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Gronau L, Duecker RP, Jerkic SP, Eickmeier O, Trischler J, Chiocchetti AG, Blumchen K, Zielen S, Schubert R. Dual Role of microRNA-146a in Experimental Inflammation in Human Pulmonary Epithelial and Immune Cells and Expression in Inflammatory Lung Diseases. Int J Mol Sci 2024; 25:7686. [PMID: 39062931 PMCID: PMC11276706 DOI: 10.3390/ijms25147686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/28/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
microRNA (miR)-146a emerges as a promising post-transcriptional regulator in various inflammatory diseases with different roles for the two isoforms miR-146a-5p and miR-146a-3p. The present study aimed to examine the dual role of miR-146a-5p and miR-146a 3p in the modulation of inflammation in human pulmonary epithelial and immune cells in vitro as well as their expression in patients with inflammatory lung diseases. Experimental inflammation in human A549, HL60, and THP1 via the NF-kB pathway resulted in the major upregulation of miR-146a-5p and miR-146a-3p expression, which was partly cell-specific. Modulation by transfection with miRNA mimics and inhibitors demonstrated an anti-inflammatory effect of miR-146a-5p and a pro-inflammatory effect of miR-146a-3p, respectively. A mutual interference between miR-146a-5p and miR-146a-3p was observed, with miR-146a-5p exerting a predominant influence. In vivo NGS analyses revealed an upregulation of miR-146a-3p in the blood of patients with cystic fibrosis and bronchiolitis obliterans, while miR-146a-5p levels were downregulated or unchanged compared to controls. The reverse pattern was observed in patients with SARS-CoV-2 infection. In conclusion, miR-146a-5p and miR-146a-3p are two distinct but interconnected miRNA isoforms with opposing functions in inflammation regulation. Understanding their interaction provides important insights into the progression and persistence of inflammatory lung diseases and might provide potential therapeutic options.
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Affiliation(s)
- Lucia Gronau
- Department of Pediatrics, Division of Pneumology, Allergology, Infectious Diseases and Gastroenterology, University Hospital, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany; (L.G.); (R.P.D.); (S.-P.J.); (O.E.); (J.T.); (K.B.)
| | - Ruth P. Duecker
- Department of Pediatrics, Division of Pneumology, Allergology, Infectious Diseases and Gastroenterology, University Hospital, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany; (L.G.); (R.P.D.); (S.-P.J.); (O.E.); (J.T.); (K.B.)
| | - Silvija-Pera Jerkic
- Department of Pediatrics, Division of Pneumology, Allergology, Infectious Diseases and Gastroenterology, University Hospital, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany; (L.G.); (R.P.D.); (S.-P.J.); (O.E.); (J.T.); (K.B.)
| | - Olaf Eickmeier
- Department of Pediatrics, Division of Pneumology, Allergology, Infectious Diseases and Gastroenterology, University Hospital, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany; (L.G.); (R.P.D.); (S.-P.J.); (O.E.); (J.T.); (K.B.)
| | - Jordis Trischler
- Department of Pediatrics, Division of Pneumology, Allergology, Infectious Diseases and Gastroenterology, University Hospital, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany; (L.G.); (R.P.D.); (S.-P.J.); (O.E.); (J.T.); (K.B.)
| | - Andreas G. Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany;
| | - Katharina Blumchen
- Department of Pediatrics, Division of Pneumology, Allergology, Infectious Diseases and Gastroenterology, University Hospital, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany; (L.G.); (R.P.D.); (S.-P.J.); (O.E.); (J.T.); (K.B.)
| | - Stefan Zielen
- Respiratory Research Institute, Medaimun GmbH, 60596 Frankfurt am Main, Germany;
| | - Ralf Schubert
- Department of Pediatrics, Division of Pneumology, Allergology, Infectious Diseases and Gastroenterology, University Hospital, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany; (L.G.); (R.P.D.); (S.-P.J.); (O.E.); (J.T.); (K.B.)
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Randolph ME, Afifi M, Gorthi A, Weil R, Wilky BA, Weinreb J, Ciero P, Hoeve NT, van Diest PJ, Raman V, Bishop AJ, Loeb DM. RNA helicase DDX3 regulates RAD51 localization and DNA damage repair in Ewing sarcoma. iScience 2024; 27:108925. [PMID: 38323009 PMCID: PMC10844834 DOI: 10.1016/j.isci.2024.108925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 12/09/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
We previously demonstrated that RNA helicase DDX3X (DDX3) can be a therapeutic target in Ewing sarcoma (EWS), but its role in EWS biology remains unclear. The present work demonstrates that DDX3 plays a unique role in DNA damage repair (DDR). We show that DDX3 interacts with several proteins involved in homologous recombination, including RAD51, RECQL1, RPA32, and XRCC2. In particular, DDX3 colocalizes with RAD51 and RNA:DNA hybrid structures in the cytoplasm of EWS cells. Inhibition of DDX3 RNA helicase activity increases cytoplasmic RNA:DNA hybrids, sequestering RAD51 in the cytoplasm, which impairs nuclear translocation of RAD51 to sites of double-stranded DNA breaks, thus increasing sensitivity of EWS to radiation treatment, both in vitro and in vivo. This discovery lays the foundation for exploring new therapeutic approaches directed at manipulating DDR protein localization in solid tumors.
