre, AP-HP, Paris, France
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Xue F, Tian J, Yu C, Du H, Guo L. Type I interferon response-related microglial Mef2c deregulation at the onset of Alzheimer's pathology in 5×FAD mice. Neurobiol Dis 2021; 152:105272. [PMID: 33540048 PMCID: PMC7956132 DOI: 10.1016/j.nbd.2021.105272] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/15/2021] [Indexed: 02/08/2023] Open
Abstract
Alzheimer’s disease (AD) is a chronic neurodegenerative disorder with multifactorial etiology. The role of microglia in the pathogenesis of AD has been increasingly recognized in recent years; however, the detailed mechanisms shaping microglial phenotypes in AD-relevant pathological settings remain largely unresolved. Myocyte-specific enhancer factor 2C (Mef2C) is a transcription factor with versatile functions. Recent studies have attributed aging-related microglial changes to type I interferon (IFN-I)-associated Mef2C deregulation. In view of the close relationship between brain aging and AD, it is of great interest to determine microglial Mef2C changes in AD-related conditions. In this study, we have found that suppressed Mef2C nuclear translocation was an early and prominent microglial phenotype in a mouse model of brain amyloidosis (5×FAD mice), which exacerbated with age. Echoing the early Mef2C deregulation and its association with microglial activation, transcriptional data showed elicited IFN-I response in microglia from young 5×FAD mice. Amyloid beta 42 (Aβ42) in its oligomeric forms promoted Mef2C deregulation in microglia on acute organotypic brain slices with augmented microglial activation and synapse elimination via microglial phagocytosis. Importantly, these oligomeric Aβ42-mediated microglial changes were substantially attenuated by blocking IFN-I signaling. The simplest interpretation of the results is that Mef2C, concurring with activated IFN-I signaling, constitutes early microglial changes in AD-related conditions. In addition to the potential contribution of Mef2C deregulation to the development of microglial phenotypes in AD, Mef2C suppression in microglia may serve as a potential mechanistic pathway linking brain aging and AD.
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Affiliation(s)
- Feng Xue
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, KS 66045, United States; The Biological Science Department, University of Texas at Dallas, TX 75080, United States
| | - Jing Tian
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, KS 66045, United States; The Biological Science Department, University of Texas at Dallas, TX 75080, United States
| | - Chunxiao Yu
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, KS 66045, United States; The Biological Science Department, University of Texas at Dallas, TX 75080, United States
| | - Heng Du
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, KS 66045, United States; Higuchi Biosciences Center, University of Kansas, KS 66045, United States; The Biological Science Department, University of Texas at Dallas, TX 75080, United States.
| | - Lan Guo
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, KS 66045, United States; Higuchi Biosciences Center, University of Kansas, KS 66045, United States; The Biological Science Department, University of Texas at Dallas, TX 75080, United States.
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Casselli T, Divan A, Vomhof-DeKrey EE, Tourand Y, Pecoraro HL, Brissette CA. A murine model of Lyme disease demonstrates that Borrelia burgdorferi colonizes the dura mater and induces inflammation in the central nervous system. PLoS Pathog 2021; 17:e1009256. [PMID: 33524035 PMCID: PMC7877756 DOI: 10.1371/journal.ppat.1009256] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 02/11/2021] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
Lyme disease, which is caused by infection with Borrelia burgdorferi and related species, can lead to inflammatory pathologies affecting the joints, heart, and nervous systems including the central nervous system (CNS). Inbred laboratory mice have been used to define the kinetics of B. burgdorferi infection and host immune responses in joints and heart, however similar studies are lacking in the CNS of these animals. A tractable animal model for investigating host-Borrelia interactions in the CNS is key to understanding the mechanisms of CNS pathogenesis. Therefore, we characterized the kinetics of B. burgdorferi colonization and associated immune responses in the CNS of mice during early and subacute infection. Using fluorescence-immunohistochemistry, intravital microscopy, bacterial culture, and quantitative PCR, we found B. burgdorferi routinely colonized the dura mater of C3H mice, with peak spirochete burden at day 7 post-infection. Dura mater colonization was observed for several Lyme disease agents including B. burgdorferi, B. garinii, and B. mayonii. RNA-sequencing and quantitative RT-PCR showed that B. burgdorferi infection was associated with increased expression of inflammatory cytokines and a robust interferon (IFN) response in the dura mater. Histopathologic changes including leukocytic infiltrates and vascular changes were also observed in the meninges of infected animals. In contrast to the meninges, we did not detect B. burgdorferi, infiltrating leukocytes, or large-scale changes in cytokine profiles in the cerebral cortex or hippocampus during infection; however, both brain regions demonstrated similar changes in expression of IFN-stimulated genes as observed in peripheral tissues and meninges. Taken together, B. burgdorferi is capable of colonizing the meninges in laboratory mice, and induces localized inflammation similar to peripheral tissues. A sterile IFN response in the absence of B. burgdorferi or inflammatory cytokines is unique to the brain parenchyma, and provides insight into the potential mechanisms of CNS pathology associated with this important pathogen.