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Affiliation(s)
- Matthew E. Randolph
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Marwa Afifi
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Aparna Gorthi
- Greehey Children’s Cancer Research Institute and Department of Cell Systems & Anatomy, UT Health San Antonio, San Antonio, TX, USA
| | - Rachel Weil
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Breelyn A. Wilky
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Joshua Weinreb
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Paul Ciero
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Natalie ter Hoeve
- Department of Pathology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Paul J. van Diest
- Department of Pathology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Venu Raman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Department of Radiology, Johns Hopkins University, Baltimore, MD, USA
- Department of Pharmacology, Johns Hopkins University, Baltimore, MD, USA
| | - Alexander J.R. Bishop
- Greehey Children’s Cancer Research Institute and Department of Cell Systems & Anatomy, UT Health San Antonio, San Antonio, TX, USA
| | - David M. Loeb
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
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3
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Randolph ME, Afifi M, Gorthi A, Weil R, Wilky BA, Weinreb J, Ciero P, ter Hoeve N, van Diest PJ, Raman V, Bishop AJR, Loeb DM. RNA Helicase DDX3 Regulates RAD51 Localization and DNA Damage Repair in Ewing Sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.10.544474. [PMID: 37333164 PMCID: PMC10274875 DOI: 10.1101/2023.06.10.544474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
We previously demonstrated that RNA helicase DDX3X (DDX3) can be a therapeutic target in Ewing sarcoma (EWS), but its role in EWS biology remains unclear. The present work demonstrates that DDX3 plays a unique role in DNA damage repair (DDR). We show that DDX3 interacts with several proteins involved in homologous recombination, including RAD51, RECQL1, RPA32, and XRCC2. In particular, DDX3 colocalizes with RAD51 and RNA:DNA hybrid structures in the cytoplasm of EWS cells. Inhibition of DDX3 RNA helicase activity increases cytoplasmic RNA:DNA hybrids, sequestering RAD51 in the cytoplasm, which impairs nuclear translocation of RAD51 to sites of double-stranded DNA breaks thus increasing sensitivity of EWS to radiation treatment, both in vitro and in vivo. This discovery lays the foundation for exploring new therapeutic approaches directed at manipulating DDR protein localization in solid tumors.
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Affiliation(s)
- Matthew E. Randolph
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY
| | - Marwa Afifi
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Aparna Gorthi
- Greehey Children’s Cancer Research Institute and Department of Cell Systems & Anatomy, UT Health San Antonio, San Antonio, TX
| | - Rachel Weil
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Breelyn A. Wilky
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Joshua Weinreb
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Paul Ciero
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY
| | - Natalie ter Hoeve
- Department of Pathology, University Medical Centre Utrecht, The Netherlands
| | - Paul J. van Diest
- Department of Pathology, University Medical Centre Utrecht, The Netherlands
| | - Venu Raman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
- Department of Radiology, Johns Hopkins University, Baltimore, MD
- Department of Pharmacology, Johns Hopkins University, Baltimore, MD
| | - Alexander J. R. Bishop
- Greehey Children’s Cancer Research Institute and Department of Cell Systems & Anatomy, UT Health San Antonio, San Antonio, TX
| | - David M. Loeb
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
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Lih TM, Cho KC, Schnaubelt M, Hu Y, Zhang H. Integrated glycoproteomic characterization of clear cell renal cell carcinoma. Cell Rep 2023; 42:112409. [PMID: 37074911 DOI: 10.1016/j.celrep.2023.112409] [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: 11/16/2022] [Revised: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC), a common form of RCC, is responsible for the high mortality rate of kidney cancer. Dysregulations of glycoproteins have been shown to associate with ccRCC. However, the molecular mechanism has not been well characterized. Here, a comprehensive glycoproteomic analysis is conducted using 103 tumors and 80 paired normal adjacent tissues. Altered glycosylation enzymes and corresponding protein glycosylation are observed, while two of the major ccRCC mutations, BAP1 and PBRM1, show distinct glycosylation profiles. Additionally, inter-tumor heterogeneity and cross-correlation between glycosylation and phosphorylation are observed. The relation of glycoproteomic features to genomic, transcriptomic, proteomic, and phosphoproteomic changes shows the role of glycosylation in ccRCC development with potential for therapeutic interventions. This study reports a large-scale tandem mass tag (TMT)-based quantitative glycoproteomic analysis of ccRCC that can serve as a valuable resource for the community.
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Affiliation(s)
- T Mamie Lih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Kyung-Cho Cho
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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5
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Gao S, Han B, Xu B, Wang N, Zhang Y, Liu X, Zhang M, Wang G, Guan X, Huang J, Liu M, Shi W. SAV Nsp2 regulates NF-κB signaling to induce inflammatory responses by targeting host DDX3. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 140:104612. [PMID: 36473548 DOI: 10.1016/j.dci.2022.104612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/02/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Salmon alphavirus (SAV) infection leads to severe pancreas disease (PD) with typical inflammatory responses in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Nsp2, an important nonstructural protein of SAV, can activate NF-κB signaling pathway to reduce inflammatory responses. However, the molecular mechanism remains unclear. In this study, the ML (279-421aa) of Nsp2 was revealed to be the key domain for activating NF-κB. We focused on a host protein, DEAD-box RNA helicase 3 (DDX3), that may interact with Nsp2 to regulate NF-κB-induced inflammatory. The interaction between DDX3 and Nsp2 was confirmed in vitro. Overexpression of DDX3 inhibited the activation of NF-κB by Nsp2. SAV Nsp2 relieves the inhibitory effect of DDX3 on NF-κB, thereby initiating the innate immune response. This study revealed the molecular mechanism of Nsp2-induced inflammatory response by targeting DDX3 to activate NF-κB, providing a theoretical basis for revealing the underlying infection mechanism and pathogenesis of SAV.
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Affiliation(s)
- Shuai Gao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Bing Han
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Baoxing Xu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Na Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yanru Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Xuefei Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Mengmeng Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Guanbo Wang
- Wellcome-Wolfson Institute for Exprerimental Medicine Queen's University Belfast, 97 Lisburn Rd, Belfast, BT9 7BL, UK
| | - Xueting Guan
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Jinshan Huang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Min Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China.
| | - Wen Shi
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China.
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Pavkova I, Kopeckova M, Link M, Vlcak E, Filimonenko V, Lecova L, Zakova J, Laskova P, Sheshko V, Machacek M, Stulik J. Francisella tularensis Glyceraldehyde-3-Phosphate Dehydrogenase Is Relocalized during Intracellular Infection and Reveals Effect on Cytokine Gene Expression and Signaling. Cells 2023; 12:cells12040607. [PMID: 36831274 PMCID: PMC9954481 DOI: 10.3390/cells12040607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/26/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is known for its multifunctionality in several pathogenic bacteria. Our previously reported data suggest that the GAPDH homologue of Francisella tularensis, GapA, might also be involved in other processes beyond metabolism. In the present study, we explored GapA's potential implication in pathogenic processes at the host cell level. Using immunoelectron microscopy, we demonstrated the localization of this bacterial protein inside infected macrophages and its peripheral distribution in bacterial cells increasing with infection time. A quantitative proteomic approach based on stable isotope labeling of amino acids in cell culture (SILAC) combined with pull-down assay enabled the identification of several of GapA's potential interacting partners within the host cell proteome. Two of these partners were further confirmed by alternative methods. We also investigated the impact of gapA deletion on the transcription of selected cytokine genes and the activation of the main signaling pathways. Our results show that ∆gapA-induced transcription of genes encoding several cytokines whose expressions were not affected in cells infected with a fully virulent wild-type strain. That might be caused, at least in part, by the detected differences in ERK/MAPK signaling activation. The experimental observations together demonstrate that the F. tularensis GAPDH homologue is directly implicated in multiple host cellular processes and, thereby, that it participates in several molecular mechanisms of pathogenesis.
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Affiliation(s)
- Ivona Pavkova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
- Correspondence: ; Tel.: +420-973-255-201
| | - Monika Kopeckova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Marek Link
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Erik Vlcak
- Institute of Molecular Genetics of the Czech Academy of Sciences, Electron Microscopy Core Facility, Videnska 1083, 142 20 Prague, Czech Republic
| | - Vlada Filimonenko
- Institute of Molecular Genetics of the Czech Academy of Sciences, Electron Microscopy Core Facility, Videnska 1083, 142 20 Prague, Czech Republic
- Institute of Molecular Genetics of the Czech Academy of Sciences, Department of Biology of the Cell Nucleus, Videnska 1083, 142 20 Prague, Czech Republic
| | - Lenka Lecova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Jitka Zakova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Pavlina Laskova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Valeria Sheshko
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Miloslav Machacek
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague, Akademika Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Jiri Stulik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
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Serfecz JC, Hong Y, Gay LA, Shekhar R, Turner PC, Renne R. DExD/H Box Helicases DDX24 and DDX49 Inhibit Reactivation of Kaposi's Sarcoma Associated Herpesvirus by Interacting with Viral mRNAs. Viruses 2022; 14:2083. [PMID: 36298642 PMCID: PMC9609691 DOI: 10.3390/v14102083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic gammaherpesvirus that is the causative agent of primary effusion lymphoma and Kaposi's sarcoma. In healthy carriers, KSHV remains latent, but a compromised immune system can lead to lytic viral replication that increases the probability of tumorigenesis. RIG-I-like receptors (RLRs) are members of the DExD/H box helicase family of RNA binding proteins that recognize KSHV to stimulate the immune system and prevent reactivation from latency. To determine if other DExD/H box helicases can affect KSHV lytic reactivation, we performed a knock-down screen that revealed DHX29-dependent activities appear to support viral replication but, in contrast, DDX24 and DDX49 have antiviral activity. When DDX24 or DDX49 are overexpressed in BCBL-1 cells, transcription of all lytic viral genes and genome replication were significantly reduced. RNA immunoprecipitation of tagged DDX24 and DDX49 followed by next-generation sequencing revealed that the helicases bind to mostly immediate-early and early KSHV mRNAs. Transfection of expression plasmids of candidate KSHV transcripts, identified from RNA pull-down, demonstrated that KSHV mRNAs stimulate type I interferon (alpha/beta) production and affect the expression of multiple interferon-stimulated genes. Our findings reveal that host DExD/H box helicases DDX24 and DDX49 recognize gammaherpesvirus transcripts and convey an antiviral effect in the context of lytic reactivation.
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Affiliation(s)
- Jacquelyn C. Serfecz
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Yuan Hong
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lauren A. Gay
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ritu Shekhar
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Peter C. Turner
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
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Panda M, Kalita E, Singh S, Kumar K, Rao A, Prajapati VK. MiRNA-SARS-CoV-2 dialogue and prospective anti-COVID-19 therapies. Life Sci 2022; 305:120761. [PMID: 35787998 PMCID: PMC9249409 DOI: 10.1016/j.lfs.2022.120761] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 02/08/2023]
Abstract
COVID-19 is a highly transmissible disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), affects 226 countries and continents, and has resulted in >6.2 million deaths worldwide. Despite the efforts of all scientific institutions worldwide to identify potential therapeutics, no specific drug has been approved by the FDA to treat the COVID-19 patient. SARS-CoV-2 variants of concerns make the potential of publicly known therapeutics to respond to and detect disease onset highly improbable. The quest for universal therapeutics pointed to the ability of RNA-based molecules to shield and detect the adverse effects of the COVID-19 illness. One such candidate, miRNA (microRNA), works on regulating the differential expression of the target gene post-transcriptionally. The prime focus of this review is to report the critical miRNA molecule and their regular expression in patients with COVID-19 infection and associated comorbidities. Viral and host miRNAs control the etiology of COVID-19 infection throughout the life cycle and host inflammatory response, where host miRNAs are identified as a double-edged showing as a proviral and antiviral response. The review also covered the role of viral miRNAs in mediating host cell signaling expression during disease pathology. Studying molecular interactions between the host and the SARS-CoV-2 virus during COVID-19 pathogenesis offers the chance to use miRNA-based therapeutics to reduce the severity of the illness. By utilizing an appropriate delivery vehicle, these small non-coding RNA could be envisioned as a promising biomarker in designing a practical RNAi-based treatment approach of clinical significance.
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Affiliation(s)
- Mamta Panda
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Elora Kalita
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Ketan Kumar
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Abhishek Rao
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India.
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Hu M, Zheng H, Wu J, Sun Y, Wang T, Chen S. DDX5: an expectable treater for viral infection- a literature review. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:712. [PMID: 35845539 PMCID: PMC9279824 DOI: 10.21037/atm-22-2375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/21/2022] [Indexed: 11/06/2022]
Abstract
Background and Objective DEAD-box protein (DDX)5 plays important roles in multiple aspects of cellular processes that require modulating RNA structure. Alongside the canonical role of DDX5 in RNA metabolism, many reports have shown that DDX5 influences viral infection by directly interacting with viral proteins. However, the functional role of DDX5 in virus-associated cancers, as well as the identity of DDX5 in virus infection-associated signaling pathways, has remained largely unexplained. Here, we further explore the precise functions of DDX5 and its potential targets for antiviral treatment. Methods We searched the PubMed and PMC databases to identify studies on role of DDXs, especially DDX5, during various viral infection published up to May 2022. Key Content and Findings DDX5 functions as both a viral infection helper and inhibitor, which depends on virus type. DDXs proteins have been identified to play roles on multiple aspects covering RNA metabolism and function. Conclusions DDX5 influences viral pathogenesis by participating in viral replication and multiple viral infection-related signaling pathways, it also plays a double-edge sword role under different viral infection conditions. Deep investigation into the mechanism of DDX5 modulating immune response in host cells revealed that it holds highly potential usage for future antiviral therapy. We reviewed current studies to provide a comprehensive update of the role of DDX5 in viral infection.