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Affiliation(s)
- Timothy Casselli
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, North Dakota, United States of America
- * E-mail: (TC); (CAB)
| | - Ali Divan
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, North Dakota, United States of America
| | - Emilie E. Vomhof-DeKrey
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, North Dakota, United States of America
- Department of Surgery, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, North Dakota, United States of America
| | - Yvonne Tourand
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, North Dakota, United States of America
| | - Heidi L. Pecoraro
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, North Dakota, United States of America
| | - Catherine A. Brissette
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, North Dakota, United States of America
- * E-mail: (TC); (CAB)
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Dual Effects of Let-7b in the Early Stage of Hepatitis C Virus Infection. J Virol 2021; 95:JVI.01800-20. [PMID: 33208444 DOI: 10.1128/jvi.01800-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022] Open
Abstract
MicroRNA let-7b expression is induced by infection of hepatitis C virus (HCV) and is involved in the regulation of HCV replication by directly targeting the HCV genome. The current study demonstrated that let-7b directly targets negative regulators of type I interferon (IFN) signaling thereby limiting HCV replication in the early stage of HCV infection. Let-7b-regulated genes which are involved in host cellular responses to HCV infection were unveiled by microarray profiling and bioinformatic analyses, followed by various molecular and cellular assays using Huh7 cells expressing wild-type (WT) or the seed region-mutated let-7b. Let-7b targeted the cytokine signaling 1 (SOCS1) protein, a negative regulator of JAK/STAT signaling, which then enhanced STAT1-Y701 phosphorylation leading to increased expression of the downstream interferon-stimulated genes (ISGs). Let-7b augmented retinoic acid-inducible gene I (RIG-I) signaling, but not MDA5, to phosphorylate and nuclear translocate IRF3 leading to increased expression of IFN-β. Let-7b directly targeted the ATG12 and IκB kinase alpha (IKKα) transcripts and reduced the interaction of the ATG5-ATG12 conjugate and RIG-I leading to increased expression of IFN, which may further stimulate JAK/STAT signaling. Let-7b induced by HCV infection elicits dual effects on IFN expression and signaling, along with targeting the coding sequences of NS5B and 5' UTR of the HCV genome, and limits HCV RNA accumulation in the early stage of HCV infection. Controlling let-7b expression is thereby crucial in the intervention of HCV infection.IMPORTANCE HCV is a leading cause of liver disease, with an estimated 71 million people infected worldwide. During HCV infection, type I interferon (IFN) signaling displays potent antiviral and immunomodulatory effects. Host factors, including microRNAs (miRNAs), play a role in upregulating IFN signaling to limit HCV replication. Let-7b is a liver-abundant miRNA that is induced by HCV infection and targets the HCV genome to suppress HCV RNA accumulation. In this study, we demonstrated that let-7b, as a positive regulator of type I IFN signaling, plays dual roles against HCV replication by increasing the expression of IFN and interferon-sensitive response element (ISRE)-driven interferon-stimulated genes (ISGs) in the early stage of HCV infection. This study sheds new insight into understanding the role of let-7b in combatting HCV infection. Clarifying IFN signaling regulated by miRNA during the early phase of HCV infection may help researchers understand the initial defense mechanisms to other RNA viruses.
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