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Affiliation(s)
- Minghui Hu
- Clinical Lab, The Affiliated Hospital of Qingdao University, Qingdao China
| | - Hongying Zheng
- Clinical Lab, The Affiliated Hospital of Qingdao University, Qingdao China
| | - Jingqi Wu
- Microbiology Department, Harbin Medical University, Harbin, China
| | - Yue Sun
- School of Public Health, Harbin Medical University, Harbin, China
| | - Tianying Wang
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao, China
| | - Shuang Chen
- Clinical Lab, Qingdao Municipal Hospital, Qingdao, China
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10
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Samir P, Kanneganti TD. DEAD/H-Box Helicases in Immunity, Inflammation, Cell Differentiation, and Cell Death and Disease. Cells 2022; 11:1608. [PMID: 35626643 PMCID: PMC9139286 DOI: 10.3390/cells11101608] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/04/2022] [Accepted: 05/07/2022] [Indexed: 12/21/2022] Open
Abstract
DEAD/H-box proteins are the largest family of RNA helicases in mammalian genomes, and they are present in all kingdoms of life. Since their discovery in the late 1980s, DEAD/H-box family proteins have been a major focus of study. They have been found to play central roles in RNA metabolism, gene expression, signal transduction, programmed cell death, and the immune response to bacterial and viral infections. Aberrant functions of DEAD/H-box proteins have been implicated in a wide range of human diseases that include cancer, neurodegeneration, and inherited genetic disorders. In this review, we provide a historical context and discuss the molecular functions of DEAD/H-box proteins, highlighting the recent discoveries linking their dysregulation to human diseases. We will also discuss the state of knowledge regarding two specific DEAD/H-box proteins that have critical roles in immune responses and programmed cell death, DDX3X and DDX58, also known as RIG-I. Given their importance in homeostasis and disease, an improved understanding of DEAD/H-box protein biology and protein-protein interactions will be critical for informing strategies to counteract the pathogenesis associated with several human diseases.
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11
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Tabassum S, Ghosh MK. DEAD-box RNA helicases with special reference to p68: Unwinding their biology, versatility, and therapeutic opportunity in cancer. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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12
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Narożna M, Rubiś B. Anti-SARS-CoV-2 Strategies and the Potential Role of miRNA in the Assessment of COVID-19 Morbidity, Recurrence, and Therapy. Int J Mol Sci 2021; 22:8663. [PMID: 34445368 PMCID: PMC8395427 DOI: 10.3390/ijms22168663] [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: 07/06/2021] [Revised: 08/07/2021] [Accepted: 08/08/2021] [Indexed: 02/06/2023] Open
Abstract
Recently, we have experienced a serious pandemic. Despite significant technological advances in molecular technologies, it is very challenging to slow down the infection spread. It appeared that due to globalization, SARS-CoV-2 spread easily and adapted to new environments or geographical or weather zones. Additionally, new variants are emerging that show different infection potential and clinical outcomes. On the other hand, we have some experience with other pandemics and some solutions in virus elimination that could be adapted. This is of high importance since, as the latest reports demonstrate, vaccine technology might not follow the new, mutated virus outbreaks. Thus, identification of novel strategies and markers or diagnostic methods is highly necessary. For this reason, we present some of the latest views on SARS-CoV-2/COVID-19 therapeutic strategies and raise a solution based on miRNA. We believe that in the face of the rapidly increasing global situation and based on analogical studies of other viruses, the possibility of using the biological potential of miRNA technology is very promising. It could be used as a promising diagnostic and prognostic factor, as well as a therapeutic target and tool.
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Affiliation(s)
- Maria Narożna
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, 4 Święcickiego St., 60-781 Poznan, Poland;
| | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, 49 Przybyszewskiego St., 60-355 Poznan, Poland
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13
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Sergeeva O, Abakumova T, Kurochkin I, Ialchina R, Kosyreva A, Prikazchikova T, Varlamova V, Shcherbinina E, Zatsepin T. Level of Murine DDX3 RNA Helicase Determines Phenotype Changes of Hepatocytes In Vitro and In Vivo. Int J Mol Sci 2021; 22:ijms22136958. [PMID: 34203429 PMCID: PMC8269429 DOI: 10.3390/ijms22136958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/26/2022] Open
Abstract
DDX3 RNA helicase is intensively studied as a therapeutic target due to participation in the replication of some viruses and involvement in cancer progression. Here we used transcriptome analysis to estimate the primary response of hepatocytes to different levels of RNAi-mediated knockdown of DDX3 RNA helicase both in vitro and in vivo. We found that a strong reduction of DDX3 protein (>85%) led to similar changes in vitro and in vivo—deregulation of the cell cycle and Wnt and cadherin pathways. Also, we observed the appearance of dead hepatocytes in the healthy liver and a decrease of cell viability in vitro after prolonged treatment. However, more modest downregulation of the DDX3 protein (60–65%) showed discordant results in vitro and in vivo—similar changes in vitro as in the case of strong knockdown and a different phenotype in vivo. These results demonstrate that the level of DDX3 protein can dramatically influence the cell phenotype in vivo and the decrease of DDX3, for more than 85% leads to cell death in normal tissues, which should be taken into account during the drug development of DDX3 inhibitors.
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Affiliation(s)
- Olga Sergeeva
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia; (T.A.); (I.K.); (R.I.); (T.P.); (V.V.); (E.S.); (T.Z.)
- Correspondence: ; Tel.: +7-926-388-0865
| | - Tatiana Abakumova
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia; (T.A.); (I.K.); (R.I.); (T.P.); (V.V.); (E.S.); (T.Z.)
| | - Ilia Kurochkin
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia; (T.A.); (I.K.); (R.I.); (T.P.); (V.V.); (E.S.); (T.Z.)
| | - Renata Ialchina
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia; (T.A.); (I.K.); (R.I.); (T.P.); (V.V.); (E.S.); (T.Z.)
| | - Anna Kosyreva
- Research Institute of Human Morphology, 117418 Moscow, Russia;
| | - Tatiana Prikazchikova
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia; (T.A.); (I.K.); (R.I.); (T.P.); (V.V.); (E.S.); (T.Z.)
| | - Varvara Varlamova
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia; (T.A.); (I.K.); (R.I.); (T.P.); (V.V.); (E.S.); (T.Z.)
| | - Evgeniya Shcherbinina
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia; (T.A.); (I.K.); (R.I.); (T.P.); (V.V.); (E.S.); (T.Z.)
| | - Timofei Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia; (T.A.); (I.K.); (R.I.); (T.P.); (V.V.); (E.S.); (T.Z.)
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
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14
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Selective cell death in HIV-1-infected cells by DDX3 inhibitors leads to depletion of the inducible reservoir. Nat Commun 2021; 12:2475. [PMID: 33931637 PMCID: PMC8087668 DOI: 10.1038/s41467-021-22608-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023] Open
Abstract
An innovative approach to eliminate HIV-1-infected cells emerging out of latency, the major hurdle to HIV-1 cure, is to pharmacologically reactivate viral expression and concomitantly trigger intracellular pro-apoptotic pathways in order to selectively induce cell death (ICD) of infected cells, without reliance on the extracellular immune system. In this work, we demonstrate the effect of DDX3 inhibitors on selectively inducing cell death in latent HIV-1-infected cell lines, primary CD4+ T cells and in CD4+ T cells from cART-suppressed people living with HIV-1 (PLWHIV). We used single-cell FISH-Flow technology to characterise the contribution of viral RNA to inducing cell death. The pharmacological targeting of DDX3 induced HIV-1 RNA expression, resulting in phosphorylation of IRF3 and upregulation of IFNβ. DDX3 inhibition also resulted in the downregulation of BIRC5, critical to cell survival during HIV-1 infection, and selectively induced apoptosis in viral RNA-expressing CD4+ T cells but not bystander cells. DDX3 inhibitor treatment of CD4+ T cells from PLWHIV resulted in an approximately 50% reduction of the inducible latent HIV-1 reservoir by quantitation of HIV-1 RNA, by FISH-Flow, RT-qPCR and TILDA. This study provides proof of concept for pharmacological reversal of latency coupled to induction of apoptosis towards the elimination of the inducible reservoir.
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15
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Ali MAM. DEAD-box RNA helicases: The driving forces behind RNA metabolism at the crossroad of viral replication and antiviral innate immunity. Virus Res 2021; 296:198352. [PMID: 33640359 DOI: 10.1016/j.virusres.2021.198352] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
DEAD-box RNA helicases, the largest family of superfamily 2 helicases, are a profoundly conserved family of RNA-binding proteins, containing a distinctive Asp-Glu-Ala-Asp (D-E-A-D) sequence motif, which is the origin of their name. Aside from the ATP-dependent unwinding of RNA duplexes, which set up these proteins as RNA helicases, DEAD-box proteins have been found to additionally stimulate RNA duplex fashioning and to uproot proteins from RNA, aiding the reformation of RNA and RNA-protein complexes. There is accumulating evidence that DEAD-box helicases play functions in the recognition of foreign nucleic acids and the modification of viral infection. As intracellular parasites, viruses must avoid identification by innate immune sensing mechanisms and disintegration by cellular machinery, whilst additionally exploiting host cell activities to assist replication. The capability of DEAD-box helicases to sense RNA in a sequence-independent way, as well as the broadness of cellular roles performed by members of this family, drive them to affect innate sensing and viral infections in numerous manners. Undoubtedly, DEAD-box helicases have been demonstrated to contribute to intracellular immune recognition, function as antiviral effectors, and even to be exploited by viruses to support their replication. Relying on the virus or the viral cycle phase, a DEAD-box helicase can function either in a proviral manner or as an antiviral factor. This review gives a comprehensive perspective on the various biochemical characteristics of DEAD-box helicases and their links to structural data. It additionally outlines the multiple functions that members of the DEAD-box helicase family play during viral infections.
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Affiliation(s)
- Mohamed A M Ali
- Department of Biochemistry, Faculty of Science, Ain Shams University, Abbassia, 11566, Cairo, Egypt.
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16
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Hua Q, Liu Y, Li M, Chen Y, Diao Q, Zeng H, Jiang Y. Tobacco-Related Exposure Upregulates Circ_0035266 to Exacerbate Inflammatory Responses in Human Bronchial Epithelial Cells. Toxicol Sci 2021; 179:70-83. [PMID: 33107911 DOI: 10.1093/toxsci/kfaa163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
One of the most carcinogenic chemicals found in cigarette tobacco smoke is 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), which has been confirmed to be associated with the etiology of diverse cancers. Lipopolysaccharide (LPS), another biologically active component of cigarette smoke, is a risk factor which enhances NNK-induced lung tumorigenesis due to chronic lung inflammation. Although inflammatory responses play critical roles in the initiation of many tumors, our knowledge about the mechanisms of NNK+LPS on inflammation is currently limited. Here, we investigated the inflammatory effects of NNK+LPS in human bronchial epithelial cells (BEAS-2B) and explored the underlying mechanisms mediated by circular RNAs (circRNAs). We identified a novel circRNA, circ_0035266, which was strongly upregulated in NNK+LPS-induced BEAS-2B cells and enhanced the inflammatory responses to NNK+LPS by regulating the secretion of pro-inflammatory cytokines interleukin (IL)-6 and IL-8. Specifically, circ_0035266 knockdown alleviated NNK+LPS-induced inflammatory responses, whereas overexpression of circ_0035266 had the opposite effect. Moreover, dual-luciferase reporter and fluorescence in situ hybridization (FISH) assays verified that circ_0035266 bound to miR-181d-5p directly in the cytoplasm. qRT-PCR, dual-luciferase reporter assays, and Western blot analyses showed that DDX3X (DDX3) was the downstream target of miR-181d-5p and that DDX3X expression levels were modulated by circ_0035266. These results suggested that circ_0035266 served as a competitive endogenous RNA for miR-181d-5p to regulate DDX3X expression, which is involved in the modulation of NNK+LPS-induced inflammatory responses in BEAS-2B cells.
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Affiliation(s)
- Qiuhan Hua
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Yufei Liu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Meizhen Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Yingnan Chen
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Qinqin Diao
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Huixian Zeng
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Yiguo Jiang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
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17
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Squeglia F, Romano M, Ruggiero A, Maga G, Berisio R. Host DDX Helicases as Possible SARS-CoV-2 Proviral Factors: A Structural Overview of Their Hijacking Through Multiple Viral Proteins. Front Chem 2020; 8:602162. [PMID: 33381492 PMCID: PMC7769135 DOI: 10.3389/fchem.2020.602162] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
As intracellular parasites, viruses hijack the host cell metabolic machinery for their replication. Among other cellular proteins, the DEAD-box (DDX) RNA helicases have been shown to be hijacked by coronaviruses and to participate in essential DDX-mediated viral replication steps. Human DDX RNA helicases play essential roles in a broad array of biological processes and serve multiple roles at the virus-host interface. The viral proteins responsible for DDX interactions are highly conserved among coronaviruses, suggesting that they might also play conserved functions in the SARS-CoV-2 replication cycle. In this review, we provide an update of the structural and functional data of DDX as possible key factors involved in SARS-CoV-2 hijacking mechanisms. We also attempt to fill the existing gaps in the available structural information through homology modeling. Based on this information, we propose possible paths exploited by the virus to replicate more efficiently by taking advantage of host DDX proteins. As a general rule, sequestration of DDX helicases by SARS-CoV-2 is expected to play a pro-viral role in two ways: by enhancing key steps of the virus life cycle and, at the same time, by suppressing the host innate immune response.
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Maria Romano
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics (IGM-CNR), Pavia, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
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18
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Winnard PT, Vesuna F, Raman V. Targeting host DEAD-box RNA helicase DDX3X for treating viral infections. Antiviral Res 2020; 185:104994. [PMID: 33301755 DOI: 10.1016/j.antiviral.2020.104994] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/19/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023]
Abstract
DDX3X or DDX3, a member of the DEAD (asp, glu, ala, asp) box RNA helicase family of proteins, is a multifunctional protein, which is usurped by several viruses and is vital to their production. To date, 18 species of virus from 12 genera have been demonstrated to be dependent on DDX3 for virulence. In addition, DDX3 has been shown to function within 7 of 10 subcellular regions that are involved in the metabolism of viruses. As such, due to its direct interaction with viral components across most or all stages of viral life cycles, DDX3 can be considered an excellent host target for pan-antiviral drug therapy and has been reported to be a possible broad-spectrum antiviral target. Along these lines, it has been demonstrated that treatment of virally infected cells with small molecule inhibitors of DDX3 blunts virion productions. On the other hand, DDX3 bolsters an innate immune response and viruses have evolved capacities to sequester or block DDX3, which dampens an innate immune response. Thus, enhancing DDX3 production or co-targeting direct viral products that interfere with DDX3's modulation of innate immunity would also diminish virion production. Here we review the evidence that supports the hypothesis that modulating DDX3's agonistic and antagonistic functions during viral infections could have an important impact on safely and efficiently subduing a broad-spectrum of viral infections.
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Affiliation(s)
- Paul T Winnard
- Division of Cancer Imaging Research, The Russell H Morgan Department of Radiology and Radiological Sciences, USA
| | - Farhad Vesuna
- Division of Cancer Imaging Research, The Russell H Morgan Department of Radiology and Radiological Sciences, USA
| | - Venu Raman
- Division of Cancer Imaging Research, The Russell H Morgan Department of Radiology and Radiological Sciences, USA; Department of Oncology, The Johns Hopkins University, School of Medicine, Baltimore, MD, USA; Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.
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19
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Exploring the wound healing, anti-inflammatory, anti-pathogenic and proteomic effects of lactic acid bacteria on keratinocytes. Sci Rep 2020; 10:11572. [PMID: 32665600 PMCID: PMC7360600 DOI: 10.1038/s41598-020-68483-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/25/2020] [Indexed: 12/26/2022] Open
Abstract
The topical application of lactic acid bacteria (LAB) is recognized as a useful approach to improve skin health. This work aims to characterize by a multidisciplinary approach, the wound healing, anti-inflammatory, anti-pathogens and proteomic effects of six LAB lysates, belonging to the genus Lactobacillus. Our results demonstrated that the lysates of tested LAB stimulated the proliferation of keratinocytes, and that L. plantarum SGL 07 and L. salivarius SGL 19 accelerated the re-epithelization by inducing keratinocyte migration. The bacterial lysates also reduced the secretion of specific pro-inflammatory mediators from keratinocytes. Furthermore, viable L. salivarius SGL 19 and L. fermentum SGL 10 had anti-pathogenic effects against S. aureus and S. pyogenes, while L. brevis SGL 12 and L. paracasei SGL 04 inhibited S. aureus and S. pyogenes, respectively. The tested lactobacilli lysates also induced specific proteome modulation of the exposed keratinocytes, involving dysregulation of proteins (such as interleukin enhancer-binding factor 2 and ATP-dependent RNA helicase) and pathways (such as cytokine, NF-kB, Hedgehog, and RUNX signaling) associated with their specific wound healing and anti-inflammatory effects. This study indicates the different potential of selected lactobacilli, suggesting that they may be successfully used in the future together with conventional therapies to bring relief from skin disorders.
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20
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Stunnenberg M, Sprokholt JK, van Hamme JL, Kaptein TM, Zijlstra-Willems EM, Gringhuis SI, Geijtenbeek TBH. Synthetic Abortive HIV-1 RNAs Induce Potent Antiviral Immunity. Front Immunol 2020; 11:8. [PMID: 32038656 PMCID: PMC6990453 DOI: 10.3389/fimmu.2020.00008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
Abstract
Strong innate and adaptive immune responses are paramount in combating viral infections. Dendritic cells (DCs) detect viral infections via cytosolic RIG-I like receptors (RLRs) RIG-I and MDA5 leading to MAVS-induced immunity. The DEAD-box RNA helicase DDX3 senses abortive human immunodeficiency virus 1 (HIV-1) transcripts and induces MAVS-dependent type I interferon (IFN) responses, suggesting that abortive HIV-1 RNA transcripts induce antiviral immunity. Little is known about the induction of antiviral immunity by DDX3-ligand abortive HIV-1 RNA. Here we synthesized a 58 nucleotide-long capped RNA (HIV-1 Cap-RNA58) that mimics abortive HIV-1 RNA transcripts. HIV-1 Cap-RNA58 induced potent type I IFN responses in monocyte-derived DCs, monocytes, macrophages and primary CD1c+ DCs. Compared with RLR agonist poly-I:C, HIV-1 Cap-RNA58 induced comparable levels of type I IFN responses, identifying HIV-1 Cap-RNA58 as a potent trigger of antiviral immunity. In monocyte-derived DCs, HIV-1 Cap-RNA58 activated the transcription factors IRF3 and NF-κB. Moreover, HIV-1 Cap-RNA58 induced DC maturation and the expression of pro-inflammatory cytokines. HIV-1 Cap-RNA58-stimulated DCs induced proliferation of CD4+ and CD8+ T cells and differentiated naïve T helper (TH) cells toward a TH2 phenotype. Importantly, treatment of DCs with HIV-1 Cap-RNA58 resulted in an efficient antiviral innate immune response that reduced ongoing HIV-1 replication in DCs. Our data strongly suggest that HIV-1 Cap-RNA58 induces potent innate and adaptive immune responses, making it an interesting addition in vaccine design strategies.
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Affiliation(s)
- Melissa Stunnenberg
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Joris K Sprokholt
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - John L van Hamme
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Tanja M Kaptein
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Esther M Zijlstra-Willems
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sonja I Gringhuis
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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21
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Zuo GF, Ren XM, Ge Q, Luo J, Ye P, Wang F, Wu W, Chao YL, Gu Y, Gao XF, Ge Z, Gao HB, Hu ZY, Zhang JJ, Chen SL. Activation of the PP2A catalytic subunit by ivabradine attenuates the development of diabetic cardiomyopathy. J Mol Cell Cardiol 2019; 130:170-183. [PMID: 30998977 DOI: 10.1016/j.yjmcc.2019.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/30/2022]
Abstract
Hyperglycemia-induced apoptosis plays a critical role in the pathogenesis of diabetic cardiomyopathy (DCM). Our previous study demonstrated that ivabradine, a selective If current antagonist, significantly attenuated myocardial apoptosis in diabetic mice, but the underlying mechanisms remained unknown. This study investigated the underlying mechanisms by which ivabradine exerts anti-apoptotic effects in experimental DCM. Pretreatment with ivabradine, but not ZD7288 (an established If current blocker), profoundly inhibited high glucose-induced apoptosis via inactivation of nuclear factor (NF)-κB signaling in neonatal rat cardiomyocytes. The effect was abolished by transfection of an siRNA targeting protein phosphatase 2A catalytic subunit (PP2Ac). In streptozotocin-induced diabetic mice, ivabradine treatment significantly inhibited left ventricular hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2) and HCN4 (major components of the If current), activated PP2Ac, and attenuated NF-κB signaling activation and apoptosis, in line with improved histological abnormalities, fibrosis, and cardiac dysfunction without affecting hyperglycemia. These effects were not observed in diabetic mice with virus-mediated knockdown of HCN2 or HCN4 after myocardial injection, but were alleviated by knockdown of PP2Acα. Molecular docking and phosphatase activity assay confirmed direct binding of ivabradine to, and activation of, PP2Ac. In conclusion, ivabradine may directly activate PP2Ac, leading to inhibition of NF-κB signaling activation, myocardial apoptosis, and fibrosis, and eventually improving cardiac function in experimental DCM. Taken together, the present findings suggest that ivabradine may be a promising drug for treatment of DCM.
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Affiliation(s)
- Guang-Feng Zuo
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiao-Min Ren
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Qing Ge
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Jie Luo
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Peng Ye
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Feng Wang
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Wen Wu
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yue-Lin Chao
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China; Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Yue Gu
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China; Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Xiao-Fei Gao
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhen Ge
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Han-Bin Gao
- The First People's Hospital of Taicang, Soochow University, Suzhou, China
| | - Zuo-Ying Hu
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.
| | - Jun-Jie Zhang
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.
| | - Shao-Liang Chen
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.
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22
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From the magic bullet to the magic target: exploiting the diverse roles of DDX3X in viral infections and tumorigenesis. Future Med Chem 2019; 11:1357-1381. [PMID: 30816053 DOI: 10.4155/fmc-2018-0451] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
DDX3X is an ATPase/RNA helicase of the DEAD-box family and one of the most multifaceted helicases known up to date, acting in RNA metabolism, cell cycle control, apoptosis, stress response and innate immunity. Depending on the virus or the viral cycle stage, DDX3X can act either in a proviral fashion or as an antiviral factor. Similarly, in different cancer types, it can act either as an oncogene or a tumor-suppressor gene. Accumulating evidence indicated that DDX3X can be considered a promising target for anticancer and antiviral chemotherapy, but also that its exploitation requires a deeper understanding of the molecular mechanisms underlying its dual role in cancer and viral infections. In this Review, we will summarize the known roles of DDX3X in different tumor types and viral infections, and the different inhibitors available, illustrating the possible advantages and potential caveats of their use as anticancer and antiviral drugs.
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Perčulija V, Ouyang S. Diverse Roles of DEAD/DEAH-Box Helicases in Innate Immunity and Diseases. HELICASES FROM ALL DOMAINS OF LIFE 2019. [PMCID: PMC7158350 DOI: 10.1016/b978-0-12-814685-9.00009-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
DEAD/DEAH-box helicases are enzymes that belong to the DEAD/H-box family of SF2 helicase superfamily. These enzymes are essential in RNA metabolism, where they are involved in a number of processes that require manipulation of RNA structure. Recent studies have found that some DEAD/DEAH-box helicases play important roles in innate immunity, where they act as sensors of cytosolic DNA/RNA, as adaptor proteins, or as regulators of signaling and gene expression. In spite of their function in immunity, DEAD/DEAH-box helicases can also be hijacked and exploited by viruses to circumvent detection and aid in viral replication. These findings not only imply that DEAD/DEAH-box helicases have a broader function than previously thought, but also give us a much better understanding of immune mechanisms and diseases that arise due to the dysregulation or evasion thereof. In this chapter, we demonstrate the known scope of activities of human DEAD/DEAH-box helicases in innate immunity and interaction with viruses or other pathogens. Additionally, we give an outline of diseases in which they are, or may be, involved in the context of immunity.
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DDX3 Participates in Translational Control of Inflammation Induced by Infections and Injuries. Mol Cell Biol 2018; 39:MCB.00285-18. [PMID: 30373933 DOI: 10.1128/mcb.00285-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/10/2018] [Indexed: 12/28/2022] Open
Abstract
Recent studies have suggested that DDX3 functions in antiviral innate immunity, but the underlying mechanism remains elusive. We previously identified target mRNAs whose translation is controlled by DDX3. Pathway enrichment analysis of these targets indicated that DDX3 is involved in various infections and inflammation. Using immunoblotting, we confirmed that PACT, STAT1, GNB2, Rac1, TAK1, and p38 mitogen-activated protein kinase (MAPK) proteins are downregulated by DDX3 knockdown in human monocytic THP-1 cells and epithelial HeLa cells. Polysome profiling revealed that DDX3 knockdown reduces the translational efficiency of target mRNAs. We further demonstrated DDX3-mediated translational control of target mRNAs by luciferase reporter assays. To examine the effects of DDX3 knockdown on macrophage migration and phagocytosis, we performed in vitro cell migration assay and flow cytometry analysis of the uptake of green fluorescent protein-expressing Escherichia coli in THP-1 cells. The DDX3 knockdown cells exhibited impaired macrophage migration and phagocytosis. Moreover, we used a human cytokine antibody array to identify the cytokines affected by DDX3 knockdown. Several chemokines were decreased considerably in DDX3 knockdown THP-1 cells after lipopolysaccharide or poly(I·C) stimulation. Lastly, we demonstrated that DDX3 is crucial for the recruitment of phagocytes to the site of inflammation in transgenic zebrafish.
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Fullam A, Gu L, Höhn Y, Schröder M. DDX3 directly facilitates IKKα activation and regulates downstream signalling pathways. Biochem J 2018; 475:3595-3607. [PMID: 30341167 DOI: 10.1042/bcj20180163] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 02/07/2023]
Abstract
DDX3 is a DEAD-box RNA helicase that we and others have previously implicated in antiviral immune signalling pathways leading to type I interferon (IFN) induction. We previously demonstrated that it directly interacts with the kinase IKKε (IκB kinase ε), enhances it activation, and then facilitates phosphorylation of the transcription factor IRF3 by IKKε. However, the TLR7/9 (Toll-like receptor 7/9)-mediated pathway, one of the most physiologically relevant IFN induction pathways, proceeds independently of IKKε or the related kinase TBK1 (TANK-binding kinase 1). This pathway induces type I IFN production via the kinases NIK (NF-κB-inducing kinase) and IKKα and is activated when plasmacytoid dendritic cells sense viral nucleic acids. In the present study, we demonstrate that DDX3 also directly interacts with IKKα and enhances its autophosphorylation and -activation. Modulation of DDX3 expression consequently affected NIK/IKKα-mediated IRF7 phosphorylation and induction of type I interferons. In addition, alternative NF-κB (nuclear factor-κB) activation, another pathway regulated by NIK and IKKα, was also down-regulated in DDX3 knockdown cells. This substantially broadens the effects of DDX3 in innate immune signalling to pathways beyond TBK1/IKKε and IFN induction. Dysregulation of these pathways is involved in disease states, and thus, our research might implicate DDX3 as a potential target for their therapeutic manipulation.
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Affiliation(s)
- Anthony Fullam
- Department of Biology, Institute of Immunology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Lili Gu
- Department of Biology, Institute of Immunology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Yvette Höhn
- Department of Biology, Institute of Immunology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Martina Schröder
- Department of Biology, Institute of Immunology, Maynooth University, Maynooth, Co. Kildare, Ireland
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Loureiro ME, Zorzetto-Fernandes AL, Radoshitzky S, Chi X, Dallari S, Marooki N, Lèger P, Foscaldi S, Harjono V, Sharma S, Zid BM, López N, de la Torre JC, Bavari S, Zúñiga E. DDX3 suppresses type I interferons and favors viral replication during Arenavirus infection. PLoS Pathog 2018; 14:e1007125. [PMID: 30001425 PMCID: PMC6042795 DOI: 10.1371/journal.ppat.1007125] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/27/2018] [Indexed: 11/19/2022] Open
Abstract
Several arenaviruses cause hemorrhagic fever (HF) diseases that are associated with high morbidity and mortality in humans. Accordingly, HF arenaviruses have been listed as top-priority emerging diseases for which countermeasures are urgently needed. Because arenavirus nucleoprotein (NP) plays critical roles in both virus multiplication and immune-evasion, we used an unbiased proteomic approach to identify NP-interacting proteins in human cells. DDX3, a DEAD-box ATP-dependent-RNA-helicase, interacted with NP in both NP-transfected and virus-infected cells. Importantly, DDX3 deficiency compromised the propagation of both Old and New World arenaviruses, including the HF arenaviruses Lassa and Junin viruses. The DDX3 role in promoting arenavirus multiplication associated with both a previously un-recognized DDX3 inhibitory role in type I interferon production in arenavirus infected cells and a positive DDX3 effect on arenavirus RNA synthesis that was dependent on its ATPase and Helicase activities. Our results uncover novel mechanisms used by arenaviruses to exploit the host machinery and subvert immunity, singling out DDX3 as a potential host target for developing new therapies against highly pathogenic arenaviruses.
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Affiliation(s)
- María Eugenia Loureiro
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | | | - Sheli Radoshitzky
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Xiaoli Chi
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Simone Dallari
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Nuha Marooki
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Psylvia Lèger
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Sabrina Foscaldi
- Centro de Virología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Vince Harjono
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Sonia Sharma
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States of America
| | - Brian M. Zid
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Nora López
- Centro de Virología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Juan Carlos de la Torre
- The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, United States of America
| | - Sina Bavari
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Elina Zúñiga
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
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